ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.2872A>G (p.Met958Val)

dbSNP: rs2105319172
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001885387 SCV002306220 likely pathogenic Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2023-11-27 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 958 of the SCN2A protein (p.Met958Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with SCN2A-related conditions (PMID: 29215089; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1342681). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SCN2A protein function. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Neurology Department, Shenzhen Children's Hospital RCV002227283 SCV002099476 pathogenic Seizures, benign familial infantile, 3 2022-02-16 no assertion criteria provided clinical testing

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