ClinVar Miner

Submissions for variant NM_018129.4(PNPO):c.264-2A>G

dbSNP: rs780977054
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000468236 SCV000550173 likely pathogenic Pyridoxal phosphate-responsive seizures 2023-03-26 criteria provided, single submitter clinical testing 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. 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: 409830). This variant has not been reported in the literature in individuals affected with PNPO-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects an acceptor splice site in intron 2 of the PNPO 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 PNPO are known to be pathogenic (PMID: 15772097, 24645144).
Athena Diagnostics Inc RCV000992669 SCV001145125 likely pathogenic not provided 2019-07-03 criteria provided, single submitter clinical testing The variant disrupts a canonical splice site, and is therefore predicted to result in the loss of a functional protein. The best available variant frequency is uninformative because there are too few occurrences in population data.

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