ClinVar Miner

Submissions for variant NM_000702.4(ATP1A2):c.2840+5G>A

gnomAD frequency: 0.00001  dbSNP: rs1254965849
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001757155 SCV001996713 uncertain significance not provided 2020-01-10 criteria provided, single submitter clinical testing Intronic +5 splice site variant in a gene for which loss-of-function is a known mechanism of disease, and both in silico predictors and evolutionary conservation support a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV002538861 SCV002978735 uncertain significance Familial hemiplegic migraine 2022-04-06 criteria provided, single submitter clinical testing This sequence change falls in intron 20 of the ATP1A2 gene. It does not directly change the encoded amino acid sequence of the ATP1A2 protein. It affects a nucleotide within the consensus splice site. 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 1310087). This variant has not been reported in the literature in individuals affected with ATP1A2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.01%).

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