ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.3490G>A (p.Ala1164Thr) (rs796053316)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189505 SCV000243148 uncertain significance not provided 2014-12-15 criteria provided, single submitter clinical testing p.Ala1164Thr (GCA>ACA): c.3490 G>A in exon 25 of the SPTAN1 gene (NM_001130438.2) The A1164T variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The A1164T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals; however, the same amino acid change (A>T) is observed in a more distantly related species. In silico analysis is inconsistent in its predictions as to whether or not the A1164T variant is damaging to the protein structure/function. Additionally, previously reported pathogenic mutations in SPTAN1 include in-frame deletions or duplications located within the last four spectrin repeats of the protein, which are essential for dimerization (Saitsu et al., 2010), and A1164T is a missense substitution located outside this region. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in EPILEPSYV2-1 panel(s).

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