ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.5872G>T (p.Gly1958Cys)

gnomAD frequency: 0.00007  dbSNP: rs920545433
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000475266 SCV000553150 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2023-11-27 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with cysteine, which is neutral and slightly polar, at codon 1958 of the SPTAN1 protein (p.Gly1958Cys). This variant is present in population databases (no rsID available, gnomAD 0.02%). 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: 411798). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available". The cysteine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect 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.
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV002056713 SCV002495974 uncertain significance Developmental and epileptic encephalopathy, 5 2022-02-11 criteria provided, single submitter clinical testing This variant has not been reported in the literature but is present in 0.02% (9/41396) of African alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/9 128624367 G T?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:411798). Evolutionary conservation and computational predictive tools suggest that this variant may not impact the protein. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Ambry Genetics RCV003343841 SCV004068302 uncertain significance Inborn genetic diseases 2023-08-09 criteria provided, single submitter clinical testing The c.5872G>T (p.G1958C) alteration is located in exon 46 (coding exon 45) of the SPTAN1 gene. This alteration results from a G to T substitution at nucleotide position 5872, causing the glycine (G) at amino acid position 1958 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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