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Gerik-Celebi HB, Bolat H, Unsel-Bolat G. Rare heterozygous genetic variants of NRXN and NLGN gene families involved in synaptic function and their association with neurodevelopmental disorders. Dev Neurobiol 2024; 84:158-168. [PMID: 38739110 DOI: 10.1002/dneu.22941] [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: 11/28/2023] [Revised: 03/02/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
The interaction of neurexins (NRXNs) in the presynaptic membrane with postsynaptic cell adhesion molecules called neuroligins (NLGNs) is critical for this synaptic function. Impaired synaptic functions are emphasized in neurodevelopmental disorders to uncover etiological factors. We evaluated variants in NRXN and NLGN genes encoding molecules located directly at the synapse in patients with neuropsychiatric disorders using clinical exome sequencing and chromosomal microarray. We presented detailed clinical findings of cases carrying heterozygous NRXN1 (c.190C > T, c.1679C > T and two copy number variations [CNVs]), NRXN2 (c.808dup, c.1901G > T), NRXN3 (c.3889C > T), and NLGN1 (c.269C > G, c.473T > A) gene variants. In addition, three novel variants were identified in the NRXN1 (c.1679C > T), NRXN3 [c.3889C > T (p.Pro1297Ser)], and NLGN1 [c.473T > A (p.Ile158Lys)] genes. We emphasize the clinical findings of CNVs of the NRXN1 gene causing a more severe clinical presentation than single nucleotide variants of the NRXN1 gene in this study. We detected an NRXN2 gene variant (c.808dup) with low allelic frequency in two unrelated cases with the same diagnosis. We emphasize the importance of this variant for future studies. We suggest that NRXN2, NRXN3, and NLGN1 genes, which are less frequently reported than NRXN1 gene variants, may also be associated with neurodevelopmental disorders.
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Affiliation(s)
| | - Hilmi Bolat
- Department of Medical Genetics, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
| | - Gul Unsel-Bolat
- Department of Child and Adolescent Psychiatry, Balıkesir University Faculty of Medicine, Balıkesir, Turkey
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2
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Saarela A, Timonen O, Kirjavainen J, Liu Y, Silvennoinen K, Mervaala E, Kälviäinen R. Novel LAMC3 pathogenic variant enriched in Finnish population causes malformations of cortical development and severe epilepsy. Epileptic Disord 2024. [PMID: 38758065 DOI: 10.1002/epd2.20244] [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: 12/01/2023] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/18/2024]
Abstract
OBJECTIVE Recessive LAMC3 mutations are recognized to cause epilepsy with cortical malformations characterized by polymicrogyria and pachygyria. The objective of this study was to describe the clinical picture and epilepsy phenotype of four patients with a previously undescribed LAMC3 variant. METHODS All epilepsy patients treated in Kuopio Epilepsy Center (located in Kuopio, Finland) are offered the possibility to participate in a scientific study investigating biomarkers in epilepsy (Epibiomarker study). We have collected a comprehensive database of the study population, and are currently re-evaluating our database regarding the patients with developmental and/or epileptic encephalopathy (DEE). If the etiology of epilepsy remains unknown in the clinical setting, we are performing whole exome sequencing to recognize the genetic causes. RESULTS Among our study population of 323 DEE patients we recognized three patients with similar homozygous LAMC3 c.1866del (p.(Phe623Serfs*10)) frameshift variant and one patient with a compound heterozygous mutation where the same frameshift variant was combined with an intronic LAMC3 c.4231-12C>G variant on another allele. All these patients have severe epilepsy and either bilateral agyria-pachygyria or bilateral polymicrogyria in their clinical MRI scanning. Cortical malformations involve the occipital lobes in all our patients. Epilepsy phenotype is variable as two of our patients have DEE with epileptic spasms progressing to Lennox-Gastaut syndrome and intellectual disability. The other two patients have focal epilepsy without marked cognitive deficit. The four patients are unrelated. LAMC3 c.1866del p.(Phe623Serfs*10) frameshift variant is enriched in the Finnish population. SIGNIFICANCE Only a few patients with epilepsy caused by LAMC3 homozygous or compound heterozygous mutations have been described in the literature. To our knowledge, the variants discovered in our patients have not previously been published. Clinical phenotype appears to be more varied than previously assumed and patients with a milder phenotype and normal cognition have probably remained unrecognized.
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Affiliation(s)
- Anni Saarela
- Department of Pediatric Neurology, Kuopio Epilepsy Center., Kuopio University Hospital. Full Member of ERN EpiCARE., Kuopio, Finland
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Oskari Timonen
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jarkko Kirjavainen
- Department of Pediatric Neurology, Kuopio Epilepsy Center., Kuopio University Hospital. Full Member of ERN EpiCARE., Kuopio, Finland
| | - Yawu Liu
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
| | - Katri Silvennoinen
- Department of Neurology, Kuopio Epilepsy Center, Kuopio University Hospital. Full Member of ERN EpiCARE, Kuopio, Finland
| | - Esa Mervaala
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Clinical Neurophysiology, Kuopio Epilepsy Center, Kuopio University Hospital. Full Member of ERN EpiCARE, Kuopio, Finland
| | - Reetta Kälviäinen
- Institute of Clinical Medicine, University of Eastern Finland, Kuopio, Finland
- Department of Neurology, Kuopio Epilepsy Center, Kuopio University Hospital. Full Member of ERN EpiCARE, Kuopio, Finland
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Cordova I, Blesson A, Savatt JM, Sveden A, Mahida S, Hazlett H, Rooney Riggs E, Chopra M. Expansion of the Genotypic and Phenotypic Spectrum of ASH1L-Related Syndromic Neurodevelopmental Disorder. Genes (Basel) 2024; 15:423. [PMID: 38674358 PMCID: PMC11049257 DOI: 10.3390/genes15040423] [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: 02/15/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Pathogenic ASH1L variants have been reported in probands with broad phenotypic presentations, including intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, seizures, congenital anomalies, and other skeletal, muscular, and sleep differences. Here, we review previously published individuals with pathogenic ASH1L variants and report three further probands with novel ASH1L variants and previously unreported phenotypic features, including mixed receptive language disorder and gait disturbances. These novel data from the Brain Gene Registry, an accessible repository of clinically derived genotypic and phenotypic data, have allowed for the expansion of the phenotypic and genotypic spectrum of this condition.
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Affiliation(s)
- Ineke Cordova
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Alyssa Blesson
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Juliann M. Savatt
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Abigail Sveden
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Sonal Mahida
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Heather Hazlett
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC 27510, USA
| | - Erin Rooney Riggs
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
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4
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Chopra M, Savatt JM, Bingaman TI, Good ME, Morgan A, Cooney C, Rossel AM, VanHoute B, Cordova I, Mahida S, Lanzotti V, Baldridge D, Gurnett CA, Piven J, Hazlett H, Pomeroy SL, Sahin M, Payne PRO, Riggs ER, Constantino JN. Clinical variants paired with phenotype: A rich resource for brain gene curation. Genet Med 2024; 26:101035. [PMID: 38059438 PMCID: PMC10939875 DOI: 10.1016/j.gim.2023.101035] [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: 05/31/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Abstract
PURPOSE Clinically ascertained variants are under-utilized in neurodevelopmental disorder research. We established the Brain Gene Registry (BGR) to coregister clinically identified variants in putative brain genes with participant phenotypes. Here, we report 179 genetic variants in the first 179 BGR registrants and analyze the proportion that were novel to ClinVar at the time of entry and those that were absent in other disease databases. METHODS From 10 academically affiliated institutions, 179 individuals with 179 variants were enrolled into the BGR. Variants were cross-referenced for previous presence in ClinVar and for presence in 6 other genetic databases. RESULTS Of 179 variants in 76 genes, 76 (42.5%) were novel to ClinVar, and 62 (34.6%) were absent from all databases analyzed. Of the 103 variants present in ClinVar, 37 (35.9%) were uncertain (ClinVar aggregate classification of variant of uncertain significance or conflicting classifications). For 5 variants, the aggregate ClinVar classification was inconsistent with the interpretation from the BGR site-provided classification. CONCLUSION A significant proportion of clinical variants that are novel or uncertain are not shared, limiting the evidence base for new gene-disease relationships. Registration of paired clinical genetic test results with phenotype has the potential to advance knowledge of the relationships between genes and neurodevelopmental disorders.
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Affiliation(s)
- Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital; Boston, MA; Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA.
| | - Juliann M Savatt
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Taylor I Bingaman
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Molly E Good
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Alexis Morgan
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Caitlin Cooney
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Allison M Rossel
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Bryanna VanHoute
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Ineke Cordova
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - Sonal Mahida
- Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Virginia Lanzotti
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Dustin Baldridge
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Christina A Gurnett
- Washington University School of Medicine Intellectual and Developmental Disability Research Center, St. Louis, MO
| | - Joseph Piven
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC
| | - Heather Hazlett
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC
| | - Scott L Pomeroy
- Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Mustafa Sahin
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital; Boston, MA; Department of Neurology, Boston Children's Hospital Intellectual Disability and Research Center; Harvard Medical School; Boston, MA
| | - Philip R O Payne
- Institute for Informatics Washington University in St. Louis, St. Louis, MO
| | - Erin Rooney Riggs
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA
| | - John N Constantino
- Division of Behavioural and Mental Health, Children's Healthcare of Atlanta, Departments of Psychiatry and Paediatrics, Emory University, Atlanta, GA
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, Sant DW, Stark Z, Whiffin N, Rehm HL, Ware JS. Toward robust clinical genome interpretation: Developing a consistent terminology to characterize Mendelian disease-gene relationships-allelic requirement, inheritance modes, and disease mechanisms. Genet Med 2024; 26:101029. [PMID: 37982373 PMCID: PMC11039201 DOI: 10.1016/j.gim.2023.101029] [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: 04/21/2023] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/21/2023] Open
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here, we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both Sequence Ontology (SO) and Human Phenotype Ontology (HPO) ontologies. Gene Curation Coalition member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom.
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Katherine S Josephs
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge, United Kingdom; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Ada Hamosh
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London, United Kingdom
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, United Kingdom
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom; Open Targets, Open Targets, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | | | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David W Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, UT
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia; University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, United Kingdom
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - James S Ware
- National Heart and Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom; Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Royal Brompton and Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, United Kingdom
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Pan X, Liu S, Feng X, Liu L, Zhang X, Qian G, Liang N, Yao H, Dong X, Tan B. Whole exome sequencing and transcriptome analysis in two unrelated patients with novel SET mutations. J Hum Genet 2023; 68:867-874. [PMID: 37737486 DOI: 10.1038/s10038-023-01196-4] [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: 06/18/2023] [Revised: 09/01/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023]
Abstract
The human SET nuclear proto-oncogene (SET) gene is a protein-coding gene that encodes proteins that affects chromatin remodeling and gene transcription. Mutations in the SET gene have been reported to cause intellectual disability (ID) and epilepsy. In this study, we collected and analyzed clinical, genetic, and transcript features of two unrelated Chinese patients with ID. Both patients were characterized by moderate intellectual disability. Whole-exome sequencing identified two novel heterozygous mutations in the SET gene: NM_001122821.1:c.532-3 T > A and NM_001122821.1:c.3 G > C (p.0?). Additionally, RNA sequencing revealed widespread dysregulation of genes involved in NF-kB signaling and neuronal system in these two patients. To our knowledge, this is the first report of SET mutations causing ID in the Chinese population, broadening the genetic and ethnic spectrum of SET-related disorders and highlighting the importance of screening for SET gene variants.
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Affiliation(s)
- Xin Pan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Sihan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xu Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guanhua Qian
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Na Liang
- College of Computer Science, Chongqing University, Chongqing, China
| | - Hong Yao
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojing Dong
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bo Tan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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Vorstman JAS, Scherer SW. Contemplating syndromic autism. Genet Med 2023; 25:100919. [PMID: 37330697 DOI: 10.1016/j.gim.2023.100919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023] Open
Affiliation(s)
- Jacob A S Vorstman
- Department of Psychiatry, Hospital for Sick Children University of Toronto, Toronto, ON, Canada; Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada.
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, Hospital for Sick Children, Toronto, ON, Canada; The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada; McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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8
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Alhajaj G, Lacroix C, Trakadis Y, Garfinkle J, Srour M. An in-frame deletion affecting the critical acid loop of PPP2R5D is associated with a neonatal lethal form of PPP2R5D-related neurodevelopmental disorder. Am J Med Genet A 2023; 191:2416-2421. [PMID: 37248744 DOI: 10.1002/ajmg.a.63307] [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: 02/17/2023] [Revised: 03/31/2023] [Accepted: 05/06/2023] [Indexed: 05/31/2023]
Abstract
Heterozygous pathogenic variants in PPP2R5D gene are associated with PPP2R5D-related neurodevelopmental disorder, a rare autosomal dominant condition, characterized by neurodevelopmental impairment in childhood, macrocephaly/megalencephaly, hypotonia, epilepsy, and dysmorphic features. Up-to-date, only approximately 100 cases have been published in the literature and the full phenotypic and genotypic spectrum have not yet been fully described. PPP2R5D gene encodes the B56δ subunit of the PP2A enzyme complex. We describe a neonatal form of PPP2R5D-related disorder with early infantile death, caused by a novel in-frame deletion causing loss of 8 amino acids and insertion of serine at position 201 (p.Phe194_Pro201delinsSer) of the B56δ subunit. This deletion is predicted to disrupt a critical acidic loop of amino acids important for binding other subunits of the PP2A enzyme complex, and harbors many of the residues previously reported to cause a mild-moderate form of this condition. This report describes a neonatal lethal presentation of the PPP2R5D-related neurodevelopmental disorder and provides additional evidence that disruption of the acidic loop is an important pathomechanism underlying PPP2R5D-related disorder.
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Affiliation(s)
- Ghadd Alhajaj
- Department of Pediatrics, Unaizah College of Medicine and Medical Sciences, Qassim University, Saudi Arabia
- Department of Pediatrics, Division of Pediatric Neurology, McGill University Health Center, Montreal, Quebec, Canada
| | - Caroline Lacroix
- Department of Diagnostic Radiology, McGill University Health Center, Montreal, Quebec, Canada
| | - Yannis Trakadis
- Department of Specialized Medicine, Division of Medical Genetics, McGill University Health Center, Montreal, Quebec, Canada
| | - Jarred Garfinkle
- Department of Pediatrics, Division of Neonatology, McGill University Health Center, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Myriam Srour
- Department of Pediatrics, Division of Pediatric Neurology, McGill University Health Center, Montreal, Quebec, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
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9
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Tan B, Liu S, Feng X, Pan X, Qian G, Liu L, Zhang X, Yao H, Dong X. Expanding the mutational and clinical spectrum of Chinese intellectual disability patients with two novel CTCF variants. Front Pediatr 2023; 11:1195862. [PMID: 37664546 PMCID: PMC10469948 DOI: 10.3389/fped.2023.1195862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023] Open
Abstract
CCCTC-Binding Factor (CTCF) is a protein-coding gene involved in transcriptional regulation, insulator activity, and regulation of chromatin structure, and is closely associated with intellectual developmental disorders. In this study, we report two unrelated Chinese patients with intellectual disability (ID). According to variant interpretation results from exome sequencing data and RNA-seq data, we present two novel heterozygous CTCF variants, NM_006565.3:c.1519_2184del (p. Glu507_Arg727delins47) and NM_006565.3:c.1838_1852del (p.Glu613_Pro617del), found in two distinct unrelated patients, respectively. Moreover, RNA-seq data of patient 1 indicated the absence of the mutant transcript, while in patient 2, the RNA-seq data revealed a CTCF mRNA transcript with a deletion of 15 nucleotides. Notably, the RNA sequencing data revealed 507 differentially expressed genes shared between these two patients. Specifically, among them, 194 were down-regulated, and 313 were up-regulated, primarily involved in gene regulation and cellular response. Our study expands the genetic and clinical spectrum of CTCF and advances our understanding of the pathogenesis of CTCF in vivo.
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Affiliation(s)
- Bo Tan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Sihan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xiaoshu Feng
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, China
| | - Xin Pan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guanhua Qian
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Li Liu
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xu Zhang
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Yao
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xiaojing Dong
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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10
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Roberts AM, DiStefano MT, Riggs ER, Josephs KS, Alkuraya FS, Amberger J, Amin M, Berg JS, Cunningham F, Eilbeck K, Firth HV, Foreman J, Hamosh A, Hay E, Leigh S, Martin CL, McDonagh EM, Perrett D, Ramos EM, Robinson PN, Rath A, van Sant D, Stark Z, Whiffin N, Rehm HL, Ware JS. Towards robust clinical genome interpretation: developing a consistent terminology to characterize disease-gene relationships - allelic requirement, inheritance modes and disease mechanisms. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.30.23287948. [PMID: 37066232 PMCID: PMC10104222 DOI: 10.1101/2023.03.30.23287948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
PURPOSE The terminology used for gene-disease curation and variant annotation to describe inheritance, allelic requirement, and both sequence and functional consequences of a variant is currently not standardized. There is considerable discrepancy in the literature and across clinical variant reporting in the derivation and application of terms. Here we standardize the terminology for the characterization of disease-gene relationships to facilitate harmonized global curation, and to support variant classification within the ACMG/AMP framework. METHODS Terminology for inheritance, allelic requirement, and both structural and functional consequences of a variant used by Gene Curation Coalition (GenCC) members and partner organizations was collated and reviewed. Harmonized terminology with definitions and use examples was created, reviewed, and validated. RESULTS We present a standardized terminology to describe gene-disease relationships, and to support variant annotation. We demonstrate application of the terminology for classification of variation in the ACMG SF 2.0 genes recommended for reporting of secondary findings. Consensus terms were agreed and formalized in both sequence ontology (SO) and human phenotype ontology (HPO) ontologies. GenCC member groups intend to use or map to these terms in their respective resources. CONCLUSION The terminology standardization presented here will improve harmonization, facilitate the pooling of curation datasets across international curation efforts and, in turn, improve consistency in variant classification and genetic test interpretation.
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Affiliation(s)
- Angharad M Roberts
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Marina T DiStefano
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erin Rooney Riggs
- Geisinger Autism & Developmental Medicine Institute, Danville, PA, USA
| | - Katherine S Josephs
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, KFSHRC, Riyadh, Saudi Arabia
| | - Joanna Amberger
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | | | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill NC, 27599
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Karen Eilbeck
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Helen V Firth
- Dept of Medical Genetics, Cambridge University Hospitals, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Ada Hamosh
- Online Mendelian Inheritance in Man (OMIM), Johns Hopkins University School of Medicine, USA
| | - Eleanor Hay
- Dept of Medical Genetics, Great Ormond Street Hospital, Great Ormond Street, London. WC1N 3JH, UK
| | - Sarah Leigh
- Genomics England, Queen Mary University of London, Dawson Hall, London, EC1M 6BQ, UK
| | | | - Ellen M McDonagh
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
- Open Targets, Cambridge, UK
| | - Daniel Perrett
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
| | - Erin M Ramos
- National Human Genome Research Institute, National Institutes of Health, USA
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA
| | - Ana Rath
- INSERM, US14-Orphanet, Paris, France
| | - David van Sant
- Department of Biomedical Informatics, University of Utah, Salt Lake City, Utah
| | - Zornitza Stark
- Australian Genomics, Melbourne 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne 3052, Australia
- University of Melbourne, Melbourne 3052, Australia
| | - Nicola Whiffin
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Big Data Institute and Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Heidi L Rehm
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - James S Ware
- National Heart & Lung Institute & MRC London Institute of Medical Sciences, Imperial College London, London, UK
- Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, United Kingdom
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