ClinVar Miner

Submissions for variant NM_001165963.4(SCN1A):c.1423_1424delinsCT (p.Ala475Leu)

dbSNP: rs2105852411
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Lifecell International Pvt. Ltd RCV001509555 SCV001712083 uncertain significance Severe myoclonic epilepsy in infancy criteria provided, single submitter clinical testing A heterozygous indel variant in exon 13 of SCN1A gene (c.1423_1424delinsCT) that results in amino acid substitution from Alanine to Valine at codon 475 (p. Ala475Val) was identified. The observed variant is not reported in 1000 Genomes and gnomAD database. The variant is conserved across the species and is predicted to be damaging by Mutation taster. Based on the above evidence this variant has been classified as variant of uncertain signficance according to the ACMG guidelines.
Lifecell International Pvt. Ltd RCV001528182 SCV001739364 pathogenic Generalized epilepsy with febrile seizures plus, type 2 criteria provided, single submitter clinical testing A heterozygous variant (c.1423_1424delinsCT) in exon 13 of the SCN1A gene that results in the amino acid substitution from Alanine to Leucine at codon 475 (p.Ala475Leu) was identified. The observed variant is not present in both the 1000 Genomes and gnomAD databases. The reference base is conserved across the species and in-silico predictions by Polyphen and SIFT are damaging. The Missense Variants Z-Score for this variant is 5.52. Missense Variants Z-Score is produced by the Exome Aggregation Consortium (60,706 adult humans) by computing a signed Z score for the deviation of observed counts from the expected number. Positive Z scores indicate increased constraint (intolerance to variation) and therefore that the gene had fewer missense variants than expected. (DOI: 10.1038/nature19057). Missense Badness and MPC scores of this varaint is 0.35 and 0.69 respectively. The Missense Badness Score is the normalized fold difference of missense substitutions between observed and expected variants from ExAC dataset. This score is then combined with orthogonal deleteriousness metrics into one score called MPC (for Missense badness, PolyPhen-2, and Constraint) designed to classify whether a missense variants is deleterious. Variants with MPC ≥ 2 have a rate nearly 6 times higher in cases than in controls. While those with intermediate MPC values (1 ≤ MPC < 2) have a more modest excess in cases. Based on the above evidence this variant has been classified as Variant of uncertain significance according to the ACMG guidelines.
Revvity Omics, Revvity Omics RCV003136093 SCV003820730 uncertain significance not provided 2019-02-28 criteria provided, single submitter clinical testing

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