ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.1648G>T (p.Ala550Ser) (rs371178746)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000519040 SCV000620962 uncertain significance not provided 2017-09-19 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the SPTAN1 gene. The A550S variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The A550S variant is observed in 2/10402 (0.02%) alleles from individuals of African background (Lek et al., 2016). The A550S 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 across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Previously reported pathogenic variants 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 the A550 residue is outside this region. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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