ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.5773G>A (p.Val1925Ile)

gnomAD frequency: 0.00001  dbSNP: rs145727224
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000734487 SCV000862635 uncertain significance not provided 2018-08-16 criteria provided, single submitter clinical testing
GeneDx RCV000734487 SCV002032744 uncertain significance not provided 2024-06-17 criteria provided, single submitter clinical testing In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This substitution is predicted to be within the C-terminal cytoplasmic domain
Labcorp Genetics (formerly Invitae), Labcorp RCV001868995 SCV002260951 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2023-11-08 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 1925 of the SCN2A protein (p.Val1925Ile). This variant is present in population databases (rs145727224, gnomAD 0.007%). 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: 598156). 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 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.

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