ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.952G>A (p.Glu318Lys) (rs149987700)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189199 SCV000242831 likely benign not specified 2017-11-08 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000557992 SCV000639651 uncertain significance Benign familial neonatal-infantile seizures; Early infantile epileptic encephalopathy 11 2019-12-16 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid with lysine at codon 318 of the SCN2A protein (p.Glu318Lys). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and lysine. This variant is present in population databases (rs149987700, ExAC 0.03%), and has an allele count higher than expected for a pathogenic variant (PMID: 28166811). This variant has not been reported in the literature in individuals with a SCN2A-related disease. ClinVar contains an entry for this variant (Variation ID: 207045). Algorithms developed to predict the effect of missense changes on protein structure and function 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.
Athena Diagnostics Inc RCV000992885 SCV001145466 likely benign not provided 2019-04-25 criteria provided, single submitter clinical testing

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