ClinVar Miner

Submissions for variant NM_003106.4(SOX2):c.869G>C (p.Ser290Thr)

gnomAD frequency: 0.00014  dbSNP: rs779686992
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001566966 SCV001790564 likely benign not provided 2021-03-12 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV002570759 SCV003262398 uncertain significance Anophthalmia/microphthalmia-esophageal atresia syndrome 2022-07-17 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1201570). This variant has not been reported in the literature in individuals affected with SOX2-related conditions. This variant is present in population databases (rs779686992, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 290 of the SOX2 protein (p.Ser290Thr).
Ambry Genetics RCV002570758 SCV003527304 likely benign Inborn genetic diseases 2021-11-15 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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