ClinVar Miner

Submissions for variant NM_006514.4(SCN10A):c.1315A>G (p.Thr439Ala)

gnomAD frequency: 0.00013  dbSNP: rs146536985
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000795088 SCV000934530 uncertain significance Brugada syndrome 2024-11-29 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 439 of the SCN10A protein (p.Thr439Ala). This variant is present in population databases (rs146536985, gnomAD 0.05%). This variant has not been reported in the literature in individuals affected with SCN10A-related conditions. ClinVar contains an entry for this variant (Variation ID: 641772). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt SCN10A protein function with a negative predictive value of 80%. 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.
Ambry Genetics RCV002386392 SCV002691701 likely benign Cardiovascular phenotype 2020-01-14 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.
Fulgent Genetics, Fulgent Genetics RCV002493451 SCV002787369 uncertain significance Episodic pain syndrome, familial, 2 2022-02-11 criteria provided, single submitter clinical testing
GeneDx RCV003156292 SCV003845505 uncertain significance not provided 2023-03-22 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function

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