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Ogawa T, Xue J, Guo L, Inoue-Arai MS, Vendramini-Pittoli S, Zechi-Ceide RM, Candido-Souza RM, Tonello C, Brandão MM, Ozawa TO, Peixoto AP, Ruiz DMCF, Nakashima T, Ikegawa S, Moriyama K, Kokitsu-Nakata NM. Identification of a de novo PUF60 variant associated with craniofacial microsomia. Am J Med Genet A 2024:e63631. [PMID: 38647383 DOI: 10.1002/ajmg.a.63631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/12/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
Craniofacial microsomia (CFM), also known as the oculo-auriculo-vertebral spectrum, is a congenital disorder characterized by hypoplasia of the mandible and external ear due to tissue malformations originating from the first and second branchial arches. However, distinguishing it from other syndromes of branchial arch abnormalities is difficult, and causal variants remain unidentified in many cases. In this report, we performed an exome sequencing analysis of a Brazilian family with CFM. The proband was a 12-month-old boy with clinical findings consistent with the diagnostic criteria for CFM, including unilateral mandibular hypoplasia, microtia, and external auditory canal abnormalities. A heterozygous de novo nonsense variant (c.713C>G, p.S238*) in PUF60 was identified, which was predicted to be pathogenic in silico. PUF60 has been reported as a causal gene in Verheij syndrome, but not in CFM. Although the boy showed craniofacial abnormalities and developmental delay that overlapped with Verheij syndrome, the facial asymmetry with unilateral hypoplasia of the mandible observed in this case did not match the previously reported phenotypes of PUF60 variants. Our findings expand the phenotypic range of PUF60 variants that cover CFM and Verheij syndrome.
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Affiliation(s)
- Takuya Ogawa
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Jingyi Xue
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
- Department of Pharmacology, School of Basic Medical Sciences, Beijing Key Laboratory of Metabolic Disturbance Related Cardiovascular Disease, Capital Medical University, Beijing, China
| | - Long Guo
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
- Department of Laboratory Animal Science, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Maristela Sayuri Inoue-Arai
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Siulan Vendramini-Pittoli
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Roseli Maria Zechi-Ceide
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Rosana Maria Candido-Souza
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Cristiano Tonello
- Department of Craniofacial Surgery, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Michele Madeira Brandão
- Department of Craniofacial Surgery, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Terumi Okada Ozawa
- Department of Orthodontics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Adriano Porto Peixoto
- Department of Orthodontics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Daniela Maria Cury Ferreira Ruiz
- Department Speech Therapy, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
| | - Tomoki Nakashima
- Department of Cell Signaling, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shiro Ikegawa
- Laboratory for Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Keiji Moriyama
- Department of Maxillofacial Orthognathics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nancy Mizue Kokitsu-Nakata
- Department of Clinical Genetics, Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru, São Paulo, Brazil
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2
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Hoogenboom A, Falix FA, van der Laan L, Kerkhof J, Alders M, Sadikovic B, van Haelst MM. Novel PUF60 variant suggesting an interaction between Verheij and Cornelia de Lange syndrome: phenotype description and review of the literature. Eur J Hum Genet 2024; 32:435-439. [PMID: 38273166 PMCID: PMC10999433 DOI: 10.1038/s41431-023-01527-1] [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: 11/07/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
Verheij syndrome [VRJS; OMIM 615583] is a rare autosomal dominant neurodevelopmental disorder characterized by distinct clinical features, including growth retardation, intellectual disability, cardiac, and renal anomalies. VRJS is caused by deletions of chromosome 8q24.3 or pathogenic variants in the PUF60 gene. Recently, pathogenic PUF60 variants have been reported in some individuals with VRJS, contributing to the variability in the clinical presentation and severity of the condition. PUF60 encodes a protein involved in regulating gene expression and cellular growth. In this report, we describe a new case of VRJS with developmental delay, cardiac-, and renal abnormalities, caused by a heterozygous pathogenic PUF60 variant. Surprisingly, DNA methylation analysis revealed a pattern resembling the Cornelia de Lange syndrome (CdLS) episignature, suggesting a potential connection between PUF60 and CdLS-related genes. This case report further delineates the clinical and molecular spectrum of VRJS and supports further research to validate the interaction between VRJS and CdLS.
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Affiliation(s)
- Amarens Hoogenboom
- Medical University of Groningen (UMCG), Groningen, the Netherlands
- Department of pediatrics, Curaçao Medical Center (CMC), Willemstad, Curaçao
| | - Farah A Falix
- Department of pediatrics, Curaçao Medical Center (CMC), Willemstad, Curaçao
| | - Liselot van der Laan
- Department of Human Genetics, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development, Amsterdam University Medical Centers (AUMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam UMC, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development, Amsterdam University Medical Centers (AUMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam UMC, Amsterdam, the Netherlands
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Mieke M van Haelst
- Department of pediatrics, Curaçao Medical Center (CMC), Willemstad, Curaçao.
- Department of Human Genetics, Amsterdam UMC, Amsterdam, the Netherlands.
- Amsterdam Reproduction & Development, Amsterdam University Medical Centers (AUMC), University of Amsterdam, Amsterdam, The Netherlands.
- Emma Center for Personalized Medicine, Amsterdam UMC, Amsterdam, The Netherlands.
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3
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Miao M, Wang J, Guo C, Su X, Sun L, Lu S. Identification of a novel de novo PUF60 variant causing Verheij syndrome in a fetus. Gene 2024; 897:148092. [PMID: 38110042 DOI: 10.1016/j.gene.2023.148092] [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: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
Verheij syndrome (VRJS) is a craniofacial spliceosomopathy with a wide phenotypic spectrum. Haploinsufficiency of the poly-uridine binding splicing factor 60 gene (PUF60) and its loss-of-function (LOF) variants are involved in VRJS. We evaluated a human fetus with congenital heart defects and preaxial polydactyly. Clinical data were obtained from the medical record. Whole-exome sequencing (WES) was used to explore the potential genetic etiology, and the detected variant verified using Sanger sequencing. Functional studies were performed to validate the pathogenic effects of the variant. Using trio-WES, we identified a novel PUF60 variant (NM_078480.2; c.1678 T > A, p.*560Argext*204) in the pedigree. Bioinformatic analyses revealed that the variant is potentially pathogenic, and functional studies indicated that it leads to degradation of the elongated protein and subsequently PUF60 LOF, producing some VRJS phenotypes. These findings confirmed the pathogenicity of the variant. This study implicates PUF60 LOF in the etiopathogenesis of VRJS. It not only expands the PUF60 variant spectrum, and also provides a basis for genetic counseling and the diagnosis of VRJS. Although trio-WES is a well-established approach for identifying the genetic etiology of rare multisystemic conditions, functional studies could aid in verifying the pathogenicity of novel variants.
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Affiliation(s)
- Mingzhu Miao
- Department of Prenatal Diagnosis, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China
| | - Jue Wang
- Department of Prenatal Diagnosis, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China
| | - Chenyan Guo
- Department of Obstetrics, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China
| | - Xiaotian Su
- Department of Bioinformatics, Berry Genomics Co., Ltd., Beijing, China
| | - Lizhou Sun
- Department of Obstetrics, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China.
| | - Shoulian Lu
- Department of Prenatal Diagnosis, Jiangsu Province People's Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing 210036, China.
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4
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Baum E, Huang W, Vincent-Delorme C, Brunelle P, Antebi A, Dafsari HS. Novel Genetic and Phenotypic Expansion in Ameliorated PUF60-Related Disorders. Int J Mol Sci 2024; 25:2053. [PMID: 38396730 PMCID: PMC10889399 DOI: 10.3390/ijms25042053] [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: 12/31/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Heterozygous variants in the Poly(U) Binding Splicing Factor 60kDa gene (PUF60) have been associated with Verheij syndrome, which has the key features of coloboma, short stature, skeletal abnormalities, developmental delay, palatal abnormalities, and congenital heart and kidney defects. Here, we report five novel patients from unrelated families with PUF60-related disorders exhibiting novel genetic and clinical findings with three truncating variants, one splice-site variant with likely reduced protein expression, and one missense variant. Protein modeling of the patient's missense variant in the PUF60 AlphaFold structure revealed a loss of polar bonds to the surrounding residues. Neurodevelopmental disorders were present in all patients, with variability in speech, motor, cognitive, social-emotional and behavioral features. Novel phenotypic expansions included movement disorders as well as immunological findings with recurrent respiratory, urinary and ear infections, atopic diseases, and skin abnormalities. We discuss the role of PUF60 in immunity with and without infection based on recent organismic and cellular studies. As our five patients showed less-severe phenotypes than classical Verheij syndrome, particularly with the absence of key features such as coloboma or palatal abnormalities, we propose a reclassification as PUF60-related neurodevelopmental disorders with multi-system involvement. These findings will aid in the genetic counseling of patients and families.
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Affiliation(s)
- Emily Baum
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Wenming Huang
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
| | | | - Perrine Brunelle
- Institut de Génétique Médicale, University of Lille, ULR7364 RADEME, CHU Lille, F-59000 Lille, France
| | - Adam Antebi
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
| | - Hormos Salimi Dafsari
- Department of Pediatrics, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
- Max-Planck-Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases (CECAD), 50931 Cologne, Germany
- Department of Pediatric Neurology, Evelina’s Children Hospital, Guy’s & St. Thomas’ Hospital NHS Foundation Trust, London SE1 7EH, UK
- Randall Division of Cell and Molecular Biophysics, Muscle Signaling Section, King’s College London, London WC2R 2LS, UK
- Center for Rare Diseases, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany
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5
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Grimes H, Ansari M, Ashraf T, Cueto-González AM, Calder A, Day M, Fernandez Alvarez P, Foster A, Lahiri N, Repetto GM, Scurr I, Varghese V, Low KJ. PUF60-related developmental disorder: A case series and phenotypic analysis of 10 additional patients with monoallelic PUF60 variants. Am J Med Genet A 2023; 191:2610-2622. [PMID: 37303278 DOI: 10.1002/ajmg.a.63313] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/11/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
PUF60-related developmental disorder (also referred to as Verheij syndrome), resulting from haploinsufficiency of PUF60, is associated with multiple congenital anomalies affecting a wide range of body systems. These anomalies include ophthalmic coloboma, and congenital anomalies of the heart, kidney, and musculoskeletal system. Behavioral and intellectual difficulties are also observed. While less common than other features associated with PUF60-related developmental disorder, for instance hearing impairment and short stature, identification of specific anomalies such as ophthalmic coloboma can aid with diagnostic identification given the limited spectrum of genes linked with this feature. We describe 10 patients with PUF60 gene variants, bringing the total number reported in the literature, to varying levels of details, to 56 patients. Patients were recruited both via locally based exome sequencing from international sites and from the DDD study in the United Kingdom. Eight of the variants reported were novel PUF60 variants. The addition of a further patient with a reported c449-457del variant to the existing literature highlights this as a recurrent variant. One variant was inherited from an affected parent. This is the first example in the literature of an inherited variant resulting in PUF60-related developmental disorder. Two patients (20%) were reported to have a renal anomaly consistent with 22% of cases in previously reported literature. Two patients received specialist endocrine treatment. More commonly observed were clinical features such as: cardiac anomalies (40%), ocular abnormalities (70%), intellectual disability (60%), and skeletal abnormalities (80%). Facial features did not demonstrate a recognizable gestalt. Of note, but remaining of unclear causality, we describe a single pediatric patient with pineoblastoma. We recommend that stature and pubertal progress should be monitored in PUF60-related developmental disorder with a low threshold for endocrine investigations as hormone therapy may be indicated. Our study reports an inherited case with PUF60-related developmental disorder which has important genetic counseling implications for families.
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Affiliation(s)
- H Grimes
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Trust, Bristol, UK
| | - M Ansari
- South East Scotland Genetics Service, Western General Hospital, Edinburgh, UK
| | - T Ashraf
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Anna Mª Cueto-González
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
- Medicine Genetics Group, Vall Hebron Research Institute (VHIR), Vall d'Hebron Barcelona Hospital Campus, Autonomous University of Barcelona, Barcelona, Spain
| | - A Calder
- Department of Radiology, Great Ormond Street Hospital, London, UK
| | - M Day
- Exeter Genetics Laboratory, Royal Devon and Exeter NHS Trust, Exeter, UK
| | - P Fernandez Alvarez
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain
| | - A Foster
- Department of Clinical Genetics, West Midlands Regional Genetics Centre, Birmingham, UK
| | - N Lahiri
- Department of Clinical Genetics, St Georges University Hospital NHS Foundation Trust, London, UK
- Department of Clinical and Molecular Science, St Georges University of London, London, UK
| | - G M Repetto
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana Universidad del Desarrollo, Santiago, Chile
| | - I Scurr
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Trust, Bristol, UK
| | - V Varghese
- All Wales Medical Genomics Services, University Hospital of Wales, Cardiff, UK
| | - Karen J Low
- Department of Clinical Genetics, University Hospitals Bristol and Weston NHS Trust, Bristol, UK
- Centre for Academic Child Health, University of Bristol, Bristol, UK
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6
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Fennell AP, Baxter AE, Berkovic SF, Ellaway CJ, Forwood C, Hildebrand MS, Kumble S, McKeown C, Mowat D, Poke G, Rajagopalan S, Regan BM, Scheffer IE, Stark Z, Stutterd CA, Tan TY, Wilkins EJ, Yeung A, Hunter MF. The diverse pleiotropic effects of spliceosomal protein PUF60: A case series of Verheij syndrome. Am J Med Genet A 2022; 188:3432-3447. [PMID: 36367278 DOI: 10.1002/ajmg.a.62950] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/17/2022] [Accepted: 06/11/2022] [Indexed: 01/31/2023]
Abstract
Verheij syndrome (VRJS) is a rare craniofacial spliceosomopathy presenting with craniofacial dysmorphism, multiple congenital anomalies and variable neurodevelopmental delay. It is caused by single nucleotide variants (SNVs) in PUF60 or interstitial deletions of the 8q24.3 region. PUF60 encodes a splicing factor which forms part of the spliceosome. To date, 36 patients with a sole diagnosis of VRJS due to disease-causing PUF60 SNVs have been reported in peer-reviewed publications. Although the depth of their phenotyping has varied greatly, they exhibit marked phenotypic heterogeneity. We report 10 additional unrelated patients, including the first described patients of Khmer, Indian, and Vietnamese ethnicities, and the eldest patient to date, with 10 heterozygous PUF60 variants identified through exome sequencing, 8 previously unreported. All patients underwent deep phenotyping identifying variable dysmorphism, growth delay, neurodevelopmental delay, and multiple congenital anomalies, including several unique features. The eldest patient is the only reported individual with a germline variant and neither neurodevelopmental delay nor intellectual disability. In combining these detailed phenotypic data with that of previously reported patients (n = 46), we further refine the known frequencies of features associated with VRJS. These include neurodevelopmental delay/intellectual disability (98%), axial skeletal anomalies (74%), appendicular skeletal anomalies (73%), oral anomalies (68%), short stature (66%), cardiac anomalies (63%), brain malformations (48%), hearing loss (46%), microcephaly (41%), colobomata (38%), and other ocular anomalies (65%). This case series, incorporating three patients from previously unreported ethnic backgrounds, further delineates the broad pleiotropy and mutational spectrum of PUF60 pathogenic variants.
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Affiliation(s)
- Andrew Paul Fennell
- Monash Genetics, Monash Health, Melbourne, Australia.,Clinical Genetics Service, Austin Health, Melbourne, Australia.,Department of Paediatrics, Monash University, Melbourne, Australia
| | | | - Samuel Frank Berkovic
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Heidelberg, Australia
| | - Carolyn Jane Ellaway
- Paediatrics North, Sydney, Australia.,Genetic Metabolic Disorders Service, The Sydney Children's Hospital Network, Sydney, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.,Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Sydney, Australia
| | - Caitlin Forwood
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Sydney, Australia
| | - Michael Stephen Hildebrand
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Heidelberg, Australia.,Murdoch Children's Research Institute, Melbourne, Australia
| | - Smitha Kumble
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Colina McKeown
- Genetic Health Service New Zealand, Wellington Hospital, Wellington, New Zealand
| | - David Mowat
- Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Sydney, Australia
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington Hospital, Wellington, New Zealand
| | | | - Brigid M Regan
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Heidelberg, Australia
| | - Ingrid Eileen Scheffer
- Epilepsy Research Centre, Department of Medicine, The University of Melbourne, Heidelberg, Australia.,Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia.,The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Chloe Alice Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Tiong Yang Tan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Ella Jane Wilkins
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia
| | - Alison Yeung
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, Australia
| | - Matthew Frank Hunter
- Monash Genetics, Monash Health, Melbourne, Australia.,Department of Paediatrics, Monash University, Melbourne, Australia
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7
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Kocaaga A, Yimenicioglu S, Atikel YÖ, Yavuz OÖ. First report of tethered cord syndrome in a patient with Verheij syndrome. Ophthalmic Genet 2022:1-5. [PMID: 36134573 DOI: 10.1080/13816810.2022.2121968] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
BACKGROUND Verheij syndrome (VRJS) is a rare microdeletion syndrome of chromosome 8q24.3 that is characterized by severe growth retardation, microcephaly, vertebral anomalies, joint laxity/dislocation, psychomotor retardation, cardiac and renal defects, and dysmorphic facial features. Pathogenic variants of PUF60 (Poly-U Binding Splicing Factor 60 kDa) have been found to cause VRJS. Here we present a Turkish patient with Verheij syndrome who has typical facial dysmorphic features and renal and cardiac abnormalities, scoliosis, tethered cord, and mild intellectual disability. METHODS This is a case report of a 11-year-old female child who presented with Verheij syndrome. Blood samples were collected from the patient and the family. We performed whole exome sequencing was used to identify potential genetic mutations. We also used 3-dimensional protein structure analysis to identify the effect of the mutation. RESULTS A de-novo in-frame variant (c.449_457delCAAAGGGGG; p.Ala150_Phe152del) of the PUF60 gene was identified by whole exome sequencing. According to ACMG guidelines in 2015, the mutation is classified as pathogenic and it has been reported in the clinvar database. Results of in-silico prediction software tools predicted the mutation was pathogenic. Protein structure analysis showed that the three residues affected by the in-frame deletion form could lead to impaired stability and function of the PUF60 protein. CONCLUSIONS To date, 25 patients have been reported with PUF60 mutations in the medical literature. In this article, we report a patient with VRJS who had the unusual findings of tethered cord syndrome and renal abnormalities. As far as we know, this is the first patient from Turkey who has been diagnosed with Verheij syndrome.
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Affiliation(s)
- A Kocaaga
- Department of Medical Genetics, Eskisehir City Hospital, Eskişehir, Turkey
| | - S Yimenicioglu
- Department of Pediatric Neurology, Eskisehir City Hospital, Eskişehir, Turkey
| | - Y Özdemir Atikel
- Department of Pediatric Nephrology, Eskisehir City Hospital, Eskişehir, Turkey
| | - O Özkale Yavuz
- Department of Pediatric Radiology, Eskisehir City Hospital, Eskişehir, Turkey
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8
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Ezan J, Moreau MM, Mamo TM, Shimbo M, Decroo M, Richter M, Peyroutou R, Rachel R, Tissir F, de Anda FC, Sans N, Montcouquiol M. Early loss of Scribble affects cortical development, interhemispheric connectivity and psychomotor activity. Sci Rep 2021; 11:9106. [PMID: 33907211 PMCID: PMC8079449 DOI: 10.1038/s41598-021-88147-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 04/01/2021] [Indexed: 12/03/2022] Open
Abstract
Neurodevelopmental disorders arise from combined defects in processes including cell proliferation, differentiation, migration and commissure formation. The evolutionarily conserved tumor-suppressor protein Scribble (Scrib) serves as a nexus to transduce signals for the establishment of apicobasal and planar cell polarity during these processes. Human SCRIB gene mutations are associated with neural tube defects and this gene is located in the minimal critical region deleted in the rare Verheij syndrome. In this study, we generated brain-specific conditional cKO mouse mutants and assessed the impact of the Scrib deletion on brain morphogenesis and behavior. We showed that embryonic deletion of Scrib in the telencephalon leads to cortical thickness reduction (microcephaly) and partial corpus callosum and hippocampal commissure agenesis. We correlated these phenotypes with a disruption in various developmental mechanisms of corticogenesis including neurogenesis, neuronal migration and axonal connectivity. Finally, we show that Scrib cKO mice have psychomotor deficits such as locomotor activity impairment and memory alterations. Altogether, our results show that Scrib is essential for early brain development due to its role in several developmental cellular mechanisms that could underlie some of the deficits observed in complex neurodevelopmental pathologies.
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Affiliation(s)
- Jerome Ezan
- Université de Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077, Bordeaux, France.
| | - Maité M Moreau
- Université de Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077, Bordeaux, France
| | - Tamrat M Mamo
- Université de Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077, Bordeaux, France
| | - Miki Shimbo
- Université de Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077, Bordeaux, France
| | - Maureen Decroo
- Université de Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077, Bordeaux, France
| | - Melanie Richter
- Germany Center for Molecular Neurobiology Hamburg (ZMNH), Research Group Neuronal Development, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronan Peyroutou
- Université de Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077, Bordeaux, France
| | - Rivka Rachel
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, NIH, Bethesda, MD, 20892, USA
| | - Fadel Tissir
- Developmental Neurobiology Group, Institute of Neuroscience, University of Louvain, Avenue Mounier 73, Box B1.73.16, 1200, Brussels, Belgium
| | - Froylan Calderon de Anda
- Germany Center for Molecular Neurobiology Hamburg (ZMNH), Research Group Neuronal Development, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nathalie Sans
- Université de Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077, Bordeaux, France
| | - Mireille Montcouquiol
- Université de Bordeaux, INSERM, Neurocentre Magendie, U1215, 33077, Bordeaux, France.
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9
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Latypova X, Dang X, Zhang J, Isidor B. Letter regarding the article "two girls with short stature, short neck, vertebral anomalies, Sprengel deformity and intellectual disability" (Isidor et al., 2015). Eur J Med Genet 2021; 64:104179. [PMID: 33636376 DOI: 10.1016/j.ejmg.2021.104179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Xenia Latypova
- Service de Génétique Médicale, Hôpital Hôtel-Dieu, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Xiao Dang
- BGI-Shenzhen, Shenzhen, 518083, China; BGI-Genomics, BGI-Shenzhen, Shenzhen, 518083, China; Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jianguo Zhang
- BGI-Shenzhen, Shenzhen, 518083, China; BGI-Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Bertrand Isidor
- Service de Génétique Médicale, Hôpital Hôtel-Dieu, Centre Hospitalier Universitaire de Nantes, Nantes, France.
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10
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Haug P, Koller S, Maggi J, Lang E, Feil S, Wlodarczyk A, Bähr L, Steindl K, Rohrbach M, Gerth-Kahlert C, Berger W. Whole Exome Sequencing in Coloboma/Microphthalmia: Identification of Novel and Recurrent Variants in Seven Genes. Genes (Basel) 2021; 12:65. [PMID: 33418956 PMCID: PMC7825129 DOI: 10.3390/genes12010065] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/25/2020] [Accepted: 12/31/2020] [Indexed: 12/16/2022] Open
Abstract
Coloboma and microphthalmia (C/M) are related congenital eye malformations, which can cause significant visual impairment. Molecular diagnosis is challenging as the genes associated to date with C/M account for only a small percentage of cases. Overall, the genetic cause remains unknown in up to 80% of patients. High throughput DNA sequencing technologies, including whole-exome sequencing (WES), are therefore a useful and efficient tool for genetic screening and identification of new mutations and novel genes in C/M. In this study, we analyzed the DNA of 19 patients with C/M from 15 unrelated families using singleton WES and data analysis for 307 genes of interest. We identified seven novel and one recurrent potentially disease-causing variants in CRIM1, CHD7, FAT1, PTCH1, PUF60, BRPF1, and TGFB2 in 47% of our families, three of which occurred de novo. The detection rate in patients with ocular and extraocular manifestations (67%) was higher than in patients with an isolated ocular phenotype (46%). Our study highlights the significant genetic heterogeneity in C/M cohorts and emphasizes the diagnostic power of WES for the screening of patients and families with C/M.
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Affiliation(s)
- Patricia Haug
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Elena Lang
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
- Department of Ophthalmology, University Hospital and University of Zurich, 8091 Zurich, Switzerland;
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Agnès Wlodarczyk
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Luzy Bähr
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren, Switzerland;
| | - Marianne Rohrbach
- Division of Metabolism and Children’s Research Centre, University Children’s Hospital Zurich, 8032 Zurich, Switzerland;
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital and University of Zurich, 8091 Zurich, Switzerland;
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland; (P.H.); (S.K.); (J.M.); (E.L.); (S.F.); (A.W.); (L.B.)
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8006 Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8006 Zurich, Switzerland
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11
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Yoon KH, Fox SC, Dicipulo R, Lehmann OJ, Waskiewicz AJ. Ocular coloboma: Genetic variants reveal a dynamic model of eye development. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:590-610. [PMID: 32852110 DOI: 10.1002/ajmg.c.31831] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 12/21/2022]
Abstract
Ocular coloboma is a congenital disorder of the eye where a gap exists in the inferior retina, lens, iris, or optic nerve tissue. With a prevalence of 2-19 per 100,000 live births, coloboma, and microphthalmia, an associated ocular disorder, represent up to 10% of childhood blindness. It manifests due to the failure of choroid fissure closure during eye development, and it is a part of a spectrum of ocular disorders that include microphthalmia and anophthalmia. Use of genetic approaches from classical pedigree analyses to next generation sequencing has identified more than 40 loci that are associated with the causality of ocular coloboma. As we have expanded studies to include singleton cases, hereditability has been very challenging to prove. As such, researchers over the past 20 years, have unraveled the complex interrelationship amongst these 40 genes using vertebrate model organisms. Such research has greatly increased our understanding of eye development. These genes function to regulate initial specification of the eye field, migration of retinal precursors, patterning of the retina, neural crest cell biology, and activity of head mesoderm. This review will discuss the discovery of loci using patient data, their investigations in animal models, and the recent advances stemming from animal models that shed new light in patient diagnosis.
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Affiliation(s)
- Kevin H Yoon
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Women & Children's Health Research Institute, University of Alberta, Edmonton, Canada
| | - Sabrina C Fox
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Women & Children's Health Research Institute, University of Alberta, Edmonton, Canada
| | - Renée Dicipulo
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Women & Children's Health Research Institute, University of Alberta, Edmonton, Canada
| | - Ordan J Lehmann
- Women & Children's Health Research Institute, University of Alberta, Edmonton, Canada.,Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada.,Department of Ophthalmology, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew J Waskiewicz
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.,Women & Children's Health Research Institute, University of Alberta, Edmonton, Canada
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12
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Yamada M, Uehara T, Suzuki H, Takenouchi T, Kosaki K. Protein elongation variant of PUF60: Milder phenotypic end of the Verheij syndrome. Am J Med Genet A 2020; 182:2709-2714. [PMID: 32851780 DOI: 10.1002/ajmg.a.61816] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/26/2020] [Accepted: 07/22/2020] [Indexed: 12/12/2022]
Abstract
The PUF60 gene encodes a ubiquitously expressed essential splicing factor that is recruited to the U2snRNA complex. The complex binds to the 3' splice site of exons in specific target genes and regulates the inclusion or exclusion of such exons. Recently, pathogenic variants of PUF60 have been shown to cause a relatively specific and potentially recognizable pattern of malformation referred to as Verheij syndrome. Here, we report a 12-year-old female patient with a de novo mutation in PUF60 whose phenotype was representative of the milder end of the phenotypic spectrum of Verheij syndrome; the de novo mutation was a frameshift mutation p.(Ser558Cysfs*21) that resulted in the addition of 21 extra amino acids at the carboxy end of the protein. Among the frequent features of Verheij syndrome, the patient exhibited coloboma, cervical spinal segmentation defects, and borderline intellectual functioning, but lacked cardiac abnormalities, deafness, and urogenital abnormalities. The results of RNA analysis using peripheral blood showed the escape of the mutant allele from nonsense-mediated mRNA decay, possibly accounting for the mild phenotype in the presently reported patient. Based on our clinical observations, we inferred that two embryologic processes, closure of the ocular plate and cervical spinal segmentation, are particularly susceptible to deficient PUF60-mediated splicing regulation, compared with other embryogenetic processes leading to the central nervous system, heart, ear, and kidney.
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Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hisato Suzuki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Toshiki Takenouchi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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13
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George A, Cogliati T, Brooks BP. Genetics of syndromic ocular coloboma: CHARGE and COACH syndromes. Exp Eye Res 2020; 193:107940. [PMID: 32032630 DOI: 10.1016/j.exer.2020.107940] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 02/07/2023]
Abstract
Optic fissure closure defects result in uveal coloboma, a potentially blinding condition affecting between 0.5 and 2.6 per 10,000 births that may cause up to 10% of childhood blindness. Uveal coloboma is on a phenotypic continuum with microphthalmia (small eye) and anophthalmia (primordial/no ocular tissue), the so-called MAC spectrum. This review gives a brief overview of the developmental biology behind coloboma and its clinical presentation/spectrum. Special attention will be given to two prominent, syndromic forms of coloboma, namely, CHARGE (Coloboma, Heart defect, Atresia choanae, Retarded growth and development, Genital hypoplasia, and Ear anomalies/deafness) and COACH (Cerebellar vermis hypoplasia, Oligophrenia, Ataxia, Coloboma, and Hepatic fibrosis) syndromes. Approaches employed to identify genes involved in optic fissure closure in animal models and recent advances in live imaging of zebrafish eye development are also discussed.
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Affiliation(s)
- Aman George
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Tiziana Cogliati
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health. Bethesda, Maryland, 20892, USA.
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14
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Alkhunaizi E, Braverman N. Clinical characterization of a PUF60 variant in a patient with Dubowitz-like syndrome. Am J Med Genet A 2018; 179:130-133. [PMID: 30569551 DOI: 10.1002/ajmg.a.60691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Ebba Alkhunaizi
- Department of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Nancy Braverman
- Department of Pediatrics and Medical Genetics, McGill University Health Centre, Montréal, Québec, Canada
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15
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Xu Q, Li CY, Wang Y, Li HP, Wu BB, Jiang YH, Xu X. Role of PUF60 gene in Verheij syndrome: a case report of the first Chinese Han patient with a de novo pathogenic variant and review of the literature. BMC Med Genomics 2018; 11:92. [PMID: 30352594 PMCID: PMC6199733 DOI: 10.1186/s12920-018-0421-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/12/2018] [Indexed: 02/06/2023] Open
Abstract
Background Verheij syndrome is a rare microdeletion syndrome of chromosome 8q24.3 that harbors PUF60, SCRIB, and NRBP2 genes. Subsequently, loss of function mutations in PUF60 have been found in children with clinical features significantly overlapping with Verheij. Case presentation Here we present the first Chinese Han patient with a de novo nonsense variant (c.1357C > T, p.Gln453*) in PUF60 by clinical whole exome sequencing. The 5-year-old boy presents with dysmorphic facial features, intellectual disability, and growth retardation but without apparent cardiac, renal, ocular, and spinal anomalies. Conclusions Our finding contributes to the understanding of the genotype and phenotype in PUF60 related disorder.
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Affiliation(s)
- Qiong Xu
- Developmental and Behavioral Pediatric Department & Child Health Care Department, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Chun-Yang Li
- Developmental and Behavioral Pediatric Department & Child Health Care Department, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Yi Wang
- Developmental and Behavioral Pediatric Department & Child Health Care Department, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Hui-Ping Li
- Developmental and Behavioral Pediatric Department & Child Health Care Department, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Bing-Bing Wu
- Developmental and Behavioral Pediatric Department & Child Health Care Department, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China
| | - Yong-Hui Jiang
- Department of Pediatrics, Duke University School of Medicine, Durham, NC, 27710, USA.,Department of Neurobiology, Duke University School of Medicine, Durham, NC, 27710, USA.,Program in Genetics and Genomics, Duke University School of Medicine, Durham, NC, 27710, USA.,Cellular Molecular Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Xiu Xu
- Developmental and Behavioral Pediatric Department & Child Health Care Department, Children's Hospital of Fudan University, 399 Wanyuan Road, Shanghai, 201102, China.
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