ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.2071+2T>C

dbSNP: rs1478905473
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000668401 SCV000792995 likely pathogenic Peroxisome biogenesis disorder 1A (Zellweger) 2017-07-25 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003594017 SCV004305120 likely pathogenic Zellweger spectrum disorders 2023-09-12 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 12 of the PEX1 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 PEX1 are known to be pathogenic (PMID: 21031596, 26387595, 31831025). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with PEX1-related conditions (PMID: 11389485). ClinVar contains an entry for this variant (Variation ID: 553031). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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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