ClinVar Genomic variation as it relates to human health

The KCNT1 c.1421G>A variant is predicted to result in the amino acid substitution p.Arg474His. This variant has been reported many times to have arisen de novo in individuals with infantile-onset epilepsy (see for examples Barcia et al. 2012. PubMed ID: 23086397; Ohba et al. 2015. PubMed ID: 26140313). A functional study found that the p.Arg474His variant causes an increase in activity of the encoded potassium channel (Kim et al. 2014. PubMed ID: 25482562), indicating a gain of function mechanism. This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating it is rare or absent in the general population. This variant has been interpreted as pathogenic by multiple independent submitters to the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/39595). Given all the evidence, we too interpret c.1421G>A (p.Arg474His) as pathogenic.

Published functional studies demonstrate a damaging effect, with increased channel activity but minor change in protein expression compared to the wild type variant (Kim et al., 2014); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 29455050, 32167590, 25482562, 25326637, 23086397, 26140313, 24315024, 25568878, 27779742, 27081515, 27652284, 28488083, 28987752, 29291456, 31872048, 31532509, 32081855, 31054119, 31532594, 31349857, 32139178, 32505479, 34489640, 33822359, 34055682, 35571021, 35365919, 36007526, 34580403, 31440721, 35715422, 34114611, 35346832, 37062836, 37177976)

PS3, PM2, PM5, PP3

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 474 of the KCNT1 protein (p.Arg474His). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with early onset epileptic encephalopathies, malignant migrating partial seizures of infancy, migrating focal seizure of infancy, and/or nocturnal frontal lobe epilepsy (PMID: 23086397, 25326637, 25482562, 26140313, 26740507). In at least one individual the variant was observed to be de novo. This variant is also known as c.1286G>A:p.R429H. ClinVar contains an entry for this variant (Variation ID: 39595). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on KCNT1 protein function. This variant disrupts the p.Arg474 amino acid residue in KCNT1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 26140313, 27652284). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

PS4, PP3, PM2_SUP, PM5

The missense variant p.R474H in KCNT1 (NM_020822.3) has been previously reported as a de novo variant in individuals with malignant migrating partial seizures of infancy (MMPSI) and West syndrome (Lee et al 2014; Barcia et al 2012; Ohba et al 2015). A different missense variant at the same position (R474C) has been reported as a pathogenic variant in individuals with epilepsy of infancy with migrating focal seizures (EIFMS) (Ohba et al, 2015). The variant has been submitted to ClinVar as Pathogenic. The p.R474H variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.R474H missense variant is predicted to be damaging by both SIFT and PolyPhen2. The arginine residue at codon 474 of KCNT1 is conserved in all mammalian species. The nucleotide c.1421 in KCNT1 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Likely Pathogenic.

ACMG classification criteria: PS3 supporting, PS4 strong, PM2 moderated, PM5 moderated, PM6 moderated, PP3 supporting

This variant has been previously reported as a de novo change in patients with malignant migrating partial seizures in infancy with and without systemic pulmonary collateral arteries (MMPSI) (PMID: 23086397, 28987752), malignant migrating focal seizures in infancy (PMID: 27779742), epilepsy of infancy with migrating focal seizures (EIMFS) (PMID: 31872048, 31532509, 32167590, 32505479) and sleep-related hypermotor epilepsy (PMID: 32167590). Overexpression studies demonstrated that this variant leads to increased Kcnt1 current amplitude (PMID: 25482562). It is absent from the gnomAD population database and thus is presumed to be rare. The c.1421G>A (p.Arg474His) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.1421G>A (p.Arg474His) variant is classified as Pathogenic.