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Yoon JG, Yu JW, Shim KW, Kim YO, Lee MG. Syndromic craniosynostosis caused by a novel missense variant in MAP4K4: Expanding the genotype-phenotype relationship in RASopathies. Clin Genet 2024; 106:199-203. [PMID: 38679877 DOI: 10.1111/cge.14539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/01/2024]
Abstract
RASopathies represent a distinct class of neurodevelopmental syndromes caused by germline variants in the Ras/MAPK pathways. Recently, a novel disease-gene association was implicated in MAPK kinase kinase kinase 4 (MAP4K4), which regulates the upstream signals of the MAPK pathways. However, to our knowledge, only two studies have reported the genotype-phenotype relationships in the MAP4K4-related disorder. This study reports on a Korean boy harboring a novel de novo missense variant in MAP4K4 (NM_001242559:c.569G>T, p.Gly190Val), revealed by trio exome sequencing, and located in the hotspot of the protein kinase domain. The patient exhibited various clinical features, including craniofacial dysmorphism, language delay, congenital heart defects, genitourinary anomalies, and sagittal craniosynostosis. Our study expands the phenotypic association of the MAP4K4-related disorder to include syndromic craniosynostosis, thereby providing further insights into the role of the RAS/MAPK pathways in the development of premature fusion of calvarial sutures.
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Affiliation(s)
- Jihoon G Yoon
- Department of Laboratory Medicine, Yonsei University College of Medicine and Gangnam Severance Hospital, Seoul, Republic of Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Woo Yu
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
- Department of Pediatric Neurosurgery, Craniofacial Reforming and Reconstruction Clinic, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyu Won Shim
- Department of Pediatric Neurosurgery, Craniofacial Reforming and Reconstruction Clinic, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yong Oock Kim
- Department of Plastic and Reconstructive Surgery, Institute for Human Tissue Restoration, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Goo Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
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2
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Massier M, Doco-Fenzy M, Egloff M, Le Guillou X, Le Guyader G, Redon S, Benech C, Le Millier K, Uguen K, Ropars J, Sacaze E, Audebert-Bellanger S, Apetrei A, Molin A, Gruchy N, Vincent-Devulder A, Spodenkiewicz M, Jacquin C, Loron G, Thibaud M, Delplancq G, Brisset S, Lesieur-Sebellin M, Malan V, Romana S, Rio M, Marlin S, Amiel J, Marquet V, Dauriat B, Moradkhani K, Mercier S, Isidor B, Arpin S, Pujalte M, Jedraszak G, Pebrel-Richard C, Salaun G, Laffargue F, Boudjarane J, Missirian C, Chelloug N, Toutain A, Chiesa J, Keren B, Mignot C, Gouy E, Jaillard S, Landais E, Poirsier C. 3q29 duplications: A cohort of 46 patients and a literature review. Am J Med Genet A 2024; 194:e63531. [PMID: 38421086 DOI: 10.1002/ajmg.a.63531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 03/02/2024]
Abstract
Duplications of the 3q29 cytoband are rare chromosomal copy number variations (CNVs) (overlapping or recurrent ~1.6 Mb 3q29 duplications). They have been associated with highly variable neurodevelopmental disorders (NDDs) with various associated features or reported as a susceptibility factor to the development of learning disabilities and neuropsychiatric disorders. The smallest region of overlap and the phenotype of 3q29 duplications remain uncertain. We here report a French cohort of 31 families with a 3q29 duplication identified by chromosomal microarray analysis (CMA), including 14 recurrent 1.6 Mb duplications, eight overlapping duplications (>1 Mb), and nine small duplications (<1 Mb). Additional genetic findings that may be involved in the phenotype were identified in 11 patients. Focusing on apparently isolated 3q29 duplications, patients present mainly mild NDD as suggested by a high rate of learning disabilities in contrast to a low proportion of patients with intellectual disabilities. Although some are de novo, most of the 3q29 duplications are inherited from a parent with a similar mild phenotype. Besides, the study of small 3q29 duplications does not provide evidence for any critical region. Our data suggest that the overlapping and recurrent 3q29 duplications seem to lead to mild NDD and that a severe or syndromic clinical presentation should warrant further genetic analyses.
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Affiliation(s)
- Marie Massier
- Department of Genetics, Reims University Hospital, Reims, France
| | - Martine Doco-Fenzy
- Department of Genetics, Reims University Hospital, Reims, France
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Matthieu Egloff
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, INSERM, LNEC, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | - Xavier Le Guillou
- Department of Genetics, Poitiers University Hospital, Poitiers, France
- University of Poitiers, CNRS, LMA, Department of Genetics, Poitiers University Hospital, Poitiers, France
| | | | - Sylvia Redon
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Caroline Benech
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | | | - Kevin Uguen
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
- University of Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Juliette Ropars
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Elise Sacaze
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Séverine Audebert-Bellanger
- Department of Genetics, Brest University Hospital, Brest, France
- Intellectual Disability Reference Center, Department of Pediatrics, Brest University Hospital, Brest, France
| | - Andreea Apetrei
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Arnaud Molin
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Nicolas Gruchy
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | - Aline Vincent-Devulder
- University of Normandy, UNICAEN, RU7450 BioTARGen, Caen University Hospital, Department of Genetics, Reference Center for Developmental Disorders and Malformative Syndromes, Anddi-Rares Network, Caen, France
| | | | - Clémence Jacquin
- Department of Genetics, Reims University Hospital, Reims, France
| | - Gauthier Loron
- Department of Neonatal Medicine and Pediatric Intensive Care, University of Reims Champagne-Ardenne, CReSTIC, Reims University Hospital, Reims, France
| | - Marie Thibaud
- Department of Pediatrics, American Memorial Hospital, Reims, France
| | | | - Sophie Brisset
- Constitutional Genetics Unit, Versailles Hospital, Le Chesnay, France
| | - Marion Lesieur-Sebellin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valérie Malan
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Serge Romana
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Marlène Rio
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Sandrine Marlin
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Jeanne Amiel
- Department of Genomic Medicine of Rare Disorders, Necker Hospital, APHP Center, University Paris Cité, Paris, France
| | - Valentine Marquet
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | - Benjamin Dauriat
- Department of Cytogenetics, Clinical Genetics and Reproductive Biology, Limoges University Hospital, Limoges, France
| | | | - Sandra Mercier
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Bertrand Isidor
- Department of Genetics, Nantes University Hospital, Nantes, France
| | - Stéphanie Arpin
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | | | - Guillaume Jedraszak
- Constitutional Genetic Laboratory, University Hospital of Amiens & UR4666 HEMATIM, University of Picardie Jules Verne, Amiens, France
| | - Céline Pebrel-Richard
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Gaëlle Salaun
- Cytogenetic Medical Department; UIC Cytogenetics of Rare Diseases and Reproduction (GRUIC ADERGEN), Rare Diseases Reference Center (CRMR): Developmental Anomalies and Malformative Syndromes in the Auvergne Region, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Fanny Laffargue
- Department of Medical Genetics, UIC ADDIR (GRIUC ADERGEN), Constitutive Reference Center CLAD South-East: Developmental anomalies and malformative syndromes, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - John Boudjarane
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Chantal Missirian
- Medical Genetics Department, Timone Enfants University Hospital, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Nora Chelloug
- Department of Medical Genetics, Toulouse University Hospital, Toulouse, France
| | - Annick Toutain
- Department of Genetics, Tours University Hospital, UMR 1253, iBrain, University of Tours, Inserm, Tours, France
| | - Jean Chiesa
- Department of Genetics, Nimes, University Hospital, Nimes University Hospital, Nimes, France
| | - Boris Keren
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Cyril Mignot
- Department of Genetics, APHP Sorbonne University, Paris, France
| | - Evan Gouy
- Department of Genetics, Hospices Civils de Lyon, Lyon, France
| | - Sylvie Jaillard
- Department of Cytogenetics and Cell Biology, Rennes university hospital, Rennes, France
| | - Emilie Landais
- Department of Genetics, Reims University Hospital, Reims, France
| | - Céline Poirsier
- Department of Genetics, Reims University Hospital, Reims, France
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3
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Türkyılmaz A, Cimbek EA, Kardeş H, Çebi AH, Acar Arslan E, Karagüzel G. A triple molecular diagnosis in a Turkish individual with hypotrichosis, deafness, and diabetes. Clin Dysmorphol 2024; 33:118-120. [PMID: 38818819 DOI: 10.1097/mcd.0000000000000499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Affiliation(s)
| | - Emine Ayça Cimbek
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
| | - Hakan Kardeş
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
| | | | - Elif Acar Arslan
- Department of Pediatric Neurology, Marmara University, Faculty of Medicine, İstanbul, Türkiye
| | - Gülay Karagüzel
- Pediatric Endocrinology, Faculty of Medicine, Karadeniz Technical University, Trabzon
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4
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Serigatto HR, Zechi-Ceide RM, Parizotto I, Kokitsu-Nakata NM. Monodactyly in a patient with CHARGE syndrome: An additional case report. Am J Med Genet A 2024; 194:e63561. [PMID: 38352994 DOI: 10.1002/ajmg.a.63561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 05/02/2024]
Abstract
CHARGE syndrome is a rare autosomal dominant syndrome characterized by multiple congenital anomalies including coloboma, heart defects, ear anomalies, and developmental delay, caused by pathogenic variants in the CHD7 gene. The discovery of the molecular basis of this syndrome increased the number of cases reported and expanded the phenotype and clinical variability. Limb anomalies are occasional clinical findings in this syndrome, present in about 30% of reported cases. The occurrence of limb anomalies in this syndrome suggests that it should be considered as part of the phenotypic spectrum. Here, we describe an individual with CHARGE syndrome presenting unilateral monodactyly.
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Affiliation(s)
| | - Roseli Maria Zechi-Ceide
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
| | - Isabella Parizotto
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, São Paulo, Brazil
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5
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Yoon JG, Yu JW, Shim KW, Kim YO, Lee MG. Multi-locus pathogenic variation identified in a patient with craniosynostosis. Am J Med Genet A 2024; 194:e63521. [PMID: 38126082 DOI: 10.1002/ajmg.a.63521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/23/2023] [Accepted: 12/09/2023] [Indexed: 12/23/2023]
Affiliation(s)
- Jihoon G Yoon
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jung Woo Yu
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyu Won Shim
- Department of Pediatric Neurosurgery, Craniofacial Reforming and Reconstruction Clinic, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yong Oock Kim
- Department of Plastic and Reconstructive Surgery, Institute for Human Tissue Restoration, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Min Goo Lee
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
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6
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Bozkurt-Yozgatli T, Pehlivan D, Gibbs RA, Sezerman U, Posey JE, Lupski JR, Coban-Akdemir Z. Multilocus pathogenic variants contribute to intrafamilial clinical heterogeneity: a retrospective study of sibling pairs with neurodevelopmental disorders. BMC Med Genomics 2024; 17:85. [PMID: 38622594 PMCID: PMC11020671 DOI: 10.1186/s12920-024-01852-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/27/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Multilocus pathogenic variants (MPVs) are genetic changes that affect multiple gene loci or regions of the genome, collectively leading to multiple molecular diagnoses. MPVs may also contribute to intrafamilial phenotypic variability between affected individuals within a nuclear family. In this study, we aim to gain further insights into the influence of MPVs on a disease manifestation in individual research subjects and explore the complexities of the human genome within a familial context. METHODS We conducted a systematic reanalysis of exome sequencing data and runs of homozygosity (ROH) regions of 47 sibling pairs previously diagnosed with various neurodevelopmental disorders (NDD). RESULTS We found siblings with MPVs driven by long ROH regions in 8.5% of families (4/47). The patients with MPVs exhibited significantly higher FROH values (p-value = 1.4e-2) and larger total ROH length (p-value = 1.8e-2). Long ROH regions mainly contribute to this pattern; the siblings with MPVs have a larger total size of long ROH regions than their siblings in all families (p-value = 6.9e-3). Whereas the short ROH regions in the siblings with MPVs are lower in total size compared to their sibling pairs with single locus pathogenic variants (p-value = 0.029), and there are no statistically significant differences in medium ROH regions between sibling pairs (p-value = 0.52). CONCLUSION This study sheds light on the significance of considering MPVs in families with affected sibling pairs and the role of ROH as an adjuvant tool in explaining clinical variability within families. Identifying individuals carrying MPVs may have implications for disease management, identification of possible disease risks to different family members, genetic counseling and exploring personalized treatment approaches.
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Affiliation(s)
- Tugce Bozkurt-Yozgatli
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Davut Pehlivan
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA
- Texas Children's Hospital, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ugur Sezerman
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James R Lupski
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.
- Texas Children's Hospital, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Zeynep Coban-Akdemir
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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7
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Donis KC, Kalil MAB, Poswar F, Kok F, Kohem CL, Poloni S, Borsatto T, Vairo FPE, Pinheiro FC, Schwartz IVD. An adult with cystathionine beta-synthase deficiency, camptodactyly-arthropathy-coxa vara-pericarditis syndrome, and deafness: A case report. Genet Mol Biol 2024; 47:e20220335. [PMID: 38593426 PMCID: PMC11003653 DOI: 10.1590/1678-4685-gmb-2022-0335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/11/2023] [Indexed: 04/11/2024] Open
Abstract
Massive sequencing platforms allow the identification of complex clinical phenotypes involving more than one autosomal recessive disorder. In this study, we report on an adult patient, born to a related couple (third degree cousins), referred for genetic evaluation due to ectopia lentis, deafness and previous diagnosis of juvenile idiopathic arthritis. He was biochemically diagnosed as having Classic Homocystinuria (HCU); Sanger sequencing of the CBS gene showed the genotype NM_000071.2(CBS):c.[833T>C];[833T>C], compatible with the diagnosis of pyridoxine-responsive HCU. As he also had symptoms not usually associated with HCU, exome sequencing was performed. In addition to the variants found in the Sanger sequencing, the following variants were identified: NM_001256317.1(TMPRSS3):c.[413C>A];[413C>A]; and the NM_005807.6(PRG4):c.[3756dup]:[3756dup], confirming the diagnosis of autosomal recessive nonsyndromic deafness and Camptodactyly-Arthropathy-Coxa Vara-Pericarditis Syndrome (CACP), respectively. Genomic analysis allowed the refinement of the diagnosis of a complex case and improvement of the patient's treatment.
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Affiliation(s)
- Karina Carvalho Donis
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
| | | | - Fabiano Poswar
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
| | - Fernando Kok
- Universidade de São Paulo, Hospital das Clínicas, Departamento de Neurologia, Unidade de Neurogenética, São Paulo, SP, Brazil
- Mendelics Análise Genômica, São Paulo, SP, Brazil
| | - Charles Lubianca Kohem
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Serviço de Reumatologia, Porto Alegre, RS, Brazil
| | - Soraia Poloni
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório BRAIN, Porto Alegre, RS, Brazil
| | - Taciane Borsatto
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório BRAIN, Porto Alegre, RS, Brazil
| | - Filippo Pinto e Vairo
- Mayo Clinic, Center for Individualized Medicine, Rochester, MN, USA
- Mayo Clinic, Department of Clinical Genomics, Rochester, MN, USA
| | - Franciele Cabral Pinheiro
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Ida Vanessa Doederlein Schwartz
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa Experimental, Laboratório BRAIN, Porto Alegre, RS, Brazil
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8
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Calame DG, Wong JH, Panda P, Nguyen DT, Leong NC, Sangermano R, Patankar SG, Abdel-Hamid M, AlAbdi L, Safwat S, Flannery KP, Dardas Z, Fatih JM, Murali C, Kannan V, Lotze TE, Herman I, Ammouri F, Rezich B, Efthymiou S, Alavi S, Murphy D, Firoozfar Z, Nasab ME, Bahreini A, Ghasemi M, Haridy NA, Goldouzi HR, Eghbal F, Karimiani EG, Srinivasan VM, Gowda VK, Du H, Jhangiani SN, Coban-Akdemir Z, Marafi D, Rodan L, Isikay S, Rosenfeld JA, Ramanathan S, Staton M, Kerby C. Oberg, Clark RD, Wenman C, Loughlin S, Saad R, Ashraf T, Male A, Tadros S, Boostani R, Abdel-Salam GM, Zaki M, Abdalla E, Manzini MC, Pehlivan D, Posey JE, Gibbs RA, Houlden H, Alkuraya FS, Bujakowska K, Maroofian R, Lupski JR, Nguyen LN. Biallelic variation in the choline and ethanolamine transporter FLVCR1 underlies a pleiotropic disease spectrum from adult neurodegeneration to severe developmental disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.09.24302464. [PMID: 38405817 PMCID: PMC10888986 DOI: 10.1101/2024.02.09.24302464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
FLVCR1 encodes Feline leukemia virus subgroup C receptor 1 (FLVCR1), a solute carrier (SLC) transporter within the Major Facilitator Superfamily. FLVCR1 is a widely expressed transmembrane protein with plasma membrane and mitochondrial isoforms implicated in heme, choline, and ethanolamine transport. While Flvcr1 knockout mice die in utero with skeletal malformations and defective erythropoiesis reminiscent of Diamond-Blackfan anemia, rare biallelic pathogenic FLVCR1 variants are linked to childhood or adult-onset neurodegeneration of the retina, spinal cord, and peripheral nervous system. We ascertained from research and clinical exome sequencing 27 individuals from 20 unrelated families with biallelic ultra-rare missense and predicted loss-of-function (pLoF) FLVCR1 variant alleles. We characterize an expansive FLVCR1 phenotypic spectrum ranging from adult-onset retinitis pigmentosa to severe developmental disorders with microcephaly, reduced brain volume, epilepsy, spasticity, and premature death. The most severely affected individuals, including three individuals with homozygous pLoF variants, share traits with Flvcr1 knockout mice and Diamond-Blackfan anemia including macrocytic anemia and congenital skeletal malformations. Pathogenic FLVCR1 missense variants primarily lie within transmembrane domains and reduce choline and ethanolamine transport activity compared with wild-type FLVCR1 with minimal impact on FLVCR1 stability or subcellular localization. Several variants disrupt splicing in a mini-gene assay which may contribute to genotype-phenotype correlations. Taken together, these data support an allele-specific gene dosage model in which phenotypic severity reflects residual FLVCR1 activity. This study expands our understanding of Mendelian disorders of choline and ethanolamine transport and demonstrates the importance of choline and ethanolamine in neurodevelopment and neuronal homeostasis.
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Affiliation(s)
- Daniel G. Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jovi Huixin Wong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Puravi Panda
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Dat Tuan Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Nancy C.P. Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Riccardo Sangermano
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Sohil G. Patankar
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Mohamed Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sylvia Safwat
- Department of Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Kyle P. Flannery
- Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, NY, USA
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chaya Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Varun Kannan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Timothy E. Lotze
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Boys Town National Research Hospital, Boys Town, NE, USA
| | - Farah Ammouri
- Boys Town National Research Hospital, Boys Town, NE, USA
- The University of Kansas Health System, Westwood, KS, USA
| | - Brianna Rezich
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - Shahryar Alavi
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, United Kingdom
| | | | | | - Amir Bahreini
- KaryoGen, Isfahan, Iran
- Department of Human Genetics, University of Pittsburgh, PA, USA
| | - Majid Ghasemi
- Department of Neurology, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Hamid Reza Goldouzi
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Eghbal
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St George’s, University of London, Cranmer Terrace London, London, UK
| | | | - Vykuntaraju K. Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait
| | - Lance Rodan
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Sedat Isikay
- Gaziantep Islam Science and Technology University, Medical Faculty, Department of Pediatric Neurology, Gaziantep, Turkey
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Subhadra Ramanathan
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Michael Staton
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Kerby C. Oberg
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Robin D. Clark
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Catharina Wenman
- Rare & Inherited Disease Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3BH, UK
| | - Sam Loughlin
- Rare & Inherited Disease Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3BH, UK
| | - Ramy Saad
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Tazeen Ashraf
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Alison Male
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Shereen Tadros
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Reza Boostani
- Department of Neurology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghada M.H. Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Maha Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Ebtesam Abdalla
- Department of Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - M. Chiara Manzini
- Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, NY, USA
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Henry Houlden
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - Fowzan S. Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Kinga Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Reza Maroofian
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - James R. Lupski
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Long Nam Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
- Immunology Program, Life Sciences Institute, National University of Singapore, Singapore 117456
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 117456
- Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456
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9
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Rezende RC, Menezes de Andrade NL, Branco Dantas NC, de Polli Cellin L, Victorino Krepischi AC, Lerario AM, de Lima Jorge AA. Exome Sequencing Identifies Multiple Genetic Diagnoses in Children with Syndromic Growth Disorders. J Pediatr 2024; 265:113841. [PMID: 37995928 DOI: 10.1016/j.jpeds.2023.113841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/25/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
OBJECTIVE To evaluate the presence of multiple genetic diagnoses in syndromic growth disorders. STUDY DESIGN We carried out a cross-sectional study to evaluate 115 patients with syndromic tall (n = 24) or short stature (n = 91) of unknown cause from a tertiary referral center for growth disorders. Exome sequencing was performed to assess germline single nucleotide, InDel, and copy number variants. All variants were classified according to ACMG/AMP guidelines. The main outcome measured was the frequency of multiple genetic diagnoses in a cohort of children with syndromic growth disorders. RESULTS The total diagnostic yield of the cohort was 54.8% (63/115). Six patients had multiple genetic diagnoses (tall stature group = 2; short stature group = 4). The proportion of multiple diagnoses within total cases was 5.2% (6/115), and within solved cases was 9.5% (6/63). No characteristics were significantly more frequent when compared with patients with single or multiple genetic findings. Among patients with multiple diagnoses, 3 had syndromes with overlapping clinical features, and the others had syndromes with distinct phenotypes. CONCLUSION Recognition of multiple genetic diagnoses as a possibility in complex cases of syndromic growth disorders opens a new perspective on treatment and genetic counseling for affected patients, defying the medical common sense of trying to fit all findings into one diagnosis.
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Affiliation(s)
- Raissa Carneiro Rezende
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Nathalia Liberatoscioli Menezes de Andrade
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Naiara Castelo Branco Dantas
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | - Laurana de Polli Cellin
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil
| | | | - Antonio Marcondes Lerario
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Alexander Augusto de Lima Jorge
- Laboratorio de Endocrinologia Celular e Molecular LIM25, Unidade de Endocrinologia Genetica/Faculdade de Medicina da Universidade de Sao Paulo (FMUSP)/Hospital das Clinicas da Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
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10
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Yamamoto S, Kanca O, Wangler MF, Bellen HJ. Integrating non-mammalian model organisms in the diagnosis of rare genetic diseases in humans. Nat Rev Genet 2024; 25:46-60. [PMID: 37491400 DOI: 10.1038/s41576-023-00633-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2023] [Indexed: 07/27/2023]
Abstract
Next-generation sequencing technology has rapidly accelerated the discovery of genetic variants of interest in individuals with rare diseases. However, showing that these variants are causative of the disease in question is complex and may require functional studies. Use of non-mammalian model organisms - mainly fruitflies (Drosophila melanogaster), nematode worms (Caenorhabditis elegans) and zebrafish (Danio rerio) - enables the rapid and cost-effective assessment of the effects of gene variants, which can then be validated in mammalian model organisms such as mice and in human cells. By probing mechanisms of gene action and identifying interacting genes and proteins in vivo, recent studies in these non-mammalian model organisms have facilitated the diagnosis of numerous genetic diseases and have enabled the screening and identification of therapeutic options for patients. Studies in non-mammalian model organisms have also shown that the biological processes underlying rare diseases can provide insight into more common mechanisms of disease and the biological functions of genes. Here, we discuss the opportunities afforded by non-mammalian model organisms, focusing on flies, worms and fish, and provide examples of their use in the diagnosis of rare genetic diseases.
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Affiliation(s)
- Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA.
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11
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Racine C, Denommé-Pichon AS, Engel C, Tran Mau-Them F, Bruel AL, Vitobello A, Safraou H, Sorlin A, Nambot S, Delanne J, Garde A, Colin E, Moutton S, Thevenon J, Jean-Marçais N, Willems M, Geneviève D, Pinson L, Perrin L, Laffargue F, Lespinasse J, Lacaze E, Molin A, Gerard M, Lambert L, Benigni C, Patat O, Bourgeois V, Poe C, Chevarin M, Couturier V, Garret P, Philippe C, Duffourd Y, Faivre L, Thauvin-Robinet C. Multiple molecular diagnoses in the field of intellectual disability and congenital anomalies: 3.5% of all positive cases. J Med Genet 2023; 61:36-46. [PMID: 37586840 DOI: 10.1136/jmg-2023-109170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 07/27/2023] [Indexed: 08/18/2023]
Abstract
PURPOSE Wide access to clinical exome/genome sequencing (ES/GS) enables the identification of multiple molecular diagnoses (MMDs), being a long-standing but underestimated concept, defined by two or more causal loci implicated in the phenotype of an individual with a rare disease. Only few series report MMDs rates (1.8% to 7.1%). This study highlights the increasing role of MMDs in a large cohort of individuals addressed for congenital anomalies/intellectual disability (CA/ID). METHODS From 2014 to 2021, our diagnostic laboratory rendered 880/2658 positive ES diagnoses for CA/ID aetiology. Exhaustive search on MMDs from ES data was performed prospectively (January 2019 to December 2021) and retrospectively (March 2014 to December 2018). RESULTS MMDs were identified in 31/880 individuals (3.5%), responsible for distinct (9/31) or overlapping (22/31) phenotypes, and potential MMDs in 39/880 additional individuals (4.4%). CONCLUSION MMDs are frequent in CA/ID and remain a strong challenge. Reanalysis of positive ES data appears essential when phenotypes are partially explained by the initial diagnosis or atypically enriched overtime. Up-to-date clinical data, clinical expertise from the referring physician, strong interactions between clinicians and biologists, and increasing gene discoveries and improved ES bioinformatics tools appear all the more fundamental to enhance chances of identifying MMDs. It is essential to provide appropriate patient care and genetic counselling.
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Affiliation(s)
- Caroline Racine
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Camille Engel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Frederic Tran Mau-Them
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Ange-Line Bruel
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Antonio Vitobello
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Hana Safraou
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Arthur Sorlin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sophie Nambot
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Julian Delanne
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Aurore Garde
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Estelle Colin
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
| | - Sébastien Moutton
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Nolwenn Jean-Marçais
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
| | - Marjolaine Willems
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - David Geneviève
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
- INSERM U1183, Université de Montpellier, Montpellier, France
| | - Lucile Pinson
- Centre de Référence "Anomalies du Développement syndromes malformatifs" Occitanie, Service de Génétique Médicale, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - Laurence Perrin
- Genetic Department, Robert-Debré Hospital Department of Genetics, Paris, France
| | - Fanny Laffargue
- Service de Génétique médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - James Lespinasse
- Unité de Génétique médicale, Centre Hospitalier Métropole Savoie, Chambery, France
| | - Elodie Lacaze
- Department of Medical Genetics, Hospital Group Le Havre, Le Havre, France
| | - Arnaud Molin
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | - Marion Gerard
- Service de Génétique, University Hospital Centre Caen, Caen, France
| | | | | | - Olivier Patat
- Department of Medical Genetics, University Hospital Centre Toulouse, Toulouse, France
| | - Valentin Bourgeois
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Charlotte Poe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Martin Chevarin
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Victor Couturier
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Philippine Garret
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christophe Philippe
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Yannis Duffourd
- Functional Unity of Innovative Diagnosis for Rare Diseases, University of Burgundy, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Anomalies du Développement et Syndromes Malformatifs de l'interrégion Est et FHU TRANSLAD, Centre Hospitalier Universitaire de Dijon Centre de Genetique, Dijon, France
- Inserm UMR1231 team GAD, University of Burgundy, Dijon, France
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12
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Alabdulrazzaq F, Alanzi T, Al‐Balool HH, Gardham A, Wakeling E, Leitch HG, AlSayed M, Abdulrahim M, Aladwani A, Romito A, Kampe K, Ferdinandusse S, Aboelanine AH, Abdullah A, Alwadani A, Bastaki L, Vaz FM, Bertoli‐Avella AM, Marafi D. Expanding the allelic spectrum of ELOVL4-related autosomal recessive neuro-ichthyosis. Mol Genet Genomic Med 2023; 11:e2256. [PMID: 37592902 PMCID: PMC10724518 DOI: 10.1002/mgg3.2256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/27/2023] [Accepted: 07/14/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Very long-chain fatty acids (VLCFAs) composed of more than 20 carbon atoms are essential in the biosynthesis of cell membranes in the brain, skin, and retina. VLCFAs are elongated beyond 28 carbon atoms by ELOVL4 enzyme. Variants in ELOVL4 are associated with three Mendelian disorders: autosomal dominant (AD) Stargardt-like macular dystrophy type 3, AD spinocerebellar ataxia, and autosomal recessive disorder congenital ichthyosis, spastic quadriplegia and impaired intellectual development (ISQMR). Only seven subjects from five unrelated families with ISQMR have been described, all of which have biallelic single-nucleotide variants. METHODS We performed clinical exome sequencing on probands from four unrelated families with neuro-ichthyosis. RESULTS We identified three novel homozygous ELOVL4 variants. Two of the families originated from the same Saudi tribe and had the exact homozygous exonic deletion in ELOVL4, while the third and fourth probands had two different novel homozygous missense variants. Seven out of the eight affected subjects had profound developmental delay, epilepsy, axial hypotonia, peripheral hypertonia, and ichthyosis. Delayed myelination and corpus callosum hypoplasia were seen in two of five subjects with brain magnetic rosonance imaging and cerebral atrophy in three. CONCLUSION Our study expands the allelic spectrum of ELOVL4-related ISQMR. The detection of the same exonic deletion in two unrelated Saudi family from same tribe suggests a tribal founder mutation.
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Affiliation(s)
- Fatima Alabdulrazzaq
- Department of PediatricsAdan Hospital, Ministry of HealthHadiyaKuwait
- Kuwait Institute of Medical SpecializationSulaibkikhatKuwait
| | - Talal Alanzi
- Division Medical Genetics and Metabolic, Department of PediatricsPrince Sultan Military Medical CityRiyadhSaudi Arabia
| | | | - Alice Gardham
- North West Thames Regional Genetics Service, Northwick Park HospitalHarrowUK
| | - Emma Wakeling
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonUK
| | - Harry G. Leitch
- North West Thames Regional Genetics Service, Northwick Park HospitalHarrowUK
- Medical Research CouncilLondon Institute of Medical SciencesLondonUK
- Institute of Clinical Sciences, Faculty of MedicineImperial College LondonLondonUK
| | - Moeenaldeen AlSayed
- Department of Medical GeneticsKing Faisal Specialist Hospital and Research CenterRiyadhSaudi Arabia
- Faculty of MedicineAlfaisal UniversityRiyadhSaudi Arabia
| | - Maha Abdulrahim
- King Abdullah Bin Abdulaziz University Hospital, Princess Nourah Bint Abdulrahman UniversityRiyadhSaudi Arabia
| | | | | | | | - Sacha Ferdinandusse
- Amsterdam UMC Location University of Amsterdam, Department of Clinical Chemistry and PediatricsLaboratory Genetic Metabolic Diseases, Emma Children's HospitalAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of MetabolismAmsterdamThe Netherlands
| | | | - Amira Abdullah
- Department of PediatricsAdan Hospital, Ministry of HealthHadiyaKuwait
| | - Amal Alwadani
- Kuwait Medical Genetics Centre, Ministry of HealthSulaibikhatKuwait
| | - Laila Bastaki
- Kuwait Medical Genetics Centre, Ministry of HealthSulaibikhatKuwait
| | - Frédéric M. Vaz
- Amsterdam UMC Location University of Amsterdam, Department of Clinical Chemistry and PediatricsLaboratory Genetic Metabolic Diseases, Emma Children's HospitalAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology Metabolism, Inborn Errors of MetabolismAmsterdamThe Netherlands
| | | | - Dana Marafi
- Department of PediatricsAdan Hospital, Ministry of HealthHadiyaKuwait
- Kuwait Medical Genetics Centre, Ministry of HealthSulaibikhatKuwait
- Department of Pediatrics, Faculty of MedicineKuwait UniversitySafatKuwait
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13
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Duan R, Marafi D, Xia ZJ, Ng BG, Maroofian R, Sumya FT, Saad AK, Du H, Fatih JM, Hunter JV, Elbendary HM, Baig SM, Abdullah U, Ali Z, Efthymiou S, Murphy D, Mitani T, Withers MA, Jhangiani SN, Coban-Akdemir Z, Calame DG, Pehlivan D, Gibbs RA, Posey JE, Houlden H, Lupashin VV, Zaki MS, Freeze HH, Lupski JR. Biallelic missense variants in COG3 cause a congenital disorder of glycosylation with impairment of retrograde vesicular trafficking. J Inherit Metab Dis 2023; 46:1195-1205. [PMID: 37711075 PMCID: PMC10873070 DOI: 10.1002/jimd.12679] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/16/2023] [Accepted: 09/13/2023] [Indexed: 09/16/2023]
Abstract
Biallelic variants in genes for seven out of eight subunits of the conserved oligomeric Golgi complex (COG) are known to cause recessive congenital disorders of glycosylation (CDG) with variable clinical manifestations. COG3 encodes a constituent subunit of the COG complex that has not been associated with disease traits in humans. Herein, we report two COG3 homozygous missense variants in four individuals from two unrelated consanguineous families that co-segregated with COG3-CDG presentations. Clinical phenotypes of affected individuals include global developmental delay, severe intellectual disability, microcephaly, epilepsy, facial dysmorphism, and variable neurological findings. Biochemical analysis of serum transferrin from one family showed the loss of a single sialic acid. Western blotting on patient-derived fibroblasts revealed reduced COG3 and COG4. Further experiments showed delayed retrograde vesicular recycling in patient cells. This report adds to the knowledge of the COG-CDG network by providing collective evidence for a COG3-CDG rare disease trait and implicating a likely pathology of the disorder as the perturbation of Golgi trafficking.
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Affiliation(s)
- Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Zhi-Jie Xia
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Bobby G. Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Farhana Taher Sumya
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Ahmed K. Saad
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jill V. Hunter
- Department of Pediatric Radiology, Texas Children’s Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Hasnaa M. Elbendary
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Shahid M. Baig
- Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi, Pakistan
- Pakistan Science Foundation (PSF), Islamabad, Pakistan
| | - Uzma Abdullah
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi, Pakistan
| | - Zafar Ali
- Centre for Biotechnology and Microbiology, University of Swat, Swat, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Marjorie A. Withers
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Daniel G. Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Vladimir V. Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Maha S. Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Hospital, Houston, Texas, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
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14
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O'Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: What's next in diagnostic testing for Mendelian conditions. Am J Hum Genet 2023; 110:1229-1248. [PMID: 37541186 PMCID: PMC10432150 DOI: 10.1016/j.ajhg.2023.06.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/06/2023] Open
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order, and emerging technologies, such as optical genome mapping and long-read DNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to research consortia focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Michael H Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children's National Research Institute, Children's National Hospital, Washington, DC 20010, USA; Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Philip M Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emily E Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Emmanuèle C Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA; Center for Genetics Medicine Research, Children's National Research and Innovation Campus, Washington, DC, USA; Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037, USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA 98195, USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lea M Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen B Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael J Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jessica X Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Matthew T Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Seth I Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children's National Hospital, Washington, DC 20010, USA
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Department of Computer Science, Rice University, 6100 Main Street, Houston, TX 77005, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.
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15
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Schmid CM, Gregor A, Costain G, Morel CF, Massingham L, Schwab J, Quélin C, Faoucher M, Kaplan J, Procopio R, Saunders CJ, Cohen ASA, Lemire G, Sacharow S, O'Donnell-Luria A, Segal RJ, Kianmahd Shamshoni J, Schweitzer D, Ebrahimi-Fakhari D, Monaghan K, Palculict TB, Napier MP, Tao A, Isidor B, Moradkhani K, Reis A, Sticht H, Chung WK, Zweier C. LHX2 haploinsufficiency causes a variable neurodevelopmental disorder. Genet Med 2023; 25:100839. [PMID: 37057675 DOI: 10.1016/j.gim.2023.100839] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023] Open
Abstract
PURPOSE LHX2 encodes the LIM homeobox 2 transcription factor (LHX2), which is highly expressed in brain and well conserved across species, but it has not been clearly linked to neurodevelopmental disorders (NDDs) to date. METHODS Through international collaboration, we identified 19 individuals from 18 families with variable neurodevelopmental phenotypes, carrying a small chromosomal deletion, likely gene-disrupting or missense variants in LHX2. Functional consequences of missense variants were investigated in cellular systems. RESULTS Affected individuals presented with developmental and/or behavioral abnormalities, autism spectrum disorder, variable intellectual disability, and microcephaly. We observed nucleolar accumulation for 2 missense variants located within the DNA-binding HOX domain, impaired interaction with co-factor LDB1 for another variant located in the protein-protein interaction-mediating LIM domain, and impaired transcriptional activation by luciferase assay for 4 missense variants. CONCLUSION We implicate LHX2 haploinsufficiency by deletion and likely gene-disrupting variants as causative for a variable NDD. Our findings suggest a loss-of-function mechanism also for likely pathogenic LHX2 missense variants. Together, our observations underscore the importance of LHX2 in the nervous system and for variable neurodevelopmental phenotypes.
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Affiliation(s)
- Cosima M Schmid
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern, Switzerland; Department for Biomedical Research, University of Bern, Bern, Switzerland
| | - Anne Gregor
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern, Switzerland; Department for Biomedical Research, University of Bern, Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, Bern, Switzerland
| | - Gregory Costain
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada; Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Chantal F Morel
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lauren Massingham
- Division of Human Genetics, Department of Pediatrics, Warren Alpert Medical School of Brown University, Hasbro Children's Hospital/Rhode Island Hospital, Providence, RI
| | - Jennifer Schwab
- Division of Human Genetics, Department of Pediatrics, Warren Alpert Medical School of Brown University, Hasbro Children's Hospital/Rhode Island Hospital, Providence, RI
| | - Chloé Quélin
- Clinical Genetics Department, CHU Hôspital Sud, Rennes, France
| | - Marie Faoucher
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France; Univ Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Julie Kaplan
- Division of Genetics, Department of Pediatrics, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Rebecca Procopio
- Division of Genetics, Department of Pediatrics, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE
| | - Carol J Saunders
- Genomic Medicine Center, Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; University of Missouri-Kansas City School of Medicine, Kansas City, MO
| | - Ana S A Cohen
- Genomic Medicine Center, Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City, Kansas City, MO; University of Missouri-Kansas City School of Medicine, Kansas City, MO
| | - Gabrielle Lemire
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Stephanie Sacharow
- Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Anne O'Donnell-Luria
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Ranit Jaron Segal
- Schneider Children's Medical Center of Israel, Petach Tikvah, Israel
| | - Jessica Kianmahd Shamshoni
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Daniela Schweitzer
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, UCLA, Los Angeles, CA
| | - Darius Ebrahimi-Fakhari
- Movement Disorders Program, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | | | | | | | - Alice Tao
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY
| | | | | | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Centre for Rare Diseases Erlangen (ZSEER), University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Heinrich Sticht
- Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY
| | - Christiane Zweier
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern, Switzerland; Department for Biomedical Research, University of Bern, Bern, Switzerland; Bern Center for Precision Medicine (BCPM), University of Bern, Bern, Switzerland.
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16
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Dawood M, Akay G, Mitani T, Marafi D, Fatih JM, Gezdirici A, Najmabadi H, Kahrizi K, Punetha J, Grochowski CM, Du H, Jolly A, Li H, Coban-Akdemir Z, Sedlazeck FJ, Hunter JV, Jhangiani SN, Muzny D, Pehlivan D, Posey JE, Carvalho CM, Gibbs RA, Lupski JR. A biallelic frameshift indel in PPP1R35 as a cause of primary microcephaly. Am J Med Genet A 2023; 191:794-804. [PMID: 36598158 PMCID: PMC9928800 DOI: 10.1002/ajmg.a.63080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/05/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023]
Abstract
Protein phosphatase 1 regulatory subunit 35 (PPP1R35) encodes a centrosomal protein required for recruiting microtubule-binding elongation machinery. Several proteins in this centriole biogenesis pathway correspond to established primary microcephaly (MCPH) genes, and multiple model organism studies hypothesize PPP1R35 as a candidate MCPH gene. Here, using exome sequencing (ES) and family-based rare variant analyses, we report a homozygous, frameshifting indel deleting the canonical stop codon in the last exon of PPP1R35 [Chr7: c.753_*3delGGAAGCGTAGACCinsCG (p.Trp251Cysfs*22)]; the variant allele maps in a 3.7 Mb block of absence of heterozygosity (AOH) in a proband with severe MCPH (-4.3 SD at birth, -6.1 SD by 42 months), pachygyria, and global developmental delay from a consanguineous Turkish kindred. Droplet digital PCR (ddPCR) confirmed mutant mRNA expression in fibroblasts. In silico prediction of the translation of mutant PPP1R35 is expected to be elongated by 18 amino acids before encountering a downstream stop codon. This complex indel allele is absent in public databases (ClinVar, gnomAD, ARIC, 1000 genomes) and our in-house database of 14,000+ exomes including 1800+ Turkish exomes supporting predicted pathogenicity. Comprehensive literature searches for PPP1R35 variants yielded two probands affected with severe microcephaly (-15 SD and -12 SD) with the same homozygous indel from a single, consanguineous, Iranian family from a cohort of 404 predominantly Iranian families. The lack of heterozygous cases in two large cohorts representative of the genetic background of these two families decreased our suspicion of a founder allele and supports the contention of a recurrent mutation. We propose two potential secondary structure mutagenesis models for the origin of this variant allele mediated by hairpin formation between complementary GC rich segments flanking the stop codon via secondary structure mutagenesis.
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Affiliation(s)
- Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - He Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Fritz J. Sedlazeck
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jill V. Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, 77030, USA
- E.B. Singleton Department of Pediatric Radiology, Texas Children’s Hospital, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Donna Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Pacific Northwest Research Institute, Seattle, WA, 98122, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030
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17
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Wojcik MH, Reuter CM, Marwaha S, Mahmoud M, Duyzend MH, Barseghyan H, Yuan B, Boone PM, Groopman EE, Délot EC, Jain D, Sanchis-Juan A, Starita LM, Talkowski M, Montgomery SB, Bamshad MJ, Chong JX, Wheeler MT, Berger SI, O’Donnell-Luria A, Sedlazeck FJ, Miller DE. Beyond the exome: what's next in diagnostic testing for Mendelian conditions. ARXIV 2023:arXiv:2301.07363v1. [PMID: 36713248 PMCID: PMC9882576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Despite advances in clinical genetic testing, including the introduction of exome sequencing (ES), more than 50% of individuals with a suspected Mendelian condition lack a precise molecular diagnosis. Clinical evaluation is increasingly undertaken by specialists outside of clinical genetics, often occurring in a tiered fashion and typically ending after ES. The current diagnostic rate reflects multiple factors, including technical limitations, incomplete understanding of variant pathogenicity, missing genotype-phenotype associations, complex gene-environment interactions, and reporting differences between clinical labs. Maintaining a clear understanding of the rapidly evolving landscape of diagnostic tests beyond ES, and their limitations, presents a challenge for non-genetics professionals. Newer tests, such as short-read genome or RNA sequencing, can be challenging to order and emerging technologies, such as optical genome mapping and long-read DNA or RNA sequencing, are not available clinically. Furthermore, there is no clear guidance on the next best steps after inconclusive evaluation. Here, we review why a clinical genetic evaluation may be negative, discuss questions to be asked in this setting, and provide a framework for further investigation, including the advantages and disadvantages of new approaches that are nascent in the clinical sphere. We present a guide for the next best steps after inconclusive molecular testing based upon phenotype and prior evaluation, including when to consider referral to a consortium such as GREGoR, which is focused on elucidating the underlying cause of rare unsolved genetic disorders.
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Affiliation(s)
- Monica H. Wojcik
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Division of Newborn Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chloe M. Reuter
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Shruti Marwaha
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Medhat Mahmoud
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Michael H. Duyzend
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Hayk Barseghyan
- Center for Genetics Medicine Research, Children’s National Research Institute, Children’s National Hospital, Washington, DC 20010 USA
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Bo Yuan
- Department of Molecular and Human Genetics and Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
| | - Philip M. Boone
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emily E. Groopman
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Emmanuèle C. Délot
- Department of Genomics and Precision Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
- Center for Genetics Medicine Research, Children’s National Research and Innovation Campus, Washington, DC, USA
- Department of Pediatrics, George Washington University, School of Medicine and Health Sciences, George Washington University, Washington, DC 20037 USA
| | - Deepti Jain
- Department of Biostatistics, School of Public Health, University of Washington, Seattle WA 98195 USA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | | | - Lea M. Starita
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
| | - Michael Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Stephen B. Montgomery
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael J. Bamshad
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Jessica X. Chong
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Matthew T. Wheeler
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Seth I. Berger
- Center for Genetics Medicine Research and Rare Disease Institute, Children’s National Hospital, Washington, DC 20010 USA
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115 USA
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030 USA
- Department of Computer Science, Rice University, 6100 Main Street, Houston, TX, 77005 USA
| | - Danny E. Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195 USA
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18
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Shravya MS, Mathew M, Vasudeva A, Girisha KM, Nayak SS. A novel biallelic variant c.2219T > A p.(Leu740*) in ADGRG6 as a cause of lethal congenital contracture syndrome 9. Clin Genet 2023; 103:127-129. [PMID: 36210633 DOI: 10.1111/cge.14237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 12/13/2022]
Affiliation(s)
- Mangalore S Shravya
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Mary Mathew
- Department of Pathology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Akhila Vasudeva
- Department of Obstetrics and Gynaecology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
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19
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Dual Molecular Diagnoses of Recessive Disorders in a Child from Consanguineous Parents: Case Report and Literature Review. Genes (Basel) 2022; 13:genes13122377. [PMID: 36553645 PMCID: PMC9778442 DOI: 10.3390/genes13122377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
The widespread use of whole exome sequencing (WES) resulted in the discovery of multilocus pathogenic variations (MPV), defined as two or more distinct or overlapping Mendelian disorders occurring in a patient, leading to a blended phenotype. In this study, we report on a child with autosomal recessive primary microcephaly-5 (MCPH5) and nephropathic cystinosis. The proband is the first child of consanguineous parents, presenting a complex phenotype including neurodevelopmental delay, microcephaly, growth restriction, significant delay of bone maturation, lissencephaly, and abnormality of neuronal migration, photophobia, and renal tubular acidosis. WES revealed two pathogenic and homozygous variants: a c.4174C>T variant in the ASPM gene and a c.382C>T variant in the CTNS gene, explaining the complex phenotype. The literature review showed that most of the patients harboring two variants in recessive disease genes are born to consanguineous parents. To the best of our knowledge, the patient herein described is the first one harboring pathogenic variants in both the ASPM and CTNS genes. These findings highlight the importance of searching for MPV in patients with complex phenotypes investigated by genome-wide testing methods, especially for those patients born to consanguineous parents.
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20
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Abstract
PURPOSE OF REVIEW Genetic studies in humans and animal models have improved our understanding of the role of numerous genes in the etiology of nonsyndromic tooth agenesis (TA). The purpose of this review is to discuss recently identified genes potentially contributing to TA. RECENT FINDINGS Despite research progress, understanding the genetic factors underlying nonsyndromic TA has been challenging given the genetic heterogeneity, variable expressivity, and incomplete penetrance of putatively pathogenic variants often observed associated with the condition. Next-generation sequencing technologies have provided a platform for novel gene and variant discoveries and informed paradigm-shifting concepts in the etiology of TA. This review summarizes the current knowledge on genes and pathways related to nonsyndromic TA with a focus on recently identified genes/variants. Evidence suggesting possible multi-locus variation in TA is also presented.
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Affiliation(s)
- Ariadne Letra
- Department of Oral and Craniofacial Sciences, and Center for Craniofacial and Dental Genetics, University of Pittsburgh School of Dental Medicine, Pittsburgh, PA, 15219, USA.
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21
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Spedicati B, Morgan A, Pianigiani G, Musante L, Rubinato E, Santin A, Nardone GG, Faletra F, Girotto G. Challenging Occam’s Razor: Dual Molecular Diagnoses Explain Entangled Clinical Pictures. Genes (Basel) 2022; 13:genes13112023. [PMID: 36360260 PMCID: PMC9690221 DOI: 10.3390/genes13112023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Dual molecular diagnoses are defined as the presence of pathogenic variants at two distinct and independently segregating loci that cause two different Mendelian conditions. In this study, we report the identification of double genetic disorders in a series of patients with complex clinical features. In the last 24 months, 342 syndromic patients have been recruited and clinically characterised. Whole Exome Sequencing analysis has been performed on the proband and on both parents and identified seven patients affected by a dual molecular diagnosis. Upon a detailed evaluation of both their clinical and molecular features, subjects are able to be divided into two groups: (A) five patients who present distinct phenotypes, due to each of the two different underlying genetic diseases; (B) two patients with overlapping clinical features that may be underpinned by both the identified genetic variations. Notably, only in one case a multilocus genomic variation was already suspected during the clinical evaluation. Overall, our findings highlight how dual molecular diagnoses represent a challenging model of complex inheritance that should always be considered whenever a patient shows atypical clinical features. Indeed, an accurate genetic characterisation is of the utmost importance to provide patients with a personalised and safe clinical management.
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Affiliation(s)
- Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Anna Morgan
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Giulia Pianigiani
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
- Correspondence: ; Tel.: +39-040-3785539
| | - Luciana Musante
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Elisa Rubinato
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Aurora Santin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | | | - Flavio Faletra
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
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22
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BCOR variants are associated with X-linked recessive partial epilepsy. Epilepsy Res 2022; 187:107036. [DOI: 10.1016/j.eplepsyres.2022.107036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/12/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022]
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23
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Duan R, Hijazi H, Gulec EY, Eker HK, Costa SR, Sahin Y, Ocak Z, Isikay S, Ozalp O, Bozdogan S, Aslan H, Elcioglu N, Bertola DR, Gezdirici A, Du H, Fatih JM, Grochowski CM, Akay G, Jhangiani SN, Karaca E, Gu S, Coban-Akdemir Z, Posey JE, Bayram Y, Sutton VR, Carvalho CM, Pehlivan D, Gibbs RA, Lupski JR. Developmental genomics of limb malformations: Allelic series in association with gene dosage effects contribute to the clinical variability. HGG ADVANCES 2022; 3:100132. [PMID: 36035248 PMCID: PMC9403727 DOI: 10.1016/j.xhgg.2022.100132] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022] Open
Abstract
Genetic heterogeneity, reduced penetrance, and variable expressivity, the latter including asymmetric body axis plane presentations, have all been described in families with congenital limb malformations (CLMs). Interfamilial and intrafamilial heterogeneity highlight the complexity of the underlying genetic pathogenesis of these developmental anomalies. Family-based genomics by exome sequencing (ES) and rare variant analyses combined with whole-genome array-based comparative genomic hybridization were implemented to investigate 18 families with limb birth defects. Eleven of 18 (61%) families revealed explanatory variants, including 7 single-nucleotide variant alleles and 3 copy number variants (CNVs), at previously reported "disease trait associated loci": BHLHA9, GLI3, HOXD cluster, HOXD13, NPR2, and WNT10B. Breakpoint junction analyses for all three CNV alleles revealed mutational signatures consistent with microhomology-mediated break-induced replication, a mechanism facilitated by Alu/Alu-mediated rearrangement. Homozygous duplication of BHLHA9 was observed in one Turkish kindred and represents a novel contributory genetic mechanism to Gollop-Wolfgang Complex (MIM: 228250), where triplication of the locus has been reported in one family from Japan (i.e., 4n = 2n + 2n versus 4n = 3n + 1n allelic configurations). Genes acting on limb patterning are sensitive to a gene dosage effect and are often associated with an allelic series. We extend an allele-specific gene dosage model to potentially assist, in an adjuvant way, interpretations of interconnections among an allelic series, clinical severity, and reduced penetrance of the BHLHA9-related CLM spectrum.
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Affiliation(s)
- Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hadia Hijazi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
| | | | - Silvia R. Costa
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
| | - Yavuz Sahin
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
| | - Zeynep Ocak
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
| | - Débora R. Bertola
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Baylor-Hopkins Center for Mendelian Genomics
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Medical Genetics, School of Medicine, Istanbul Medeniyet University, Istanbul, Turkey
- Department of Medical Genetics, Konya City Hospital, Konya, Turkey
- Human Genome and Stem Cell Research Center, Institute of Bioscience, Universidade de São Paulo, São Paulo, Brazil
- Medical Genetics, Genoks Genetics Center, Ankara, Turkey
- Department of Medical Genetics, Faculty of Medicine, Istinye University, Istanbul, Turkey
- Department of Pediatric Neurology, Faculty of Medicine, Gaziantep University, Gaziantep, Turkey
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana, Turkey
- Department of Medical Genetics, Faculty of Medicine, Cukurova University, Adana, Turkey
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul, Turkey
- Eastern Mediterranean University Medical School, Magosa, 10 Mersin, Turkey
- Genetics Unit, Instituto da Criança do Hospital das Clínicas da Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul, Turkey
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | | | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shen Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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24
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Reid KM, Spaull R, Salian S, Barwick K, Meyer E, Zhen J, Hirata H, Sheipouri D, Benkerroum H, Gorman KM, Papandreou A, Simpson MA, Hirano Y, Farabella I, Topf M, Grozeva D, Carss K, Smith M, Pall H, Lunt P, De Gressi S, Kamsteeg E, Haack TB, Carr L, Guerreiro R, Bras J, Maher ER, Scott RH, Vandenberg RJ, Raymond FL, Chong WK, Sudhakar S, Mankad K, Reith ME, Campeau PM, Harvey RJ, Kurian MA. MED27, SLC6A7, and MPPE1 Variants in a Complex Neurodevelopmental Disorder with Severe Dystonia. Mov Disord 2022; 37:2139-2146. [PMID: 35876425 PMCID: PMC9796674 DOI: 10.1002/mds.29147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/19/2022] [Accepted: 06/13/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Despite advances in next generation sequencing technologies, the identification of variants of uncertain significance (VUS) can often hinder definitive diagnosis in patients with complex neurodevelopmental disorders. OBJECTIVE The objective of this study was to identify and characterize the underlying cause of disease in a family with two children with severe developmental delay associated with generalized dystonia and episodic status dystonicus, chorea, epilepsy, and cataracts. METHODS Candidate genes identified by autozygosity mapping and whole-exome sequencing were characterized using cellular and vertebrate model systems. RESULTS Homozygous variants were found in three candidate genes: MED27, SLC6A7, and MPPE1. Although the patients had features of MED27-related disorder, the SLC6A7 and MPPE1 variants were functionally investigated. SLC6A7 variant in vitro overexpression caused decreased proline transport as a result of reduced cell-surface expression, and zebrafish knockdown of slc6a7 exhibited developmental delay and fragile motor neuron morphology that could not be rescued by L-proline transporter-G396S RNA. Lastly, patient fibroblasts displayed reduced cell-surface expression of glycophosphatidylinositol-anchored proteins linked to MPPE1 dysfunction. CONCLUSIONS We report a family harboring a homozygous MED27 variant with additional loss-of-function SLC6A7 and MPPE1 gene variants, which potentially contribute to a blended phenotype caused by multilocus pathogenic variants. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Kimberley M. Reid
- Molecular Neurosciences, Developmental Neurosciences, Zayed Centre for Research into Rare Disease in ChildrenUCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Robert Spaull
- Molecular Neurosciences, Developmental Neurosciences, Zayed Centre for Research into Rare Disease in ChildrenUCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom,Department of NeurologyGreat Ormond Street HospitalLondonUnited Kingdom
| | - Smrithi Salian
- Department of Pediatrics, CHU Sainte‐Justine Research CenterUniversity of MontrealMontrealQuebecCanada
| | - Katy Barwick
- Molecular Neurosciences, Developmental Neurosciences, Zayed Centre for Research into Rare Disease in ChildrenUCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Esther Meyer
- Molecular Neurosciences, Developmental Neurosciences, Zayed Centre for Research into Rare Disease in ChildrenUCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Juan Zhen
- Cell Therapy and Cell Engineering FacilityMemorial Sloan Kettering Cancer CenterNew YorkNew YorkUSA
| | - Hiromi Hirata
- Department of Chemistry and Biological ScienceCollege of Science and Engineering, Aoyama Gakuin UniversitySagamiharaJapan
| | - Diba Sheipouri
- School of Medical Sciences, University of SydneySydneyNew South WalesAustralia
| | - Hind Benkerroum
- Department of Pediatrics, CHU Sainte‐Justine Research CenterUniversity of MontrealMontrealQuebecCanada
| | - Kathleen M. Gorman
- Department of Neurology and Clinical NeurophysiologyChildren's Health Ireland at Temple StreetDublinIreland,School of Medicine and Medical SciencesUniversity College DublinDublinIreland
| | - Apostolos Papandreou
- Molecular Neurosciences, Developmental Neurosciences, Zayed Centre for Research into Rare Disease in ChildrenUCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom,Department of NeurologyGreat Ormond Street HospitalLondonUnited Kingdom
| | - Michael A. Simpson
- Division of Genetics and Molecular MedicineKing's College London School of MedicineLondonUnited Kingdom
| | - Yoshinobu Hirano
- Department of Chemistry and Biological ScienceCollege of Science and Engineering, Aoyama Gakuin UniversitySagamiharaJapan
| | - Irene Farabella
- Institute of Structural and Molecular Biology, Crystallography/Department of Biological SciencesBirkbeck College, University of LondonLondonUnited Kingdom,CNAG‐CRG, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - Maya Topf
- Leibniz Institute for Virology (HPI) and Universitätsklinikum Hamburg Eppendorf (UKE)Centre for Structural Systems Biology (CSSB)HamburgGermany,Institute of Structural and Molecular Biology, Crystallography/Department of Biological SciencesBirkbeck College, University of LondonLondonUnited Kingdom
| | - Detelina Grozeva
- Department of Medical GeneticsCambridge Institute for Medical Research, University of CambridgeCambridgeUnited Kingdom,Centre for Trials Research, Neuadd MeirionnyddCardiff UniversityCardiffUnited Kingdom
| | - Keren Carss
- Wellcome Trust Sanger InstituteCambridgeUnited Kingdom
| | - Martin Smith
- Department of NeurologyJohn Radcliffe HospitalOxfordUnited Kingdom
| | - Hardev Pall
- Department of NeurologyQueen Elizabeth HospitalBirminghamUnited Kingdom
| | - Peter Lunt
- Clinical Genetic ServiceGloucester Royal HospitalGloucesterUnited Kingdom
| | - Susanna De Gressi
- Department of PaediatricsCheltenham General HospitalGloucestershireUnited Kingdom
| | - Erik‐Jan Kamsteeg
- Department of Human GeneticsRadboud University Medical CenterNijmegenNetherlands
| | - Tobias B. Haack
- Institute of Medical Genetics and Applied GenomicsUniversity of TuebingenTuebingenGermany
| | - Lucinda Carr
- Department of NeurologyGreat Ormond Street HospitalLondonUnited Kingdom
| | - Rita Guerreiro
- Department of Neurodegenerative ScienceVan Andel InstituteGrand RapidsMichiganUSA
| | - Jose Bras
- Department of Neurodegenerative ScienceVan Andel InstituteGrand RapidsMichiganUSA
| | - Eamonn R. Maher
- Department of Medical GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Richard H. Scott
- Department of Clinical GeneticsGreat Ormond Street HospitalLondonUnited Kingdom
| | | | - F. Lucy Raymond
- Centre for Trials Research, Neuadd MeirionnyddCardiff UniversityCardiffUnited Kingdom
| | - Wui K. Chong
- Department of RadiologyGreat Ormond Street HospitalLondonUnited Kingdom,Developmental Neurosciences DepartmentUCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Sniya Sudhakar
- Department of RadiologyGreat Ormond Street HospitalLondonUnited Kingdom,Developmental Neurosciences DepartmentUCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Kshitij Mankad
- Department of RadiologyGreat Ormond Street HospitalLondonUnited Kingdom,Developmental Neurosciences DepartmentUCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom
| | - Maarten E. Reith
- Department of PsychiatryNew York University School of MedicineNew YorkNew YorkUSA
| | - Philippe M. Campeau
- Department of Pediatrics, CHU Sainte‐Justine Research CenterUniversity of MontrealMontrealQuebecCanada
| | - Robert J. Harvey
- School of Health and Behavioural SciencesUniversity of the Sunshine CoastSippy DownsQueenslandAustralia,Sunshine Coast Health InstituteBirtinyaQueenslandAustralia
| | - Manju A. Kurian
- Molecular Neurosciences, Developmental Neurosciences, Zayed Centre for Research into Rare Disease in ChildrenUCL Great Ormond Street Institute of Child HealthLondonUnited Kingdom,Department of NeurologyGreat Ormond Street HospitalLondonUnited Kingdom
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25
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Sakka R, Abdelhedi F, Sellami H, Pichon B, Lajmi Y, Mnif M, Kebaili S, Derbel R, Kamoun H, Gdoura R, Delbaere A, Desir J, Abramowicz M, Vialard F, Dupont JM, Ammar-Keskes L. An unusual familial Xp22.12 microduplication including EIF1AX: A novel candidate dosage-sensitive gene for premature ovarian insufficiency. Eur J Med Genet 2022; 65:104613. [PMID: 36113757 DOI: 10.1016/j.ejmg.2022.104613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 07/22/2022] [Accepted: 09/09/2022] [Indexed: 11/19/2022]
Abstract
We report on the results of array-CGH and Whole exome sequencing (WES) studies carried out in a Tunisian family with 46,XX premature ovarian insufficiency (POI). This study has led to the identification of a familial Xp22.12 tandem duplication with a size of 559.4 kb, encompassing only three OMIM genes (RPS6KA3, SH3KBP1and EIF1AX), and a new heterozygous variant in SPIDR gene: NM_001080394.3:c.1845_1853delTATAATTGA (p.Ile616_Asp618del) segregating with POI. Increased mRNA expression levels were detected for SH3KBP1 and EIF1AX, while a normal transcript level for RPS6KA3 was detected in the three affected family members, explaining the absence of intellectual disability (ID). To the best of our knowledge, this is the first duplication involving the Xp22.12 region, reported in a family without ID, but rather with secondary amenorrhea (SA) and female infertility. As EIF1AX is a regulatory gene escaping X-inactivation, which has an extreme dosage sensitivity and highly expressed in the ovary, we suggest that this gene might be a candidate gene for ovarian function. Homozygous nonsense pathogenic variants of SPIDR gene have been reported in familial cases in POI. It has been suggested that chromosomal instability associated with SPIDR molecular defects supports the role of SPIDR protein in double-stranded DNA damage repair in vivo in humans and its causal role in POI. In this family, the variant (p.Ile616_Asp618del), present in a heterozygous state, is located in the domain that interacts with BLM and might disrupt the BLM binding ability of SPIDR protein. These findings strengthen the hypothesis that the additional effect of this variant could lead to POI in this family. Although the work represents the first evidence that EIF1AX duplication might be responsible for POI through its over-expression, further functional studies are needed to clarify and prove EIF1AX involvement in POI phenotype.
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Affiliation(s)
- Rim Sakka
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia; Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Fatma Abdelhedi
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia; Medical Genetics Department, Hedi Chaker Hospital, Sfax, Tunisia.
| | - Hanen Sellami
- Water Researches and Technologies Center (CERTE), University of Carthage, Tourist Road Soliman, Nabeul, Tunisia; Toxicology, Environmental Microbiology and Health Research Laboratory (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Bruno Pichon
- Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Yosra Lajmi
- Cytogenetics Department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris, Sorbonne Paris Cité, Paris Descartes University, Medical School, Paris, France
| | - Mouna Mnif
- Department of Endocrinology, Hedi Chaker Hospital, Sfax, Tunisia
| | - Sahbi Kebaili
- Department of Gynecology, HediChaker Hospital, Sfax, Tunisia
| | - Rihab Derbel
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia
| | - Hassen Kamoun
- Medical Genetics Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Radhouane Gdoura
- Toxicology, Environmental Microbiology and Health Research Laboratory (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Tunisia
| | - Anne Delbaere
- Fertility Clinic, Department of Gynecology and Obstetrics, Erasme Hospital, UniversitéLibre de Bruxelles, Brussels, Belgium
| | - Julie Desir
- Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Marc Abramowicz
- Center of Medical Genetics, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - François Vialard
- Genetics Department, CHI Poissy St Germain-en-Laye, F-78300, Poissy, France; RHuMA Team, UMR-BREED, INRAE-UVSQ-ENVA, UFR-SVS, F-78180, Montigny le Bretonneux, France
| | - Jean-Michel Dupont
- Cytogenetics Department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris, Sorbonne Paris Cité, Paris Descartes University, Medical School, Paris, France
| | - Leila Ammar-Keskes
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Tunisia
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26
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Marafi D, Kozar N, Duan R, Bradley S, Yokochi K, Al Mutairi F, Saadi NW, Whalen S, Brunet T, Kotzaeridou U, Choukair D, Keren B, Nava C, Kato M, Arai H, Froukh T, Faqeih EA, AlAsmari AM, Saleh MM, Pinto e Vairo F, Pichurin PN, Klee EW, Schmitz CT, Grochowski CM, Mitani T, Herman I, Calame DG, Fatih JM, Du H, Coban-Akdemir Z, Pehlivan D, Jhangiani SN, Gibbs RA, Miyatake S, Matsumoto N, Wagstaff LJ, Posey JE, Lupski JR, Meijer D, Wagner M. A reverse genetics and genomics approach to gene paralog function and disease: Myokymia and the juxtaparanode. Am J Hum Genet 2022; 109:1713-1723. [PMID: 35948005 PMCID: PMC9502070 DOI: 10.1016/j.ajhg.2022.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
The leucine-rich glioma-inactivated (LGI) family consists of four highly conserved paralogous genes, LGI1-4, that are highly expressed in mammalian central and/or peripheral nervous systems. LGI1 antibodies are detected in subjects with autoimmune limbic encephalitis and peripheral nerve hyperexcitability syndromes (PNHSs) such as Isaacs and Morvan syndromes. Pathogenic variations of LGI1 and LGI4 are associated with neurological disorders as disease traits including familial temporal lobe epilepsy and neurogenic arthrogryposis multiplex congenita 1 with myelin defects, respectively. No human disease has been reported associated with either LGI2 or LGI3. We implemented exome sequencing and family-based genomics to identify individuals with deleterious variants in LGI3 and utilized GeneMatcher to connect practitioners and researchers worldwide to investigate the clinical and electrophysiological phenotype in affected subjects. We also generated Lgi3-null mice and performed peripheral nerve dissection and immunohistochemistry to examine the juxtaparanode LGI3 microarchitecture. As a result, we identified 16 individuals from eight unrelated families with loss-of-function (LoF) bi-allelic variants in LGI3. Deep phenotypic characterization showed LGI3 LoF causes a potentially clinically recognizable PNHS trait characterized by global developmental delay, intellectual disability, distal deformities with diminished reflexes, visible facial myokymia, and distinctive electromyographic features suggestive of motor nerve instability. Lgi3-null mice showed reduced and mis-localized Kv1 channel complexes in myelinated peripheral axons. Our data demonstrate bi-allelic LoF variants in LGI3 cause a clinically distinguishable disease trait of PNHS, most likely caused by disturbed Kv1 channel distribution in the absence of LGI3.
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Affiliation(s)
- Dana Marafi
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, Safat 13110, Kuwait,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nina Kozar
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stephen Bradley
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Kenji Yokochi
- Department of Pediatrics, Toyohashi Municipal Hospital, Toyohashi, Aichi 441-8570, Japan,Department of Pediatrics, Seirei Mikatahara General Hospital, Shizuoka 433-8558, Japan
| | - Fuad Al Mutairi
- Genetics and Precision Medicine Department, King Abdullah Specialized Children’s Hospital, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, P.O. Box 22490, Riyadh 11426, Kingdom of Saudi Arabia,King Abdullah International Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Kingdom of Saudi Arabia
| | - Nebal Waill Saadi
- College of Medicine, University of Baghdad, Baghdad 10001, Iraq,Children Welfare Teaching Hospital, Medical City Complex, Baghdad 10001, Iraq
| | - Sandra Whalen
- UF de Génétique Clinique et Centre de Reference Anomalies du Développement et Syndromes Malformatifs, APHP, Sorbonne Université, Hôpital Trousseau, 75005 Paris, France
| | - Theresa Brunet
- Institute of Human Genetics, Faculty of Medicine, Technical University Munich, Munich, Germany,Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Urania Kotzaeridou
- Division of Child Neurology and Inherited Metabolic Diseases, Centre for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Division of Pediatric Endocrinology, Centre for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Boris Keren
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris 75013, France
| | - Caroline Nava
- Département de Génétique, Hôpital Pitié-Salpêtrière, Assistance Publique - Hôpitaux de Paris, Paris 75013, France
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo 142-8666, Japan
| | - Hiroshi Arai
- Department of Pediatric Neurology, Bobath Memorial Hospital, Osaka 536-0023, Japan
| | - Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Eissa Ali Faqeih
- Section of Medical Genetics, King Fahad Medical City, Children’s Specialist Hospital, Riyadh, Saudi Arabia
| | - Ali M. AlAsmari
- Section of Medical Genetics, King Fahad Medical City, Children’s Specialist Hospital, Riyadh, Saudi Arabia
| | - Mohammed M. Saleh
- Section of Medical Genetics, King Fahad Medical City, Children’s Specialist Hospital, Riyadh, Saudi Arabia
| | - Filippo Pinto e Vairo
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | | | - Eric W. Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA,Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA,Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | | | | | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Isabella Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA,Texas Children’s Hospital, Houston, TX 77030, USA
| | - Daniel G. Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA,Texas Children’s Hospital, Houston, TX 77030, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA,Texas Children’s Hospital, Houston, TX 77030, USA
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Laura J. Wagstaff
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, UK
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA,Texas Children’s Hospital, Houston, TX 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA,Corresponding author
| | - Dies Meijer
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.
| | - Matias Wagner
- Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany,Institute of Human Genetics, Technical University Munich, Munich, Germany
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27
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Zaklyazminskaya E, Shestak A, Podolyak D, Komoliatova V, Makarov L, Novitskaya A, Revishvili A. Diagnostic yield and variant reassessment in the genes encoding Nav1.5 channel in Russian patients with Brugada syndrome. Front Pharmacol 2022; 13:984299. [PMID: 36091819 PMCID: PMC9449364 DOI: 10.3389/fphar.2022.984299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Brugada syndrome (BrS) is an inherited cardiac arrhythmia characterized by ST-elevation, negative T-wave, and a high risk of sudden cardiac death (SCD) due to ventricular tachycardia. It is associated with mutations in over 20 genes but only SCN5A is recommended for routine genetic screening. This study was performed to estimate diagnostic yield and pathogenicity assessment of rare genetic variants in the genes encoding Nav1.5 channel in Russian patients with Brugada syndrome (BrS). Targeted genes panel sequencing of the five genes were screened using IonTorrent PGM with following Sanger confirmation. Detailed clinical evaluation of 75 unrelated BrS probands with a deep phenotyping of SCN5A (+) probands was performed. Twelve rare genetic variants (six missense, six truncating) were initially identified and classified as disease-causing. Reassessment of the clinical significance in the light of the current guidelines revealed: 2 Pathogenic (P) variants; 8 Likely Pathogenic (LP); two missense variants (p.G274S and p. S1778H) were re-classified later as a variant of uncertain significance (VUS). Unique VUS (p.Arg100Ser) was detected in the SCN4B gene. Lone Brugada-pattern was observed in 46% probands; 54% patients had concomitant arrhythmias. PR interval, the only electrocardiography parameter correlating with SCN5A-mutation, was longer (207 ± 24 ms) than normal in SCN5A (+) probands. SCD cases were registered in 31 families. Depression was the only recurring extra-cardiac complaint in SCN5A (+) probands; it was self-reported in five SCN5A (+) probands, and co-segregated with Brugada pattern in 2 families. After variants reassessment, the ratio of SCN5A (+) probands with Brugada syndrome accounts for 13% in Russian cohort.
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Affiliation(s)
- Elena Zaklyazminskaya
- Petrovsky National Research Centre of Surgery, Moscow, Russia
- Bochkov Research Centre for Medical Genetics, Moscow, Russia
- *Correspondence: Elena Zaklyazminskaya,
| | - Anna Shestak
- Petrovsky National Research Centre of Surgery, Moscow, Russia
| | - Dmitry Podolyak
- Petrovsky National Research Centre of Surgery, Moscow, Russia
| | - Vera Komoliatova
- Centre of Syncope and Cardiac Arrhythmias in Children and Adolescents, Moscow, Russia
| | - Leonid Makarov
- Centre of Syncope and Cardiac Arrhythmias in Children and Adolescents, Moscow, Russia
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28
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Huang Y, Ma M, Mao X, Pehlivan D, Kanca O, Un-Candan F, Shu L, Akay G, Mitani T, Lu S, Candan S, Wang H, Xiao B, Lupski JR, Bellen HJ. Novel dominant and recessive variants in human ROBO1 cause distinct neurodevelopmental defects through different mechanisms. Hum Mol Genet 2022; 31:2751-2765. [PMID: 35348658 PMCID: PMC9402236 DOI: 10.1093/hmg/ddac070] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/17/2022] [Accepted: 03/20/2022] [Indexed: 07/27/2023] Open
Abstract
The Roundabout (Robo) receptors, located on growth cones of neurons, induce axon repulsion in response to the extracellular ligand Slit. The Robo family of proteins controls midline crossing of commissural neurons during development in flies. Mono- and bi-allelic variants in human ROBO1 (HGNC: 10249) have been associated with incomplete penetrance and variable expressivity for a breath of phenotypes, including neurodevelopmental defects such as strabismus, pituitary defects, intellectual impairment, as well as defects in heart and kidney. Here, we report two novel ROBO1 variants associated with very distinct phenotypes. A homozygous missense p.S1522L variant in three affected siblings with nystagmus; and a monoallelic de novo p.D422G variant in a proband who presented with early-onset epileptic encephalopathy. We modeled these variants in Drosophila and first generated a null allele by inserting a CRIMIC T2A-GAL4 in an intron. Flies that lack robo1 exhibit reduced viability but have very severe midline crossing defects in the central nervous system. The fly wild-type cDNA driven by T2A-Gal4 partially rescues both defects. Overexpression of the human reference ROBO1 with T2A-GAL4 is toxic and reduces viability, whereas the recessive p.S1522L variant is less toxic, suggesting that it is a partial loss-of-function allele. In contrast, the dominant variant in fly robo1 (p.D413G) affects protein localization, impairs axonal guidance activity and induces mild phototransduction defects, suggesting that it is a neomorphic allele. In summary, our studies expand the phenotypic spectrum associated with ROBO1 variant alleles.
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Affiliation(s)
- Yan Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mengqi Ma
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xiao Mao
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Feride Un-Candan
- Department of Neuroloy, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Li Shu
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shenzhao Lu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sukru Candan
- Department of Medical Genetics, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Hua Wang
- National Health Commission Key Laboratory for Birth Defect Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan 410008, China
- Department of Medical Genetics, Maternal and Child Health Hospital of Hunan Province, Changsha, Hunan 410008, China
| | - Bo Xiao
- Neurology Department, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA
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29
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Calame DG, Herman I, Marshall AE, Maroofian R, Donis KC, Fatih JM, Mitani T, Du H, Grochowski CM, Sousa S, Bakhtiari S, Ito YA, Rocca C, Hunter JV, Sutton VR, Emrick LT, Boycott KM, Lossos A, Fellig Y, Prus E, Kalish Y, Meiner V, Suerink M, Ruivenkamp C, Muirhead K, Saadi NW, Zaki MS, Skidmore DL, Osmond M, Silva TO, Houlden H, Murphy D, Ghayoorarimiani E, Jamshidi Y, Jaddoa AG, Tajsharghi H, Jin SC, Coban-Akdemir Z, Travaglini L, Nicita F, Jhangiani SN, Gibbs RA, Posey JE, Kruer MC, Kernohan KD, Morales Saute JA, Vanderver A, Pehlivan D, Marafi D, Lupski JR. Biallelic Variants in the Ectonucleotidase ENTPD1 Cause a Complex Neurodevelopmental Disorder with Intellectual Disability, Distinct White Matter Abnormalities, and Spastic Paraplegia. Ann Neurol 2022; 92:304-321. [PMID: 35471564 PMCID: PMC10054521 DOI: 10.1002/ana.26381] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 04/18/2022] [Accepted: 04/21/2022] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Human genomics established that pathogenic variation in diverse genes can underlie a single disorder. For example, hereditary spastic paraplegia is associated with >80 genes, with frequently only few affected individuals described for each gene. Herein, we characterize a large cohort of individuals with biallelic variation in ENTPD1, a gene previously linked to spastic paraplegia 64 (Mendelian Inheritance in Man # 615683). METHODS Individuals with biallelic ENTPD1 variants were recruited worldwide. Deep phenotyping and molecular characterization were performed. RESULTS A total of 27 individuals from 17 unrelated families were studied; additional phenotypic information was collected from published cases. Twelve novel pathogenic ENTPD1 variants are described (NM 001776.6): c.398_399delinsAA; p.(Gly133Glu), c.540del; p.(Thr181Leufs*18), c.640del; p.(Gly216Glufs*75), c.185 T > G; p.(Leu62*), c.1531 T > C; p.(*511Glnext*100), c.967C > T; p.(Gln323*), c.414-2_414-1del, and c.146 A > G; p.(Tyr49Cys) including 4 recurrent variants c.1109 T > A; p.(Leu370*), c.574-6_574-3del, c.770_771del; p.(Gly257Glufs*18), and c.1041del; p.(Ile348Phefs*19). Shared disease traits include childhood onset, progressive spastic paraplegia, intellectual disability (ID), dysarthria, and white matter abnormalities. In vitro assays demonstrate that ENTPD1 expression and function are impaired and that c.574-6_574-3del causes exon skipping. Global metabolomics demonstrate ENTPD1 deficiency leads to impaired nucleotide, lipid, and energy metabolism. INTERPRETATION The ENTPD1 locus trait consists of childhood disease onset, ID, progressive spastic paraparesis, dysarthria, dysmorphisms, and white matter abnormalities, with some individuals showing neurocognitive regression. Investigation of an allelic series of ENTPD1 (1) expands previously described features of ENTPD1-related neurological disease, (2) highlights the importance of genotype-driven deep phenotyping, (3) documents the need for global collaborative efforts to characterize rare autosomal recessive disease traits, and (4) provides insights into disease trait neurobiology. ANN NEUROL 2022;92:304-321.
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Affiliation(s)
- Daniel G. Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Aren E. Marshall
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Reza Maroofian
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Karina Carvalho Donis
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | | | | | - Somayeh Bakhtiari
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, 85016, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine–Phoenix, Phoenix, AZ, USA
| | - Yoko A. Ito
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Clarissa Rocca
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Jill V. Hunter
- Texas Children’s Hospital, Houston, Texas, 77030, USA
- Division of Neuroradiology, Edward B. Singleton Department of Radiology, Texas Children’s Hospital, Houston, Texas
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Lisa T. Emrick
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Kym M. Boycott
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Alexander Lossos
- Department of Neurology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Yakov Fellig
- Department of Pathology, Hadassah Medical Organization and Faculty of Medicine, Hebrew University, Jerusalem 91120, Israel
| | - Eugenia Prus
- Hematology and Bone Marrow Transplantation Division, Hadassah Medical Center and the Hebrew University, POB 12000, 91120, Jerusalem, Israel
| | - Yosef Kalish
- Hematology and Bone Marrow Transplantation Division, Hadassah Medical Center and the Hebrew University, POB 12000, 91120, Jerusalem, Israel
| | - Vardiella Meiner
- Department of Genetics, Hadassah Medical Center and the Hebrew University, POB 12000, 91120, Jerusalem, Israel
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Claudia Ruivenkamp
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Kayla Muirhead
- Division of Neurology, Children’s Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Nebal W. Saadi
- College of Medicine / University of Baghdad, Children Welfare Teaching Hospital, Medical City Complex, Baghdad 10001, Iraq
| | - Maha S. Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, Centre of Excellence of Human Genetics, National Research Centre, Cairo, Egypt
| | - David L. Skidmore
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew Osmond
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
| | - Thiago Oliveira Silva
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Henry Houlden
- Department of Neuromuscular Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, United Kingdom
| | - Ehsan Ghayoorarimiani
- Genetics Section, Molecular and Clinical Sciences Institute, St. George’s University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Yalda Jamshidi
- Genetics Section, Molecular and Clinical Sciences Institute, St. George’s University of London, Cranmer Terrace, London SW17 0RE, UK
| | | | - Homa Tajsharghi
- School of Health Sciences, Division Biomedicine, University of Skovde, Skovde, Sweden
| | - Sheng Chih Jin
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Lorena Travaglini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Laboratory of Molecular Medicine, Department of Neuroscience, IRCCS Bambino Gesù Children’s Hospital, 00146 Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Laboratory of Molecular Medicine, Department of Neuroscience, IRCCS Bambino Gesù Children’s Hospital, 00146 Rome, Italy
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Michael C. Kruer
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children’s Hospital, Phoenix, AZ, 85016, USA
- Departments of Child Health, Neurology, and Cellular & Molecular Medicine, and Program in Genetics, University of Arizona College of Medicine–Phoenix, Phoenix, AZ, USA
| | - Kristin D. Kernohan
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, K1H 8L1, Canada
- Newborn Screening Ontario, Ottawa, Canada, K1H 8L1, Canada
| | - Jonas A. Morales Saute
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Internal Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- Neurology Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Adeline Vanderver
- Division of Neurology, Children’s Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, USA
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
- Texas Children’s Hospital, Houston, Texas, 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA
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Rosina E, Pezzani L, Pezzoli L, Marchetti D, Bellini M, Pilotta A, Calabrese O, Nicastro E, Cirillo F, Cereda A, Scatigno A, Milani D, Iascone M. Atypical, Composite, or Blended Phenotypes: How Different Molecular Mechanisms Could Associate in Double-Diagnosed Patients. Genes (Basel) 2022; 13:genes13071275. [PMID: 35886058 PMCID: PMC9319862 DOI: 10.3390/genes13071275] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 12/10/2022] Open
Abstract
In the last few years, trio-Whole Exome Sequencing (WES) analysis has revolutionized the diagnostic process for patients with rare genetic syndromes, demonstrating its potential even in non-specific clinical pictures and in atypical presentations of known diseases. Multiple disorders in a single patient have been estimated to occur in approximately 2–7.5% of diagnosed cases, with higher frequency in consanguineous families. Here, we report the clinical and molecular characterisation of eight illustrative patients for whom trio-WES allowed for identifing more than one genetic condition. Double homozygosity represented the causal mechanism in only half of them, whereas the other half showed peculiar multilocus combinations. The paper takes into consideration difficulties and learned lessons from our experience and therefore supports the powerful role of wide analyses for ascertaining multiple genetic diseases in complex patients, especially when a clinical suspicion could account for the majority of clinical signs. It finally makes clear how a patient’s “deep phenotyping” might not be sufficient to suggest the presence of multiple genetic diagnoses but remains essential to validate an unexpected multilocus result from genetic tests.
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Affiliation(s)
- Erica Rosina
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
| | - Lidia Pezzani
- Paediatric Unit, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (E.N.); (A.C.); (A.S.)
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy
| | - Laura Pezzoli
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
| | - Daniela Marchetti
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
| | - Matteo Bellini
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
| | - Alba Pilotta
- Auxo-Endocrinology, Diabetology and Medical Genetic Unit, Department of Paediatrics, ASST Spedali Civili, 25123 Brescia, Italy;
| | - Olga Calabrese
- Medical Genetics Unit, Azienda Ospedaliera Universitaria di Modena, 41125 Modena, Italy;
| | - Emanuele Nicastro
- Paediatric Unit, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (E.N.); (A.C.); (A.S.)
| | - Francesco Cirillo
- Pediatric Hepatology and Paediatric Liver Transplantation, Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione, 90127 Palermo, Italy;
| | - Anna Cereda
- Paediatric Unit, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (E.N.); (A.C.); (A.S.)
| | - Agnese Scatigno
- Paediatric Unit, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (L.P.); (E.N.); (A.C.); (A.S.)
| | - Donatella Milani
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milano, Italy
- Correspondence: ; Tel.: +39-02-55032560
| | - Maria Iascone
- Laboratory of Medical Genetics, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy; (E.R.); (L.P.); (D.M.); (M.B.); (M.I.)
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31
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Abdelrahman HA, Akawi N, Al-Shamsi AM, Al-Gazali L, Ali BR. Pontocerebellar Hypoplasia Type 9: A New Case with a Novel Mutation and Review of Literature. J Pediatr Genet 2022. [DOI: 10.1055/s-0042-1748018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractPontocerebellar hypoplasia type 9 (PCH-9) is a very rare autosomal recessive neurodegenerative disorder. Affected infants present early with severe developmental delay, spasticity, with the unique magnetic resonance imaging picture of thin corpus callosum, atrophied pons, and cerebellum. It is caused by loss of function mutations in the AMPD2 gene, encoding for the adenosine monophosphate deaminase enzyme-paralog 2. This gene is expressed in different somatic tissues with high level of expression in cerebellum and its encoded enzyme catalyzes a critical step in de novo biosynthesis of purines and its deficiency in the developing neurons severely affects neuronal differentiation and cell viability. We clinically evaluated an Emirati patient presented with severe developmental and growth delay, as well as corpus callosum agenesis and atrophy of brainstem and cerebellum. We performed exome sequencing, Sanger sequencing, and segregation analysis to identify the genetic cause of the phenotype, followed by in silico and in vitro analysis. We identified the novel variant (NM_004037.9:c.1471G > A) in AMPD2 gene leading to a single amino acid substitution (p.Gly491Arg) in adenosine monophosphate deaminase-2 enzyme. This variant is predicted to be pathogenic using several in silico tools, and resulted in a decrease in the enzyme function in the patient's polymorphonuclear cells by 82% (95% confidence interval: 73.3–91.7%, p = 0.029) compared with the control. This data establishes that the affected child is affected by PCH-9. Furthermore, we review all reported cases in literature to summarize the main clinical features of this rare disease.
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Affiliation(s)
- Hanadi A. Abdelrahman
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | - Nadia Akawi
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
| | | | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Heath Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Bassam R. Ali
- Department of Genetics and Genomics, College of Medicine and Heath Sciences, United Arab Emirates University Al-Ain, United Arab Emirates
- Zayed Center for Health sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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Priolo M, Mancini C, Pizzi S, Chiriatti L, Radio FC, Cordeddu V, Pintomalli L, Mammì C, Dallapiccola B, Tartaglia M. Complex Presentation of Hao-Fountain Syndrome Solved by Exome Sequencing Highlighting Co-Occurring Genomic Variants. Genes (Basel) 2022; 13:genes13050889. [PMID: 35627274 PMCID: PMC9141324 DOI: 10.3390/genes13050889] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/02/2022] [Accepted: 05/11/2022] [Indexed: 01/05/2023] Open
Abstract
Objective: The co-occurrence of pathogenic variants has emerged as a relatively common finding underlying complex phenotypes. Here, we used whole-exome sequencing (WES) to solve an unclassified multisystem clinical presentation. Patients and Methods: A 20-year-old woman affected by moderate intellectual disability (ID), dysmorphic features, hypertrichosis, scoliosis, recurrent bronchitis, and pneumonia with bronchiectasis, colelithiasis, chronic severe constipation, and a family history suggestive of autosomal dominant recurrence of polycystic kidney disease was analyzed by WES to identify the genomic events underlying the condition. Results: Four co-occurring genomic events fully explaining the proband’s clinical features were identified. A de novo truncating USP7 variant was disclosed as the cause of Hao–Fountain syndrome, a disorder characterized by syndromic ID and distinctive behavior. Compound heterozygosity for a major cystic fibrosis-causing variant and the modulator allele, IVS8-5T, in CFTR explained the recurrent upper and lower respiratory way infections, bronchiectasis, cholelithiasis, and chronic constipation. Finally, a truncating PKD2 variant co-segregating with polycystic kidney disease in the family allowed presymptomatic disease diagnosis. Conclusions: The co-occurring variants in USP7 and CFTR variants explained the multisystem disorder of the patient. The comprehensive dissection of the phenotype and early diagnosis of autosomal dominant polycystic kidney disease allowed us to manage the CFTR-related disorder symptoms and monitor renal function and other complications associated with PKD2 haploinsufficiency, addressing proper care and surveillance.
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Affiliation(s)
- Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
- Correspondence: ; Tel.: +39-09-6539-7319
| | - Cecilia Mancini
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Simone Pizzi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Luigi Chiriatti
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
| | - Francesca Clementina Radio
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Viviana Cordeddu
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Letizia Pintomalli
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
| | - Corrado Mammì
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.C.); (L.P.); (C.M.)
| | - Bruno Dallapiccola
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
| | - Marco Tartaglia
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (C.M.); (S.P.); (F.C.R.); (B.D.); (M.T.)
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Marafi D, Fatih JM, Kaiyrzhanov R, Ferla MP, Gijavanekar C, Al-Maraghi A, Liu N, Sites E, Alsaif HS, Al-Owain M, Zakkariah M, El-Anany E, Guliyeva U, Guliyeva S, Gaba C, Haseeb A, Alhashem AM, Danish E, Karageorgou V, Beetz C, Subhi AA, Mullegama SV, Torti E, Sebastin M, Breilyn MS, Duberstein S, Abdel-Hamid MS, Mitani T, Du H, Rosenfeld JA, Jhangiani SN, Coban Akdemir Z, Gibbs RA, Taylor JC, Fakhro KA, Hunter JV, Pehlivan D, Zaki MS, Gleeson JG, Maroofian R, Houlden H, Posey JE, Sutton VR, Alkuraya FS, Elsea SH, Lupski JR. Biallelic variants in SLC38A3 encoding a glutamine transporter cause epileptic encephalopathy. Brain 2022; 145:909-924. [PMID: 34605855 PMCID: PMC9050560 DOI: 10.1093/brain/awab369] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/13/2021] [Accepted: 08/26/2021] [Indexed: 11/14/2022] Open
Abstract
The solute carrier (SLC) superfamily encompasses >400 transmembrane transporters involved in the exchange of amino acids, nutrients, ions, metals, neurotransmitters and metabolites across biological membranes. SLCs are highly expressed in the mammalian brain; defects in nearly 100 unique SLC-encoding genes (OMIM: https://www.omim.org) are associated with rare Mendelian disorders including developmental and epileptic encephalopathy and severe neurodevelopmental disorders. Exome sequencing and family-based rare variant analyses on a cohort with neurodevelopmental disorders identified two siblings with developmental and epileptic encephalopathy and a shared deleterious homozygous splicing variant in SLC38A3. The gene encodes SNAT3, a sodium-coupled neutral amino acid transporter and a principal transporter of the amino acids asparagine, histidine, and glutamine, the latter being the precursor for the neurotransmitters GABA and glutamate. Additional subjects with a similar developmental and epileptic encephalopathy phenotype and biallelic predicted-damaging SLC38A3 variants were ascertained through GeneMatcher and collaborations with research and clinical molecular diagnostic laboratories. Untargeted metabolomic analysis was performed to identify novel metabolic biomarkers. Ten individuals from seven unrelated families from six different countries with deleterious biallelic variants in SLC38A3 were identified. Global developmental delay, intellectual disability, hypotonia, and absent speech were common features while microcephaly, epilepsy, and visual impairment were present in the majority. Epilepsy was drug-resistant in half. Metabolomic analysis revealed perturbations of glutamate, histidine, and nitrogen metabolism in plasma, urine, and CSF of selected subjects, potentially representing biomarkers of disease. Our data support the contention that SLC38A3 is a novel disease gene for developmental and epileptic encephalopathy and illuminate the likely pathophysiology of the disease as perturbations in glutamine homeostasis.
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Affiliation(s)
- Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait
- Correspondence to: Dana Marafi, MD, MSc Department of Pediatrics, Faculty of Medicine, Kuwait University P.O. Box 24923, 13110 Safat, Kuwait E-mail:
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rauan Kaiyrzhanov
- Department of Neuromuscular Disorders Institute of Neurology, University College London, Queen Square, London, UK
| | - Matteo P Ferla
- NIHR Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Charul Gijavanekar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
| | | | - Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Emily Sites
- Division of Molecular and Human Genetics, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Hessa S Alsaif
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Mohammad Al-Owain
- Department of Medical Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University 11533, Riyadh, Saudi Arabia
| | - Mohamed Zakkariah
- Section of Child Neurology, Department of Pediatrics, Al-adan Hospital, Riqqa, Kuwait
| | - Ehab El-Anany
- Section of Child Neurology, Department of Pediatrics, Al-adan Hospital, Riqqa, Kuwait
| | | | | | - Colette Gaba
- Department of Pediatrics, Bon Secours Mercy Health, Toledo, OH 43608, USA
| | - Ateeq Haseeb
- Mercy Children’s Hospital, Toledo, OH 43608, USA
| | - Amal M Alhashem
- Division of Medical Genetic and Metabolic Medicine, Department of Pediatrics, Prince Sultan Medical Military City, Riyadh, Saudi Arabia
| | - Enam Danish
- Department of Ophthalmology, King Fahad Armed Forces Hospital, Jeddah, Saudi Arabia
| | | | | | - Alaa A Subhi
- Neurosciences Department, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | | | | | - Monisha Sebastin
- Albert Einstein College of Medicine and the Children's Hospital at Montefiore, Bronx, New York 10467, USA
- Division of Genetics, Department of Pediatrics, Montefiore Medical Center and Albert Einstein College of Medicine, Bronx, New York, 10467, USA
| | - Margo Sheck Breilyn
- Albert Einstein College of Medicine and the Children's Hospital at Montefiore, Bronx, New York 10467, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Susan Duberstein
- Isabelle Rapin Division of Child Neurology in the Saul R Korey Department of Neurology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Mohamed S Abdel-Hamid
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jenny C Taylor
- NIHR Oxford Biomedical Research Centre, Oxford OX4 2PG, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha 26999, Qatar
- Department of Genetic Medicine, Weill Cornell Medical College, Doha, Qatar
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha 34110, Qatar
| | - Jill V Hunter
- E.B. Singleton Department of Pediatric Radiology, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Radiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Maha S Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, Howard Hughes Medical Institute, University of California, San Diego, CA 92123, USA
| | - Reza Maroofian
- Department of Neuromuscular Disorders Institute of Neurology, University College London, Queen Square, London, UK
| | - Henry Houlden
- Department of Neuromuscular Disorders Institute of Neurology, University College London, Queen Square, London, UK
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Baylor Genetics Laboratory, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence may also be addressed to: James R. Lupski, MD, PhD, DSc (hon) Department of Molecular and Human Genetics, Baylor College of Medicine One Baylor Plaza, Room 604B, Houston, TX 77030, USA E-mail:
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34
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Passos-Bueno MR, Costa CIS, Zatz M. Dystrophin genetic variants and autism. DISCOVER MENTAL HEALTH 2022; 2:4. [PMID: 37861890 PMCID: PMC10501027 DOI: 10.1007/s44192-022-00008-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/07/2022] [Indexed: 10/21/2023]
Abstract
Loss-of-function variants in the dystrophin gene, a well-known cause of muscular dystrophies, have emerged as a mutational risk mechanism for autism spectrum disorder (ASD), which in turn is a highly prevalent (~ 1%) genetically heterogeneous neurodevelopmental disorder. Although the association of intellectual disability with the dystrophinopathies Duchenne (DMD) and Becker muscular dystrophy (BMD) has been long established, their association with ASD is more recent, and the dystrophin genotype-ASD phenotype correlation is unclear. We therefore present a review of the literature focused on the ASD prevalence among dystrophinopathies, the relevance of the dystrophin isoforms, and most particularly the relevance of the genetic background to the etiology of ASD in these patients. Four families with ASD-DMD/BMD patients are also reported here for the first time. These include a single ASD individual, ASD-discordant and ASD-concordant monozygotic twins, and non-identical ASD triplets. Notably, two unrelated individuals, which were first ascertained because of the ASD phenotype at ages 15 and 5 years respectively, present rare dystrophin variants still poorly characterized, suggesting that some dystrophin variants may compromise the brain more prominently. Whole exome sequencing in these ASD-DMD/BMD individuals together with the literature suggest, although based on preliminary data, a complex and heterogeneous genetic architecture underlying ASD in dystrophinopathies, that include rare variants of large and medium effect. The need for the establishment of a consortia for genomic investigation of ASD-DMD/BMD patients, which may shed light on the genetic architecture of ASD, is discussed.
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Affiliation(s)
- Maria Rita Passos-Bueno
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Claudia Ismania Samogy Costa
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Mayana Zatz
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-Tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
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35
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Herman I, Jolly A, Du H, Dawood M, Abdel-Salam GMH, Marafi D, Mitani T, Calame DG, Coban-Akdemir Z, Fatih JM, Hegazy I, Jhangiani SN, Gibbs RA, Pehlivan D, Posey JE, Lupski JR. Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. Am J Med Genet A 2022; 188:735-750. [PMID: 34816580 PMCID: PMC8837671 DOI: 10.1002/ajmg.a.62565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 12/19/2022]
Abstract
Genomic sequencing and clinical genomics have demonstrated that substantial subsets of atypical and/or severe disease presentations result from multilocus pathogenic variation (MPV) causing blended phenotypes. In an infant with a severe neurodevelopmental disorder, four distinct molecular diagnoses were found by exome sequencing (ES). The blended phenotype that includes brain malformation, dysmorphism, and hypotonia was dissected using the Human Phenotype Ontology (HPO). ES revealed variants in CAPN3 (c.259C > G:p.L87V), MUSK (c.1781C > T:p.A594V), NAV2 (c.1996G > A:p.G666R), and ZC4H2 (c.595A > C:p.N199H). CAPN3, MUSK, and ZC4H2 are established disease genes linked to limb-girdle muscular dystrophy (OMIM# 253600), congenital myasthenia (OMIM# 616325), and Wieacker-Wolff syndrome (WWS; OMIM# 314580), respectively. NAV2 is a retinoic-acid responsive novel disease gene candidate with biological roles in neurite outgrowth and cerebellar dysgenesis in mouse models. Using semantic similarity, we show that no gene identified by ES individually explains the proband phenotype, but rather the totality of the clinically observed disease is explained by the combination of disease-contributing effects of the identified genes. These data reveal that multilocus pathogenic variation can result in a blended phenotype with each gene affecting a different part of the nervous system and nervous system-muscle connection. We provide evidence from this n = 1 study that in patients with MPV and complex blended phenotypes resulting from multiple molecular diagnoses, quantitative HPO analysis can allow for dissection of phenotypic contribution of both established disease genes and novel disease gene candidates not yet proven to cause human disease.
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Affiliation(s)
- Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ghada M. H. Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Pediatrics, Faculty of Medicine, Kuwait University, P.O. Box 24923, 13110 Safat, Kuwait,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Daniel G. Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Ibrahim Hegazy
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N. Jhangiani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, 77030, USA,Texas Children's Hospital, Houston, Texas, 77030, USA,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, 77030, USA,Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030
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36
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Methods to Improve Molecular Diagnosis in Genomic Cold Cases in Pediatric Neurology. Genes (Basel) 2022; 13:genes13020333. [PMID: 35205378 PMCID: PMC8871714 DOI: 10.3390/genes13020333] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
During the last decade, genetic testing has emerged as an important etiological diagnostic tool for Mendelian diseases, including pediatric neurological conditions. A genetic diagnosis has a considerable impact on disease management and treatment; however, many cases remain undiagnosed after applying standard diagnostic sequencing techniques. This review discusses various methods to improve the molecular diagnostic rates in these genomic cold cases. We discuss extended analysis methods to consider, non-Mendelian inheritance models, mosaicism, dual/multiple diagnoses, periodic re-analysis, artificial intelligence tools, and deep phenotyping, in addition to integrating various omics methods to improve variant prioritization. Last, novel genomic technologies, including long-read sequencing, artificial long-read sequencing, and optical genome mapping are discussed. In conclusion, a more comprehensive molecular analysis and a timely re-analysis of unsolved cases are imperative to improve diagnostic rates. In addition, our current understanding of the human genome is still limited due to restrictions in technologies. Novel technologies are now available that improve upon some of these limitations and can capture all human genomic variation more accurately. Last, we recommend a more routine implementation of high molecular weight DNA extraction methods that is coherent with the ability to use and/or optimally benefit from these novel genomic methods.
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37
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Zhang C, Jolly A, Shayota BJ, Mazzeu JF, Du H, Dawood M, Soper PC, Ramalho de Lima A, Ferreira BM, Coban-Akdemir Z, White J, Shears D, Thomson FR, Douglas SL, Wainwright A, Bailey K, Wordsworth P, Oldridge M, Lester T, Calder AD, Dumic K, Banka S, Donnai D, Jhangiani SN, Potocki L, Chung WK, Mora S, Northrup H, Ashfaq M, Rosenfeld JA, Mason K, Pollack LC, McConkie-Rosell A, Kelly W, McDonald M, Hauser NS, Leahy P, Powell CM, Boy R, Honjo RS, Kok F, Martelli LR, Filho VO, Genomics England Research Consortium, Muzny DM, Gibbs RA, Posey JE, Liu P, Lupski JR, Sutton VR, Carvalho CM. Novel pathogenic variants and quantitative phenotypic analyses of Robinow syndrome: WNT signaling perturbation and phenotypic variability. HGG ADVANCES 2022; 3:100074. [PMID: 35047859 PMCID: PMC8756549 DOI: 10.1016/j.xhgg.2021.100074] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/24/2021] [Indexed: 11/20/2022] Open
Abstract
Robinow syndrome (RS) is a genetically heterogeneous disorder with six genes that converge on the WNT/planar cell polarity (PCP) signaling pathway implicated (DVL1, DVL3, FZD2, NXN, ROR2, and WNT5A). RS is characterized by skeletal dysplasia and distinctive facial and physical characteristics. To further explore the genetic heterogeneity, paralog contribution, and phenotypic variability of RS, we investigated a cohort of 22 individuals clinically diagnosed with RS from 18 unrelated families. Pathogenic or likely pathogenic variants in genes associated with RS or RS phenocopies were identified in all 22 individuals, including the first variant to be reported in DVL2. We retrospectively collected medical records of 16 individuals from this cohort and extracted clinical descriptions from 52 previously published cases. We performed Human Phenotype Ontology (HPO) based quantitative phenotypic analyses to dissect allele-specific phenotypic differences. Individuals with FZD2 variants clustered into two groups with demonstrable phenotypic differences between those with missense and truncating alleles. Probands with biallelic NXN variants clustered together with the majority of probands carrying DVL1, DVL2, and DVL3 variants, demonstrating no phenotypic distinction between the NXN-autosomal recessive and dominant forms of RS. While phenotypically similar diseases on the RS differential matched through HPO analysis, clustering using phenotype similarity score placed RS-associated phenotypes in a unique cluster containing WNT5A, FZD2, and ROR2 apart from non-RS-associated paralogs. Through human phenotype analyses of this RS cohort and OMIM clinical synopses of Mendelian disease, this study begins to tease apart specific biologic roles for non-canonical WNT-pathway proteins.
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Affiliation(s)
- Chaofan Zhang
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Angad Jolly
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Medical Scientist Training Program, BCM, Houston, TX 77030, USA
| | - Brian J. Shayota
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Juliana F. Mazzeu
- University of Brasilia, Brasilia 70050, Brazil
- Robinow Syndrome Foundation, Anoka, MN 55303, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Medical Scientist Training Program, BCM, Houston, TX 77030, USA
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | | | | | | | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, UTHealth, Houston, TX 77030, USA
| | - Janson White
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Deborah Shears
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Fraser Robert Thomson
- Cardiothoracic Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | | | - Andrew Wainwright
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Kathryn Bailey
- Pediatric Rheumatology, Nuffield Orthopedic Centre, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7HE, UK
| | - Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, Oxford OX3 7LD, UK
| | - Mike Oldridge
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Tracy Lester
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Alistair D. Calder
- Radiology Department, Great Ormond Street Hospital NHS Foundation Trust, London WC1N 3JH, UK
| | - Katja Dumic
- Department of Pediatric Endocrinology and Diabetes, University Clinical Center Zagreb, Zagreb 10000, Croatia
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9WL, UK
- Manchester Center for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Dian Donnai
- Manchester Center for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | | | - Lorraine Potocki
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Wendy K. Chung
- Department of Pediatrics and Medicine, Columbia University, NY 10032, USA
| | - Sara Mora
- GeneDx Inc., Gaithersburg, MD 20878, USA
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children’s Memorial Hermann Hospital, Houston, TX 77030, USA
| | - Myla Ashfaq
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth Houston) and Children’s Memorial Hermann Hospital, Houston, TX 77030, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Kati Mason
- GeneDx Inc., Gaithersburg, MD 20878, USA
- Arnold Palmer Hospital for Children, Orlando, FL 32806, USA
| | | | | | - Wei Kelly
- Division of Medical Genetics, Duke University Medical Center, Durham, NC 27708, USA
| | - Marie McDonald
- Division of Medical Genetics, Duke University Medical Center, Durham, NC 27708, USA
| | - Natalie S. Hauser
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA 22042, USA
| | - Peter Leahy
- Cook Children's Hospital, Fort Worth, TX 76104, USA
| | - Cynthia M. Powell
- Division of Pediatric Genetics and Metabolism, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Raquel Boy
- State University of Rio de Janeiro, Rio de Janeiro 21941, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética, Instituto da Criança - Hospital das Clinicas HCFMUSP, Faculdade de Medicina, University of Sao Paulo, São Paulo 05508, Brasil
| | - Fernando Kok
- Mendelics Análise Genômica, São Paulo 04013, Brasil
| | - Lucia R. Martelli
- Department of Genetics, Ribeirao Preto Medical School, University of Sao Paulo, São Paulo 05508, Brazil
| | - Vicente Odone Filho
- Instituto de Tratamento do Câncer Infantil, São Paulo University Medical School, Hospital Israelita Albert Einstein, São Paulo 05508, Brasil
| | | | - Donna M. Muzny
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Baylor Genetics, Houston, TX 77021, USA
| | - James R. Lupski
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
- Human Genome Sequencing Center, BCM, Houston, TX 77030, USA
- Department of Pediatrics, BCM, Houston, TX 77030, USA
| | - V. Reid Sutton
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Texas Children's Hospital, Houston, TX 77030, USA
| | - Claudia M.B. Carvalho
- Department of Molecular and Human Genetics, BCM, Houston, TX 77030, USA
- Pacific Northwest Research Institute (PNRI), Seattle, WA 98122, USA
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Abstract
PURPOSE OF REVIEW A single genetic diagnosis, especially from the analysis of a limited number of genes, may not signal the end of a diagnostic odyssey. When a patient with a genetic syndrome presents with symptoms that are not usually associated with their disease phenotype, additional genetic testing is warranted. RECENT FINDINGS Although multiple co-existing genetic diagnoses may sound unlikely, many recent studies and case reports have demonstrated that this scenario is more common than expected. Studies involving whole exome and genome sequencing have identified a frequency of multiple genetic diagnoses and have identified clinical findings that make a second diagnosis more likely, which we have seen reflected in recent cases from our own clinic and consult service. These include multisystem disease, consanguinity, well described aneuploidies with rare or new symptoms, and complex structural chromosomal anomalies which may include multiple chromosomes and breakpoints that disrupt gene function. SUMMARY Identifying a second diagnosis can have vast implications for patient management and counseling. Patients can be followed with appropriate medical screening and early interventions to support optimal child development. Furthermore, the patient's family can be impacted by ending the diagnostic odyssey, providing testing for other at-risk family members, and offering prenatal options.
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Affiliation(s)
- Kristin B Linscott
- Department of Genetics
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jennifer A Cassady
- Department of Genetics
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nathaniel H Robin
- Department of Genetics
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Abdel-Salam GMH, Duan R, Abdel-Hamid MS, Sayed ISM, Jhangiani SN, Khan Z, Du H, Gibbs RA, Posey JE, Marafi D, Lupski JR. Expanding the phenotypic and allelic spectrum of SMG8: Clinical observations reveal overlap with SMG9-associated disease trait. Am J Med Genet A 2021; 188:648-657. [PMID: 34761517 DOI: 10.1002/ajmg.a.62561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/03/2021] [Accepted: 10/22/2021] [Indexed: 11/06/2022]
Abstract
SMG8 (MIM *617315) is a regulatory subunit involved in nonsense-mediated mRNA decay (NMD), a cellular protective pathway that regulates mRNA transcription, transcript stability, and degrades transcripts containing premature stop codons. SMG8 binds SMG9 and SMG1 to form the SMG1C complex and inhibit the kinase activity of SMG1. Biallelic deleterious variants in SMG9 are known to cause a heart and brain malformation syndrome (HBMS; MIM #616920), whereas biallelic deleterious variants in SMG8 were recently described to cause a novel neurodevelopmental disorder (NDD) with dysmorphic facies and cataracts, now defined as Alzahrani-Kuwahara syndrome (ALKUS: MIM #619268). Only eight subjects from four families with ALKUS have been described to date. Through research reanalysis of a nondiagnostic clinical exome, we identified a subject from a fifth unrelated family with a homozygous deleterious variant in SMG8 and features consistent with ALKUS. Interestingly, the subject also had unilateral microphthalmia, a clinical feature that has been described in SMG9-related disorder. Our study expands the phenotypic spectrum of SMG8-related disorder, demonstrates an overlapping phenotype between SMG8- and SMG9-related rare disease traits, provides further evidence for the SMG8 and SMG9 protein interactions, and highlights the importance of revisiting nondiagnostic exome data to identify and affirm emerging novel genes for rare disease traits.
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Affiliation(s)
- Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National ResearchCentre, Cairo, Egypt
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Mohamed S Abdel-Hamid
- Medical Molecular Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Inas S M Sayed
- Orodental Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Ziad Khan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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40
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Longo F, De Ritis D, Miluzio A, Fraticelli D, Baets J, Scarlato M, Santorelli FM, Biffo S, Maltecca F. Assessment of Sacsin Turnover in Patients With ARSACS: Implications for Molecular Diagnosis and Pathogenesis. Neurology 2021; 97:e2315-e2327. [PMID: 34649874 PMCID: PMC8665432 DOI: 10.1212/wnl.0000000000012962] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/07/2021] [Indexed: 11/15/2022] Open
Abstract
Background and Objectives Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is caused by variations in SACS gene encoding sacsin, a huge multimodular protein of unknown function. More than 200 SACS variations have been described worldwide to date. Because ARSACS presents phenotypic variability, previous empirical studies attempted to correlate the nature and position of SACS variations with the age at onset or with disease severity, although not considering the effect of the various variations on protein stability. In this work, we studied genotype-phenotype correlation in ARSACS at a functional level. Methods We analyzed a large set of skin fibroblasts derived from patients with ARSACS, including both new and already published cases, carrying variations of different types affecting diverse domains of the protein. Results We found that sacsin is almost absent in patients with ARSACS, regardless of the nature of the variation. As expected, we did not detect sacsin in patients with truncating variations. We found it strikingly reduced or absent also in compound heterozygotes carrying diverse missense variations. In this case, we excluded SACS mRNA decay, defective translation, or faster posttranslational degradation as possible causes of protein reduction. Conversely, our results demonstrate that nascent mutant sacsin protein undergoes cotranslational ubiquitination and degradation. Discussion Our results provide a mechanistic explanation for the lack of genotype-phenotype correlation in ARSACS. We also propose a new and unambiguous criterion for ARSACS diagnosis that is based on the evaluation of sacsin level. Last, we identified preemptive degradation of a mutant protein as a novel cause of a human disease.
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Affiliation(s)
- Fabiana Longo
- Mitochondrial Dysfunctions in Neurodegeneration Unit, Ospedale San Raffaele, Milan, Italy
| | - Daniele De Ritis
- Mitochondrial Dysfunctions in Neurodegeneration Unit, Ospedale San Raffaele, Milan, Italy
| | - Annarita Miluzio
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Davide Fraticelli
- Mitochondrial Dysfunctions in Neurodegeneration Unit, Ospedale San Raffaele, Milan, Italy
| | - Jonathan Baets
- Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerpen, Belgium.,Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerpen, Belgium
| | - Marina Scarlato
- Department of Neurology, Ospedale San Raffaele, Milan, Italy
| | | | - Stefano Biffo
- Istituto Nazionale di Genetica Molecolare, INGM, "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Biosciences, University of Milan, Milan, Italy
| | - Francesca Maltecca
- Mitochondrial Dysfunctions in Neurodegeneration Unit, Ospedale San Raffaele, Milan, Italy .,Università Vita-Salute San Raffaele, Milan, Italy
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41
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Khayat MM, Hu J, Jiang Y, Li H, Chander V, Dawood M, Hansen AW, Li S, Friedman J, Cross L, Bijlsma EK, Ruivenkamp CA, Sansbury FH, Innis JW, Omark O’Shea J, Meng Q, Rosenfeld JA, McWalter K, Wangler MF, Lupski JR, Posey JE, Murdock D, Gibbs RA. AHDC1 missense mutations in Xia-Gibbs syndrome. HGG ADVANCES 2021; 2:100049. [PMID: 34950897 PMCID: PMC8694554 DOI: 10.1016/j.xhgg.2021.100049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/04/2021] [Indexed: 12/19/2022] Open
Abstract
Xia-Gibbs syndrome (XGS; MIM: 615829) is a phenotypically heterogeneous neurodevelopmental disorder (NDD) caused by newly arising mutations in the AT-Hook DNA-Binding Motif-Containing 1 (AHDC1) gene that are predicted to lead to truncated AHDC1 protein synthesis. More than 270 individuals have been diagnosed with XGS worldwide. Despite the absence of an independent assay for AHDC1 protein function to corroborate potential functional consequences of rare variant genetic findings, there are also reports of individuals with XGS-like trait manifestations who have de novo missense AHDC1 mutations and who have been provided a molecular diagnosis of the disorder. To investigate a potential contribution of missense mutations to XGS, we mapped the missense mutations from 10 such individuals to the AHDC1 conserved protein domain structure and detailed the observed phenotypes. Five newly identified individuals were ascertained from a local XGS Registry, and an additional five were taken from external reports or databases, including one publication. Where clinical data were available, individuals with missense mutations all displayed phenotypes consistent with those observed in individuals with AHDC1 truncating mutations, including delayed motor milestones, intellectual disability (ID), hypotonia, and speech delay. A subset of the 10 reported missense mutations cluster in two regions of the AHDC1 protein with known conserved domains, likely representing functional motifs. Variants outside the clustered regions score lower for computational prediction of their likely damaging effects. Overall, de novo missense variants in AHDC1 are likely diagnostic of XGS when in silico analysis of their position relative to conserved regions is considered together with disease trait manifestations.
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Affiliation(s)
- Michael M. Khayat
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Yunyun Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Varuna Chander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Moez Dawood
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA
| | - Adam W. Hansen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shoudong Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer Friedman
- UCSD Departments of Neuroscience and Pediatrics, Rady Children’s Hospital Division of Neurology, Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | - Laura Cross
- Department of Pediatrics and Genetics, Children’s Mercy Hospitals, Kansas City, MO, USA
| | - Emilia K. Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Francis H. Sansbury
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Jeffrey W. Innis
- Departments of Human Genetics, Pediatrics, and Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Michael F. Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Neurological Research Institute, Houston, TX, USA
| | - James R. Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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Mitani T, Isikay S, Gezdirici A, Gulec EY, Punetha J, Fatih JM, Herman I, Akay G, Du H, Calame DG, Ayaz A, Tos T, Yesil G, Aydin H, Geckinli B, Elcioglu N, Candan S, Sezer O, Erdem HB, Gul D, Demiral E, Elmas M, Yesilbas O, Kilic B, Gungor S, Ceylan AC, Bozdogan S, Ozalp O, Cicek S, Aslan H, Yalcintepe S, Topcu V, Bayram Y, Grochowski CM, Jolly A, Dawood M, Duan R, Jhangiani SN, Doddapaneni H, Hu J, Muzny DM, Marafi D, Akdemir ZC, Karaca E, Carvalho CMB, Gibbs RA, Posey JE, Lupski JR, Pehlivan D. High prevalence of multilocus pathogenic variation in neurodevelopmental disorders in the Turkish population. Am J Hum Genet 2021; 108:1981-2005. [PMID: 34582790 PMCID: PMC8546040 DOI: 10.1016/j.ajhg.2021.08.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 02/06/2023] Open
Abstract
Neurodevelopmental disorders (NDDs) are clinically and genetically heterogenous; many such disorders are secondary to perturbation in brain development and/or function. The prevalence of NDDs is > 3%, resulting in significant sociocultural and economic challenges to society. With recent advances in family-based genomics, rare-variant analyses, and further exploration of the Clan Genomics hypothesis, there has been a logarithmic explosion in neurogenetic "disease-associated genes" molecular etiology and biology of NDDs; however, the majority of NDDs remain molecularly undiagnosed. We applied genome-wide screening technologies, including exome sequencing (ES) and whole-genome sequencing (WGS), to identify the molecular etiology of 234 newly enrolled subjects and 20 previously unsolved Turkish NDD families. In 176 of the 234 studied families (75.2%), a plausible and genetically parsimonious molecular etiology was identified. Out of 176 solved families, deleterious variants were identified in 218 distinct genes, further documenting the enormous genetic heterogeneity and diverse perturbations in human biology underlying NDDs. We propose 86 candidate disease-trait-associated genes for an NDD phenotype. Importantly, on the basis of objective and internally established variant prioritization criteria, we identified 51 families (51/176 = 28.9%) with multilocus pathogenic variation (MPV), mostly driven by runs of homozygosity (ROHs) - reflecting genomic segments/haplotypes that are identical-by-descent. Furthermore, with the use of additional bioinformatic tools and expansion of ES to additional family members, we established a molecular diagnosis in 5 out of 20 families (25%) who remained undiagnosed in our previously studied NDD cohort emanating from Turkey.
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Affiliation(s)
- Tadahiro Mitani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sedat Isikay
- Department of Pediatric Neurology, Faculty of Medicine, University of Gaziantep, Gaziantep 27310, Turkey
| | - Alper Gezdirici
- Department of Medical Genetics, Basaksehir Cam and Sakura City Hospital, Istanbul 34480, Turkey
| | - Elif Yilmaz Gulec
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, 34303 Istanbul, Turkey
| | - Jaya Punetha
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Isabella Herman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Akif Ayaz
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey; Departments of Medical Genetics, School of Medicine, Istanbul Medipol University, Istanbul 34810, Turkey
| | - Tulay Tos
- University of Health Sciences Zubeyde Hanim Research and Training Hospital of Women's Health and Diseases, Department of Medical Genetics, Ankara 06080, Turkey
| | - Gozde Yesil
- Istanbul Faculty of Medicine, Department of Medical Genetics, Istanbul University, Istanbul 34093, Turkey
| | - Hatip Aydin
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Private Reyap Istanbul Hospital, Istanbul 34515, Turkey
| | - Bilgen Geckinli
- Centre of Genetics Diagnosis, Zeynep Kamil Maternity and Children's Training and Research Hospital, Istanbul, Turkey; Department of Medical Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey
| | - Nursel Elcioglu
- Department of Pediatric Genetics, School of Medicine, Marmara University, Istanbul 34722, Turkey; Eastern Mediterranean University Medical School, Magosa, Mersin 10, Turkey
| | - Sukru Candan
- Medical Genetics Section, Balikesir Ataturk Public Hospital, Balikesir 10100, Turkey
| | - Ozlem Sezer
- Department of Medical Genetics, Samsun Education and Research Hospital, Samsun 55100, Turkey
| | - Haktan Bagis Erdem
- Department of Medical Genetics, University of Health Sciences, Diskapi Yildirim Beyazit Training and Research Hospital, Ankara 06110, Turkey
| | - Davut Gul
- Department of Medical Genetics, Gulhane Military Medical School, Ankara 06010, Turkey
| | - Emine Demiral
- Department of Medical Genetics, School of Medicine, University of Inonu, Malatya 44280, Turkey
| | - Muhsin Elmas
- Department of Medical Genetics, Afyon Kocatepe University, School of Medicine, Afyon 03218, Turkey
| | - Osman Yesilbas
- Division of Critical Care Medicine, Department of Pediatrics, School of Medicine, Bezmialem Foundation University, Istanbul 34093, Turkey; Department of Pediatrics, Division of Pediatric Critical Care Medicine, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Betul Kilic
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Serdal Gungor
- Department of Pediatrics and Pediatric Neurology, Faculty of Medicine, Inonu University, Malatya 34218, Turkey
| | - Ahmet C Ceylan
- Department of Medical Genetics, University of Health Sciences, Ankara Training and Research Hospital, Ankara 06110, Turkey
| | - Sevcan Bozdogan
- Department of Medical Genetics, Cukurova University Faculty of Medicine, Adana 01330, Turkey
| | - Ozge Ozalp
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Salih Cicek
- Department of Medical Genetics, Konya Training and Research Hospital, Konya 42250, Turkey
| | - Huseyin Aslan
- Department of Medical Genetics, Adana City Training and Research Hospital, Adana 01170, Turkey
| | - Sinem Yalcintepe
- Department of Medical Genetics, School of Medicine, Trakya University, Edirne 22130, Turkey
| | - Vehap Topcu
- Department of Medical Genetics, Ankara City Hospital, Ankara 06800, Turkey
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Angad Jolly
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Moez Dawood
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ruizhi Duan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Claudia M B Carvalho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA.
| | - Davut Pehlivan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA.
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Xia W, Ni Z, Zhang Z, Sang H, Liu H, Chen Z, Jiang L, Yin C, Huang J, Li L, Lei X. Case Report: A Boy From a Consanguineous Family Diagnosed With Congenital Muscular Dystrophy Caused by Integrin Alpha 7 ( ITGA7) Mutation. Front Genet 2021; 12:706823. [PMID: 34552617 PMCID: PMC8450528 DOI: 10.3389/fgene.2021.706823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 07/30/2021] [Indexed: 12/20/2022] Open
Abstract
Introduction: Congenital muscular dystrophy (CMD) is a group of early-onset disorders with clinical and genetic heterogeneity. Patients always present with muscle weakness typically from birth to early infancy, delay or arrest of gross motor development, and joint and/or spinal rigidity. There are various genes related to the development of CMD. Among them, mutations in integrin alpha 7 (ITGA7) is a rare subtype. The identification of disease-causing genes facilitates the diagnosis and treatment of CMD. Methods: We screened ITGA7 mutations in four people by whole exome sequencing and targeted sequencing from a consanguineous family. We then carried out electromyography and neuroelectrophysiological examinations to clarify a clinical picture of the patient diagnosed with CMD. Results: We report a Chinese boy diagnosed with CMD who carries a homozygous variant (c.1088dupG, p.H364Sfs*15) of the ITGA7 gene. According to the genotype analysis of his family members, this is an autosomal recessive inheritance. Conclusions: Our case further shows that ITGA7 mutation is related to CMD. Genetic counseling and multidisciplinary management of CMD play an important role in helping patients and their family. Further elucidation of the significant clinical and genetic heterogeneity, therapeutic targets, and the clinical care for patients remains our challenge for the future.
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Affiliation(s)
- Wenqing Xia
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
- Department of Neurology, Hangzhou First People's Hospital, Hangzhou, China
| | - Zhumei Ni
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zheng Zhang
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Hongfei Sang
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
- Department of Neurology, Hangzhou First People's Hospital, Hangzhou, China
| | - Huifang Liu
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong, SAR China
| | - Zhenzhen Chen
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
- Department of Hematology, Affiliated Hangzhou First People's Hospital, Zhejiang University, Hangzhou, China
| | - Lin Jiang
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
- Department of Neurology, Hangzhou First People's Hospital, Hangzhou, China
| | - Congguo Yin
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
- Department of Neurology, Hangzhou First People's Hospital, Hangzhou, China
| | - Jinyu Huang
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
- Department of Cardiology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lingfei Li
- The Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
- Department of Neurology, Hangzhou First People's Hospital, Hangzhou, China
| | - Xiaoguang Lei
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming Medical University, Kunming, China
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Biallelic loss-of-function variants in the splicing regulator NSRP1 cause a severe neurodevelopmental disorder with spastic cerebral palsy and epilepsy. Genet Med 2021; 23:2455-2460. [PMID: 34385670 DOI: 10.1038/s41436-021-01291-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Alternative splicing plays a critical role in mouse neurodevelopment, regulating neurogenesis, cortical lamination, and synaptogenesis, yet few human neurodevelopmental disorders are known to result from pathogenic variation in splicing regulator genes. Nuclear Speckle Splicing Regulator Protein 1 (NSRP1) is a ubiquitously expressed splicing regulator not known to underlie a Mendelian disorder. METHODS Exome sequencing and rare variant family-based genomics was performed as a part of the Baylor-Hopkins Center for Mendelian Genomics Initiative. Additional families were identified via GeneMatcher. RESULTS We identified six patients from three unrelated families with homozygous loss-of-function variants in NSRP1. Clinical features include developmental delay, epilepsy, variable microcephaly (Z-scores -0.95 to -5.60), hypotonia, and spastic cerebral palsy. Brain abnormalities included simplified gyral pattern, underopercularization, and/or vermian hypoplasia. Molecular analysis identified three pathogenic NSRP1 predicted loss-of-function variant alleles: c.1359_1362delAAAG (p.Glu455AlafsTer20), c.1272dupG (p.Lys425GlufsTer5), and c.52C>T (p.Gln18Ter). The two frameshift variants result in a premature termination codon in the last exon, and the mutant transcripts are predicted to escape nonsense mediated decay and cause loss of a C-terminal nuclear localization signal required for NSRP1 function. CONCLUSION We establish NSRP1 as a gene for a severe autosomal recessive neurodevelopmental disease trait characterized by developmental delay, epilepsy, microcephaly, and spastic cerebral palsy.
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Innella G, Bonora E, Neri I, Virdi A, Guglielmo A, Pradella LM, Ceccarelli C, Amato LB, Lanzoni A, Miccoli S, Gasparre G, Zuntini R, Turchetti D. PTEN Hamartoma Tumor Syndrome: Skin Manifestations and Insights Into Their Molecular Pathogenesis. Front Med (Lausanne) 2021; 8:688105. [PMID: 34386506 PMCID: PMC8353102 DOI: 10.3389/fmed.2021.688105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/30/2021] [Indexed: 12/13/2022] Open
Abstract
Germline PTEN pathogenic variants cause a spectrum of disorders collectively labeled PTEN Hamartoma Tumor Syndrome (PHTS) and featured by hamartomas, developmental anomalies and increased cancer risk. Studies on experimental models provided evidence that PTEN is a “haploinsufficient” tumor-suppressor gene, however, mechanisms involved in the pathogenesis of clinical manifestations in PHTS patients remain elusive. Beyond analyzing clinical and molecular features of a series of 20 Italian PHTS patients, we performed molecular investigations to explore the mechanisms involved in the pathogenesis of PTEN-associated manifestations, with special focus on mucocutaneous manifestations. Typical mucocutaneous features were present in all patients assessed, confirming that these are the most important clue to the diagnosis. The most frequent were papules located in the trunk or extremities (73.7%), oral mucosa papules (68.4%), acral/palmoplantar keratosis and facial papules (both 57.9%), according with literature data. Molecular analyses on one trichilemmoma suggested that the wild-type PTEN allele was retained and expressed, reinforcing the evidence that PTEN does not require a second somatic hit to initiate pathogenic processes. Unexpectedly, one patient also displayed a cutaneous phenotype consistent with atypical mole/melanoma syndrome; no variants were detected in known melanoma genes, but Whole Exome Sequencing showed the rare truncating variant c.495G>A in the CDH13 gene that might have cooperated with PTEN-haploinsufficiency to generate such phenotype. Our findings confirm the reproducibility of known PHTS manifestations in real-world practice, highlighting the role of mucocutaneous manifestations in facilitating prompt diagnosis of the syndrome, and provide some insights into the pathogenic process induced by PTEN alterations, which may contribute to its understanding.
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Affiliation(s)
- Giovanni Innella
- Department of Medical and Surgical Sciences, Center for Studies on Hereditary Cancer, University of Bologna, Bologna, Italy.,Unit of Medical Genetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Elena Bonora
- Department of Medical and Surgical Sciences, Center for Studies on Hereditary Cancer, University of Bologna, Bologna, Italy
| | - Iria Neri
- Unit of Dermatology, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Annalucia Virdi
- Unit of Dermatology, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Alba Guglielmo
- Unit of Dermatology, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Laura Maria Pradella
- Department of Medical and Surgical Sciences, Center for Studies on Hereditary Cancer, University of Bologna, Bologna, Italy
| | - Claudio Ceccarelli
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum University of Bologna, Bologna, Italy
| | - Laura Benedetta Amato
- Department of Medical and Surgical Sciences, Center for Studies on Hereditary Cancer, University of Bologna, Bologna, Italy
| | - Anna Lanzoni
- Unit of Dermatology, Ospedale Bellaria-Maggiore di Bologna, Bologna, Italy
| | - Sara Miccoli
- Unit of Medical Genetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences, Center for Studies on Hereditary Cancer, University of Bologna, Bologna, Italy.,Center for Applied Biomedical Research (CRBA), Bologna, Italy
| | - Roberta Zuntini
- Department of Medical and Surgical Sciences, Center for Studies on Hereditary Cancer, University of Bologna, Bologna, Italy
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences, Center for Studies on Hereditary Cancer, University of Bologna, Bologna, Italy.,Unit of Medical Genetics, IRCCS (Istituto di Ricovero e Cura a Carattere Scientifico) Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
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Priolo M, Radio FC, Pizzi S, Pintomalli L, Pantaleoni F, Mancini C, Cordeddu V, Africa E, Mammì C, Dallapiccola B, Tartaglia M. Co-Occurring Heterozygous CNOT3 and SMAD6 Truncating Variants: Unusual Presentation and Refinement of the IDDSADF Phenotype. Genes (Basel) 2021; 12:genes12071009. [PMID: 34208845 PMCID: PMC8303239 DOI: 10.3390/genes12071009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/23/2021] [Accepted: 06/26/2021] [Indexed: 11/29/2022] Open
Abstract
Objective, the application of genomic sequencing in clinical practice has allowed us to appreciate the contribution of co-occurring pathogenic variants to complex and unclassified clinical phenotypes. Besides the clinical relevance, these findings have provided evidence of previously unrecognized functional links between genes in the context of developmental processes and physiology. Patients and Methods, a 5-year-old patient showing an unclassified phenotype characterized by developmental delay, speech delay, peculiar behavioral features, facial dysmorphism and severe cardiopathy was analyzed by trio-based whole exome sequencing (WES) analysis to identify the genomic events underlying the condition. Results, two co-occurring heterozygous truncating variants in CNOT3 and SMAD6 were identified. Heterozygous loss-of-function variants in CNOT3, encoding a subunit of the CCR4-NOT protein complex, have recently been reported to cause a syndromic condition known as intellectual developmental disorder with speech delay, autism and dysmorphic facies (IDDSADF). Enrichment of rare/private variants in the SMAD6 gene, encoding a protein negatively controlling transforming growth factor β/bone morphogenetic protein (TGFB/BMP) signaling, has been described in association with a wide spectrum of congenital heart defects. We dissected the contribution of individual variants to the complex clinical manifestations and profiled a previously unappreciated set of facial features and signs characterizing IDDSADF. Conclusions, two concomitant truncating variants in CNOT3 and SMAD6 are the cause of the combination of features documented in the patient resulting in the unique multisystem neurodevelopmental condition. These findings provide evidence for a functional link between the CCR4-NOT complex and TGFB/BMP signaling in processes controlling cardiac development. Finally, the present revision provides evidence that IDDSADF is characterized by a distinctive facial gestalt.
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Affiliation(s)
- Manuela Priolo
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
| | - Francesca Clementina Radio
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Simone Pizzi
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Letizia Pintomalli
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Francesca Pantaleoni
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Cecilia Mancini
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Viviana Cordeddu
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Emilio Africa
- UOC di Neuroradiologia, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy;
| | - Corrado Mammì
- Unità di Genetica Medica, Grande Ospedale Metropolitano “Bianchi-Melacrino-Morelli”, 89124 Reggio Calabria, Italy; (L.P.); (C.M.)
| | - Bruno Dallapiccola
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
| | - Marco Tartaglia
- Area di Ricerca Genetica e Malattie Rare, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146 Rome, Italy; (F.C.R.); (S.P.); (F.P.); (C.M.); (B.D.)
- Correspondence: (M.P.); (M.T.); Tel.: +39-0965397319 (M.P.); +39-0668593742 (M.T.)
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47
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Andolfo I, Martone S, Rosato BE, Marra R, Gambale A, Forni GL, Pinto V, Göransson M, Papadopoulou V, Gavillet M, Elalfy M, Panarelli A, Tomaiuolo G, Iolascon A, Russo R. Complex Modes of Inheritance in Hereditary Red Blood Cell Disorders: A Case Series Study of 155 Patients. Genes (Basel) 2021; 12:genes12070958. [PMID: 34201899 PMCID: PMC8304671 DOI: 10.3390/genes12070958] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 12/19/2022] Open
Abstract
Hereditary erythrocytes disorders include a large group of conditions with heterogeneous molecular bases and phenotypes. We analyzed here a case series of 155 consecutive patients with clinical suspicion of hereditary erythrocyte defects referred to the Medical Genetics Unit from 2018 to 2020. All of the cases followed a diagnostic workflow based on a targeted next-generation sequencing panel of 86 genes causative of hereditary red blood cell defects. We obtained an overall diagnostic yield of 84% of the tested patients. Monogenic inheritance was seen for 69% (107/155), and multi-locus inheritance for 15% (23/155). PIEZO1 and SPTA1 were the most mutated loci. Accordingly, 16/23 patients with multi-locus inheritance showed dual molecular diagnosis of dehydrated hereditary stomatocytosis/xerocytosis and hereditary spherocytosis. These dual inheritance cases were fully characterized and were clinically indistinguishable from patients with hereditary spherocytosis. Additionally, their ektacytometry curves highlighted alterations of dual inheritance patients compared to both dehydrated hereditary stomatocytosis and hereditary spherocytosis. Our findings expand the genotypic spectrum of red blood cell disorders and indicate that multi-locus inheritance should be considered for analysis and counseling of these patients. Of note, the genetic testing was crucial for diagnosis of patients with a complex mode of inheritance.
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Affiliation(s)
- Immacolata Andolfo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
| | - Stefania Martone
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
| | - Barbara Eleni Rosato
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
| | - Roberta Marra
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
| | - Antonella Gambale
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
- Department of Laboratory Medicine (DAIMedLab), UOC Medical Genetics, ‘Federico II’ University Hospital, 80131 Naples, Italy
| | - Gian Luca Forni
- Centro della Microcitemia e delle Anemie Congenite, Ospedale Galliera, 16128 Genoa, Italy; (G.L.F.); (V.P.)
| | - Valeria Pinto
- Centro della Microcitemia e delle Anemie Congenite, Ospedale Galliera, 16128 Genoa, Italy; (G.L.F.); (V.P.)
| | - Magnus Göransson
- Department of Paediatrics, The Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, 41345 Gothenburg, Sweden;
| | - Vasiliki Papadopoulou
- Service and Central Laboratory of Haematology, Department of Oncology and Department of Laboratory Medicine and Pathology, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; (V.P.); (M.G.)
| | - Mathilde Gavillet
- Service and Central Laboratory of Haematology, Department of Oncology and Department of Laboratory Medicine and Pathology, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland; (V.P.); (M.G.)
| | - Mohsen Elalfy
- Thalassemia Centre, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt;
| | | | - Giovanna Tomaiuolo
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
- Department of Chemical Engineering, Materials and Industrial Production, ‘Federico II’ University of Naples, 80125 Naples, Italy
| | - Achille Iolascon
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
- CEINGE Biotecnologie Avanzate, 80145 Naples, Italy; (A.G.); (A.P.); (G.T.)
- Correspondence:
| | - Roberta Russo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; (I.A.); (S.M.); (B.E.R.); (R.M.); (R.R.)
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48
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Pham DH, Pitman MR, Kumar R, Jolly LA, Schulz R, Gardner AE, de Nys R, Heron SE, Corbett MA, Kothur K, Gill D, Rajagopalan S, Kolc KL, Halliday BJ, Robertson SP, Regan BM, Kirsch HE, Berkovic SF, Scheffer IE, Pitson SM, Petrovski S, Gecz J. Integrated in silico and experimental assessment of disease relevance of PCDH19 missense variants. Hum Mutat 2021; 42:1030-1041. [PMID: 34082468 DOI: 10.1002/humu.24237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/27/2021] [Accepted: 05/31/2021] [Indexed: 11/09/2022]
Abstract
PCDH19 is a nonclustered protocadherin molecule involved in axon bundling, synapse function, and transcriptional coregulation. Pathogenic variants in PCDH19 cause infantile-onset epilepsy known as PCDH19-clustering epilepsy or PCDH19-CE. Recent advances in DNA-sequencing technologies have led to a significant increase in the number of reported PCDH19-CE variants, many of uncertain significance. We aimed to determine the best approaches for assessing the disease relevance of missense variants in PCDH19. The application of the American College of Medical Genetics and Association for Molecular Pathology (ACMG-AMP) guidelines was only 50% accurate. Using a training set of 322 known benign or pathogenic missense variants, we identified MutPred2, MutationAssessor, and GPP as the best performing in silico tools. We generated a protein structural model of the extracellular domain and assessed 24 missense variants. We also assessed 24 variants using an in vitro reporter assay. A combination of these tools was 93% accurate in assessing known pathogenic and benign PCDH19 variants. We increased the accuracy of the ACMG-AMP classification of 45 PCDH19 variants from 50% to 94%, using these tools. In summary, we have developed a robust toolbox for the assessment of PCDH19 variant pathogenicity to improve the accuracy of PCDH19-CE variant classification.
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Affiliation(s)
- Duyen H Pham
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Melissa R Pitman
- Molecular Therapeutics, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia
| | - Raman Kumar
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lachlan A Jolly
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Renee Schulz
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia
| | - Alison E Gardner
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Rebekah de Nys
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Sarah E Heron
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Mark A Corbett
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kavitha Kothur
- Department of Paediatrics and Child Health, Kids Neuroscience Centre, The University of Sydney, Sydney, New South Wales, Australia.,TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Deepak Gill
- Department of Paediatrics and Child Health, Kids Neuroscience Centre, The University of Sydney, Sydney, New South Wales, Australia.,TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Sulekha Rajagopalan
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia
| | - Kristy L Kolc
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
| | - Benjamin J Halliday
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Stephen P Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Brigid M Regan
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia
| | - Heidi E Kirsch
- Department of Neurology, University of California, San Francisco, California, USA
| | - Samuel F Berkovic
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, Victoria, Australia.,Department of Paediatrics, Royal Children's Hospital, University of Melbourne, Flemington, Victoria, Australia.,Epilepsy Research Centre, Florey Institute of Neuroscience and Mental Health, Heidelberg, Victoria, Australia
| | - Stuart M Pitson
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Molecular Therapeutics, Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia, Australia.,School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Slave Petrovski
- Centre for Genomics Research, Precision Medicine and Genomics, IMED Biotech Unit, AstraZeneca, Cambridge, UK.,Department of Medicine, University of Melbourne, Parkville, Victoria, Australia
| | - Jozef Gecz
- Neurogenetics, Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, Australia.,Paediatrics and Reproductive Health, Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia.,School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia.,Women and Kids, South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
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49
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Calame DG, Herman I, Fatih JM, Du H, Akay G, Jhangiani SN, Coban-Akdemir Z, Milewicz DM, Gibbs RA, Posey JE, Marafi D, Hunter JV, Fan Y, Lupski JR, Miyake CY. Risk of sudden cardiac death in EXOSC5-related disease. Am J Med Genet A 2021; 185:2532-2540. [PMID: 34089229 DOI: 10.1002/ajmg.a.62352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/20/2021] [Accepted: 05/07/2021] [Indexed: 11/07/2022]
Abstract
The RNA exosome is a multi-subunit complex involved in the processing, degradation, and regulated turnover of RNA. Several subunits are linked to Mendelian disorders, including pontocerebellar hypoplasia (EXOSC3, MIM #614678; EXOSC8, MIM #616081: and EXOSC9, MIM #618065) and short stature, hearing loss, retinitis pigmentosa, and distinctive facies (EXOSC2, MIM #617763). More recently, EXOSC5 (MIM *606492) was found to underlie an autosomal recessive neurodevelopmental disorder characterized by developmental delay, hypotonia, cerebellar abnormalities, and dysmorphic facies. An unusual feature of EXOSC5-related disease is the occurrence of complete heart block requiring a pacemaker in a subset of affected individuals. Here, we provide a detailed clinical and molecular characterization of two siblings with microcephaly, developmental delay, cerebellar volume loss, hypomyelination, with cardiac conduction and rhythm abnormalities including sinus node dysfunction, intraventricular conduction delay, atrioventricular block, and ventricular tachycardia (VT) due to compound heterozygous variants in EXOSC5: (1) NM_020158.4:c.341C > T (p.Thr114Ile; pathogenic, previously reported) and (2) NM_020158.4:c.302C > A (p.Thr101Lys; novel variant). A review of the literature revealed an additional family with biallelic EXOSC5 variants and cardiac conduction abnormalities. These clinical and molecular data provide compelling evidence that cardiac conduction abnormalities and arrhythmias are part of the EXOSC5-related disease spectrum and argue for proactive screening due to potential risk of sudden cardiac death.
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Affiliation(s)
- Daniel G Calame
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Isabella Herman
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA.,Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jawid M Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Gulsen Akay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Dianna M Milewicz
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Center at Houston, Houston, Texas, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Jill V Hunter
- Department of Radiology, Baylor College of Medicine, Houston, Texas, USA.,E.B. Singleton Department of Pediatric Radiology, Texas Children's Hospital, Houston, Texas, USA
| | - Yuxin Fan
- John Welsh Cardiovascular Diagnostic Laboratory, Departments of Pediatrics and Pathology & Immunology, Baylor College of Medicine, Houston, Texas, USA
| | - James R Lupski
- Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Christina Y Miyake
- Department of Pediatrics, Division of Cardiology, Texas Children's Hospital, Houston, Texas, USA.,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, USA
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50
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Calame DG, Fatih J, Herman I, Akdemir ZC, Du H, Jhangiani SN, Gibbs RA, Marafi D, Pehlivan D, Posey JE, Lotze T, Mancias P, Bhattacharjee MB, Lupski JR. Biallelic Pathogenic Variants in TNNT3 Associated With Congenital Myopathy. Neurol Genet 2021; 7:e589. [PMID: 33977145 PMCID: PMC8105884 DOI: 10.1212/nxg.0000000000000589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/11/2021] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Pathogenic variants in TNNT3, the gene encoding fast skeletal muscle troponin T, were first described in autosomal dominant distal arthrogryposis type 2B2. Recently, a homozygous splice site variant, c.681+1G>A, was identified in a patient with nemaline myopathy and distal arthrogryposis. Here, we describe the second individual with congenital myopathy associated with biallelic TNNT3 variants. METHODS Clinical exome sequencing data from a patient with molecularly undiagnosed congenital myopathy underwent research reanalysis. Clinical and histopathologic data were collected and compared with the single reported patient with TNNT3-related congenital myopathy. RESULTS A homozygous TNNT3 variant, c.481-1G>A, was identified. This variant alters a consensus splice acceptor and is predicted to affect splicing by multiple in silico prediction tools. Both the patient reported here and the previously published patient exhibited limb, bulbar, and respiratory muscle weakness from birth, which improved over time. Other shared features include history of polyhydramnios, hypotonia, scoliosis, and high-arched palate. Distal arthrogryposis and nemaline rods, findings reported in the first patient with TNNT3-related congenital myopathy, were not observed in the patient reported here. CONCLUSIONS This report provides further evidence for the association of biallelic TNNT3 variants with severe recessive congenital myopathy with or without nemaline rods and distal arthrogryposis. TNNT3 sequencing and copy number analysis should be incorporated into the workup of congenital myopathies.
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Affiliation(s)
- Daniel G. Calame
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Jawid Fatih
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Isabella Herman
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Zeynep Coban Akdemir
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Haowei Du
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Shalini N. Jhangiani
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Richard A. Gibbs
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Dana Marafi
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Davut Pehlivan
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Jennifer E. Posey
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Timothy Lotze
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Pedro Mancias
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - Meenakshi Bidwai Bhattacharjee
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
| | - James R. Lupski
- From the Division of Neurology and Developmental Neuroscience (D.G.C., I.H., D.P., T.L.), Department of Pediatrics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital (D.G.C., I.H., D.P., J.R.L.), Houston, TX; Department of Molecular and Human Genetics (D.G.C., J.F., I.H., Z.C.A., H.D., R.A.G., D.M., D.P., J.E.P., J.R.L.), Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center (S.N.J., R.A.G., J.R.L.), Baylor College of Medicine, Houston, TX; Department of Pediatrics (D.M.), Faculty of Medicine, Kuwait University, Safat, Kuwait; Division of Child and Adolescent Neurology (P.M.), Department of Pediatrics, University of Texas Health Science Center, Houston, TX; Pathology and Laboratory Medicine (M.B.B.), University of Texas Health Science Center at Houston-McGovern Medical School, Houston, TX; and Department of Pediatrics (J.R.L.), Baylor College of Medicine, Houston, TX
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