ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.6184C>T (p.Arg2062Trp)

dbSNP: rs2131953982
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes RCV001374982 SCV001572270 uncertain significance Neurodevelopmental disorder 2020-08-06 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV001780272 SCV002026323 likely pathogenic Developmental and epileptic encephalopathy, 5 2017-09-01 criteria provided, single submitter research
Genome-Nilou Lab RCV001780272 SCV002056577 likely pathogenic Developmental and epileptic encephalopathy, 5 2021-07-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001865870 SCV002174136 pathogenic Early infantile epileptic encephalopathy with suppression bursts 2024-10-26 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 2062 of the SPTAN1 protein (p.Arg2062Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of SPTAN1-related conditions (PMID: 29050398; internal data). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 1064825). 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) has been performed 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 SPTAN1 protein function. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV004590360 SCV005078253 pathogenic not provided 2024-06-26 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; This variant is associated with the following publications: (PMID: 34590414, 34440880, 29050398)

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