ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.2875C>T (p.Arg959Ter)

dbSNP: rs1057517481
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000410455 SCV000487533 likely pathogenic Peroxisome biogenesis disorder 1A (Zellweger) 2016-03-04 criteria provided, single submitter clinical testing
Counsyl RCV000411996 SCV000487534 likely pathogenic Peroxisome biogenesis disorder 1B 2016-03-04 criteria provided, single submitter clinical testing
Baylor Genetics RCV001004319 SCV001163200 pathogenic Peroxisome biogenesis disorder 1A (Zellweger); Peroxisome biogenesis disorder 1B criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001201668 SCV001372750 pathogenic Zellweger spectrum disorders 2024-01-27 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg959*) in the PEX1 gene. It is expected to result in an absent or disrupted protein product. 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 premature translational stop signal has been observed in individual(s) with clinical features of a Zellweger spectrum disorder (PMID: 27848944). ClinVar contains an entry for this variant (Variation ID: 371716). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV003319350 SCV004024033 pathogenic not provided 2023-02-02 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27848944, 34974531)
Baylor Genetics RCV003475982 SCV004203256 pathogenic Heimler syndrome 1 2024-01-20 criteria provided, single submitter clinical testing
Natera, Inc. RCV001201668 SCV002076836 pathogenic Zellweger spectrum disorders 2021-02-16 no assertion criteria provided clinical testing

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