ClinVar Miner

Submissions for variant NM_000702.4(ATP1A2):c.2563+2T>C

gnomAD frequency: 0.00003  dbSNP: rs775008062
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001374157 SCV001570939 likely pathogenic Familial hemiplegic migraine 2022-09-19 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This sequence change affects a donor splice site in intron 18 of the ATP1A2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ATP1A2 are known to be pathogenic (PMID: 30690204). This variant is present in population databases (rs775008062, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with ATP1A2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1064213). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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