ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.5922G>C (p.Lys1974Asn)

gnomAD frequency: 0.00001  dbSNP: rs777407223
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189470 SCV000243111 likely benign not specified 2017-07-05 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001321393 SCV001512220 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2022-12-13 criteria provided, single submitter clinical testing 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. This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 1974 of the SPTAN1 protein (p.Lys1974Asn). This variant is present in population databases (rs777407223, gnomAD 0.002%). 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: 207297). This variant disrupts the p.Lys1974 amino acid residue in SPTAN1. Other variant(s) that disrupt this residue have been determined to be pathogenic (Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 RCV001808496 SCV002056574 uncertain significance Developmental and epileptic encephalopathy, 5 2021-07-15 criteria provided, single submitter clinical testing

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