ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.1684G>T (p.Ala562Ser)

gnomAD frequency: 0.00001  dbSNP: rs773328719
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002314584 SCV000848359 uncertain significance Inborn genetic diseases 2016-11-29 criteria provided, single submitter clinical testing The p.A562S variant (also known as c.1684G>T), located in coding exon 13 of the SPTAN1 gene, results from a G to T substitution at nucleotide position 1684. The alanine at codon 562 is replaced by serine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Invitae RCV001044778 SCV001208593 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2019-01-26 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with SPTAN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 588495). This variant is present in population databases (rs773328719, ExAC 0.003%). This sequence change replaces alanine with serine at codon 562 of the SPTAN1 protein (p.Ala562Ser). The alanine residue is highly conserved and there is a moderate physicochemical difference between alanine and serine.
Genome-Nilou Lab RCV001809781 SCV002056743 uncertain significance Developmental and epileptic encephalopathy, 5 2021-07-15 criteria provided, single submitter clinical testing

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