ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.3637-3_3637-1del

dbSNP: rs2116039871
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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 RCV001379471 SCV001577274 likely pathogenic Zellweger spectrum disorders 2020-10-02 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 22 of the PEX1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. 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. Donor and acceptor splice site variants typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PEX1 are known to be pathogenic (PMID: 9398847, 16086329, 16141001, 21031596, 26387595, 31831025). 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. This variant has not been reported in the literature in individuals with PEX1-related conditions. This variant is not present in population databases (ExAC no frequency).
Natera, Inc. RCV001379471 SCV002076801 likely pathogenic Zellweger spectrum disorders 2018-06-04 no assertion criteria provided clinical testing

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