ClinVar Miner

Submissions for variant NM_001165963.4(SCN1A):c.5006C>A (p.Ala1669Glu)

dbSNP: rs397514458
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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 RCV001379443 SCV001577246 pathogenic Early infantile epileptic encephalopathy with suppression bursts 2022-03-03 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 1669 of the SCN1A protein (p.Ala1669Glu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with SCN1A-related conditions (PMID: 21555645; Invitae). ClinVar contains an entry for this variant (Variation ID: 29883). 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 expected to disrupt SCN1A protein function. This variant disrupts the p.Ala1669 amino acid residue in SCN1A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 27113213). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000022764 SCV000044053 pathogenic Severe myoclonic epilepsy in infancy 2011-05-01 no assertion criteria provided literature only

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