ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.2033C>G (p.Thr678Arg)

dbSNP: rs1446046264
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001327824 SCV001518914 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2020-05-04 criteria provided, single submitter clinical testing This sequence change replaces threonine with arginine at codon 678 of the SCN2A protein (p.Thr678Arg). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and arginine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SCN2A-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.
GeneDx RCV003317477 SCV004021767 uncertain significance not provided 2023-01-24 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This substitution is predicted to be within the C-terminal cytoplasmic domain

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