ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.2538G>T (p.Leu846Phe)

dbSNP: rs1699366355
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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 RCV003770380 SCV004585920 pathogenic Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2024-09-06 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 846 of the SCN2A protein (p.Leu846Phe). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with SCN2A-related conditions (PMID: 31175295, 34114234; internal data). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 984898). 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 expected to disrupt SCN2A protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
GenomeConnect - Simons Searchlight RCV001265505 SCV001443649 likely pathogenic Complex neurodevelopmental disorder 2017-07-12 no assertion criteria provided provider interpretation Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2017-07-12 and interpreted as Likely Pathogenic. Variant was initially reported on 2017-02-16 by GTR ID of laboratory name 206966. The reporting laboratory might also submit to ClinVar.

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