ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.4693T>A (p.Trp1565Arg)

dbSNP: rs1701902994
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001206716 SCV001378038 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2023-03-30 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SCN2A protein function. ClinVar contains an entry for this variant (Variation ID: 937654). This variant has not been reported in the literature in individuals affected with SCN2A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces tryptophan, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 1565 of the SCN2A protein (p.Trp1565Arg).
GeneDx RCV002282481 SCV002571537 uncertain significance not provided 2022-03-07 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are often considered pathogenic (HGMD); This substitution is predicted to be within the transmembrane segment S2 of the fourth homologous domain; Has not been previously published as pathogenic or benign to our knowledge
Revvity Omics, Revvity RCV002282481 SCV003820779 uncertain significance not provided 2019-11-27 criteria provided, single submitter clinical testing

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