ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.5468C>T (p.Pro1823Leu)

gnomAD frequency: 0.00002  dbSNP: rs561973288
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000443505 SCV000526178 likely benign not specified 2016-06-30 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.
Invitae RCV001041521 SCV001205142 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2023-08-17 criteria provided, single submitter clinical testing 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. This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 1823 of the SPTAN1 protein (p.Pro1823Leu). This variant is present in population databases (rs561973288, gnomAD 0.004%). 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: 385053). 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.
Genome-Nilou Lab RCV001808815 SCV002056596 likely benign Developmental and epileptic encephalopathy, 5 2021-07-15 criteria provided, single submitter clinical testing

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