ClinVar Miner

Submissions for variant NM_001145358.2(SIN3A):c.1657C>T (p.Arg553Ter)

dbSNP: rs1555444885
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000622315 SCV000740908 pathogenic Inborn genetic diseases 2016-12-05 criteria provided, single submitter clinical testing
Clinical Genetics and Genomics, Karolinska University Hospital RCV001269798 SCV001450068 likely pathogenic not provided 2020-01-29 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003403431 SCV004122964 pathogenic SIN3A-related intellectual disability syndrome 2023-10-16 criteria provided, single submitter clinical testing Variant summary: SIN3A c.1657C>T (p.Arg553X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant was absent in 251464 control chromosomes. c.1657C>T has been reported in the literature in individuals affected with Witteveen-Kolk syndrome (e.g. Jacobson_2022). These data indicate that the variant is likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 35144002). Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, classifying the variant as pathogenic (n=1) or likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.
GeneDx RCV001269798 SCV005333447 pathogenic not provided 2023-06-29 criteria provided, single submitter clinical testing Identified in an individual with a neurodevelopmental disorder, but segregation and detailed clinical information was not provided (Wang et al., 2020); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 33004838)

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