ClinVar Miner

Submissions for variant NM_000702.3(ATP1A2):c.2438T>A (p.Met813Lys) (rs796052277)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000679915 SCV000807346 uncertain significance Familial hemiplegic migraine type 2 2017-09-01 criteria provided, single submitter clinical testing Likely pathogenicity based on finding it de novo in a 2-year-old male with developmental delay, seizure disorder, alternating hemiplegic migraine, and left hemiparesis.
GeneDx RCV000505754 SCV000240369 likely pathogenic not provided 2016-12-09 criteria provided, single submitter clinical testing p.Met813Lys (ATG>AAG): c.2438 T>A in exon 17 of the ATP1A2 gene (NM_000702.3). The Met813Lys missense change has not been published as a pathogenic variant, nor has it been reported as a benign variant 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 amino acid substitution is non-conservative as a uncharged, non-polar Methionine residue is replaced by a positively charged, polar Lysine residue. Met813Lys alters a conserved position in the M6 transmembrane domain of the ATP1A2 protein and several in-silico algorithms predict it may be damaging to the structure/function of the protein. The Met813Lys variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.

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