ClinVar Miner

Submissions for variant NM_004974.4(KCNA2):c.1118C>T (p.Thr373Ile)

dbSNP: rs1553181282
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000520764 SCV000621412 pathogenic not provided 2025-03-18 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Mendelics RCV000986393 SCV001135389 likely pathogenic Developmental and epileptic encephalopathy, 32 2019-05-28 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000986393 SCV001221242 pathogenic Developmental and epileptic encephalopathy, 32 2024-01-15 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 373 of the KCNA2 protein (p.Thr373Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of autosomal dominant KCNA2-related conditions (Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 452594). 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 KCNA2 protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.

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