ClinVar Miner

Submissions for variant NM_003106.4(SOX2):c.480C>G (p.Tyr160Ter)

dbSNP: rs55683010
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000403743 SCV000329530 pathogenic not provided 2021-02-08 criteria provided, single submitter clinical testing Published functional studies demonstrate a damaging effect: reduced transactivation activity compared to wildtype (Suzuki et al., 2014); Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 158 amino acids are lost, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (Stenson et al., 2014); Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 17522144, 28832562, 29453417, 26938784, 27427475, 18987493, 16712695, 28121235, 24804704)
Eurofins Ntd Llc (ga) RCV000403743 SCV000340722 pathogenic not provided 2016-03-21 criteria provided, single submitter clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000403743 SCV001447404 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001387936 SCV001588695 pathogenic Anophthalmia/microphthalmia-esophageal atresia syndrome 2023-12-11 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Tyr160*) in the SOX2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 158 amino acid(s) of the SOX2 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with SOX2-related conditions (PMID: 16712695, 24804704, 26938784, 27427475, 28121235). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 279896). This variant disrupts a region of the SOX2 protein in which other variant(s) (p.Tyr180*) have been determined to be pathogenic (PMID: 19921648). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV001387936 SCV002021904 pathogenic Anophthalmia/microphthalmia-esophageal atresia syndrome 2021-09-16 criteria provided, single submitter clinical testing
Genetics and Molecular Pathology, SA Pathology RCV001387936 SCV002556870 pathogenic Anophthalmia/microphthalmia-esophageal atresia syndrome 2020-10-26 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV001387936 SCV002765100 pathogenic Anophthalmia/microphthalmia-esophageal atresia syndrome 2022-12-05 criteria provided, single submitter clinical testing _x000D_ Criteria applied: PVS1_STR, PS4, PS3_SUP, PM2_SUP
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein RCV001387936 SCV003807350 pathogenic Anophthalmia/microphthalmia-esophageal atresia syndrome 2022-09-27 criteria provided, single submitter clinical testing ACMG classification criteria: PVS1 very strong, PS4 strong, PM2 moderated, PM6 moderated

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