ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.4135G>A (p.Val1379Met)

gnomAD frequency: 0.00002  dbSNP: rs779140322
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000479253 SCV000574275 likely benign not provided 2020-12-14 criteria provided, single submitter clinical testing
Invitae RCV000557760 SCV000639626 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2024-01-29 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 1379 of the SCN2A protein (p.Val1379Met). This variant is present in population databases (rs779140322, gnomAD 0.01%). This missense change has been observed in individuals with clinical features of SCN2A-related conditions (Invitae). ClinVar contains an entry for this variant (Variation ID: 424464). 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 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 RCV002329163 SCV002628903 benign Inborn genetic diseases 2018-11-28 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: 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.

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