ClinVar Miner

Submissions for variant NM_000702.4(ATP1A2):c.2439+5G>A

dbSNP: rs1651923862
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001305217 SCV001494540 uncertain significance Familial hemiplegic migraine 2021-03-06 criteria provided, single submitter clinical testing This sequence change falls in intron 17 of the ATP1A2 gene. It does not directly change the encoded amino acid sequence of the ATP1A2 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with ATP1A2-related conditions. Nucleotide substitutions within 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, but this prediction has not been confirmed by published transcriptional studies. 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.
Ambry Genetics RCV002451688 SCV002736712 uncertain significance Inborn genetic diseases 2019-06-13 criteria provided, single submitter clinical testing The c.2439+5G>A intronic variant results from a G to A substitution 5 nucleotides after coding exon 17 in the ATP1A2 gene. This nucleotide position is well conserved in available vertebrate species. Using two different splice site prediction tools, this alteration is predicted by BDGP to abolish the native splice donor site, but is predicted to weaken (but not abolish) the efficiency of the native splice donor site by ESEfinder; however, direct evidence is unavailable. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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