ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.9799C>T (p.Arg3267Trp)

dbSNP: rs538720577
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001050423 SCV001214530 uncertain significance not provided 2022-08-09 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 disruptive. ClinVar contains an entry for this variant (Variation ID: 846979). This variant has not been reported in the literature in individuals affected with SZT2-related conditions. This variant is present in population databases (rs538720577, gnomAD 0.2%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 3210 of the SZT2 protein (p.Arg3210Trp).
New York Genome Center RCV001836936 SCV002097717 uncertain significance Developmental and epileptic encephalopathy, 18 2020-12-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV002374902 SCV002690667 likely benign Inborn genetic diseases 2024-04-08 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.
GeneDx RCV001050423 SCV004014405 uncertain significance not provided 2024-03-07 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as a pathogenic or benign germline variant to our knowledge; This variant is associated with the following publications: (PMID: 32055024)
Genome-Nilou Lab RCV001836936 SCV004178098 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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