ClinVar Miner

Submissions for variant NM_020699.4(GATAD2B):c.1438C>T (p.Gln480Ter)

dbSNP: rs1674313030
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001267967 SCV001446506 likely pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV002471073 SCV002769063 pathogenic Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome 2022-02-02 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with GAND syndrome (MIM#615074). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (ClinVar, DECIPHER). (SP) 0802 - This variant has moderate previous evidence of pathogenicity in unrelated individuals. It has been reported de novo in at least one individual with neurodevelopmental disorder and classified as likely pathogenic by a diagnostic laboratory in ClinVar (PMID: 32688057). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1204 - This variant has been shown to be de novo in the proband (parental status not tested but assumed). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Genome-Nilou Lab RCV002471073 SCV004050285 likely pathogenic Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome 2023-04-11 criteria provided, single submitter clinical testing

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