ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.5921A>G (p.Lys1974Arg)

dbSNP: rs1858423393
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001379316 SCV001577100 likely pathogenic Early infantile epileptic encephalopathy with suppression bursts 2024-01-30 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 1974 of the SPTAN1 protein (p.Lys1974Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with features of SPTAN1-related conditions (Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 1067924). 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 currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
GeneDx RCV003227034 SCV003923793 uncertain significance not provided 2023-07-29 criteria provided, single submitter clinical testing De novo variant with confirmed parentage in a patient referred for genetic testing at GeneDx; however, the reported clinical features are only partially consistent with the features typically observed in individuals with pathogenic variants in this gene; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant does not alter protein structure/function

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