ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.130-1G>T

gnomAD frequency: 0.00002  dbSNP: rs1028247729
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001004525 SCV001163570 pathogenic Peroxisome biogenesis disorder 1A (Zellweger); Peroxisome biogenesis disorder 1B criteria provided, single submitter clinical testing
Invitae RCV001378209 SCV001575730 likely pathogenic Zellweger spectrum disorders 2023-12-04 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 1 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). This variant has not been reported in the literature in individuals affected with PEX1-related conditions. ClinVar contains an entry for this variant (Variation ID: 813453). 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.
Natera, Inc. RCV001378209 SCV002079356 likely pathogenic Zellweger spectrum disorders 2019-06-19 no assertion criteria provided clinical testing
Baylor Genetics RCV002290989 SCV002583275 likely pathogenic Peroxisome biogenesis disorder 1A (Zellweger) no assertion criteria provided clinical testing

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