ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.6496C>T (p.Arg2166Cys)

gnomAD frequency: 0.00004  dbSNP: rs775190610
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189529 SCV000243172 likely benign not provided 2020-10-07 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001314638 SCV001505176 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2024-02-28 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 2166 of the SPTAN1 protein (p.Arg2166Cys). This variant is present in population databases (rs775190610, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with SPTAN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 207355). 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 SPTAN1 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Genome-Nilou Lab RCV001808522 SCV002056602 uncertain significance Developmental and epileptic encephalopathy, 5 2021-07-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV002362991 SCV002658212 likely benign Inborn genetic diseases 2022-06-06 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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