ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.3133C>T (p.Arg1045Trp)

gnomAD frequency: 0.00001  dbSNP: rs794727356
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000176280 SCV000227911 uncertain significance not provided 2015-01-23 criteria provided, single submitter clinical testing
Invitae RCV001343594 SCV001537587 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2023-12-02 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 1045 of the SPTAN1 protein (p.Arg1045Trp). This variant is present in population databases (rs794727356, gnomAD 0.006%). 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: 195664). 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 RCV001808450 SCV002056752 uncertain significance Developmental and epileptic encephalopathy, 5 2021-07-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV003278676 SCV003961146 likely benign Inborn genetic diseases 2023-03-31 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: 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.
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital RCV000678849 SCV000805040 uncertain significance Landau-Kleffner syndrome 2017-04-05 no assertion criteria provided clinical testing

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