ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.3049G>C (p.Val1017Leu)

gnomAD frequency: 0.00001  dbSNP: rs769267899
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000531828 SCV000639621 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2025-01-20 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1017 of the SCN2A protein (p.Val1017Leu). This variant is present in population databases (rs769267899, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with SCN2A-related conditions. ClinVar contains an entry for this variant (Variation ID: 464905). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt SCN2A protein function with a negative predictive value of 95%. 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 RCV001848941 SCV002104329 uncertain significance not provided 2023-10-11 criteria provided, single submitter clinical testing Missense variants in this gene are a common cause of disease and they are underrepresented in the general population; In silico analysis supports that this missense variant does not alter protein structure/function; This substitution is predicted to be in the cytoplasmic loop between the second and third homologous domains; Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV002491014 SCV002783187 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11; Episodic ataxia, type 9 2022-01-06 criteria provided, single submitter clinical testing

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