ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.3180dup (p.Gly1061fs)

gnomAD frequency: 0.00001  dbSNP: rs61750430
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001193612 SCV001362560 pathogenic Peroxisome biogenesis disorder 2021-03-14 criteria provided, single submitter clinical testing Variant summary: PEX1 c.3180dupT (p.Gly1061TrpfsX16) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been been reported in patients with Zellweger syndrome (HGMD database). The variant was absent in 251100 control chromosomes. c.3180dupT has been reported in the literature in individuals affected with Zellweger Syndrome and subsequently cited by others (example, Collins_1999, Rosewich_2005). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV001380781 SCV001578943 pathogenic Zellweger spectrum disorders 2024-01-24 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gly1061Trpfs*16) 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 Zellweger syndrome spectrum (PMID: 10447258). ClinVar contains an entry for this variant (Variation ID: 928943). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003473733 SCV004203337 pathogenic Heimler syndrome 1 2023-06-06 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001193612 SCV005913835 pathogenic Peroxisome biogenesis disorder 2023-07-15 criteria provided, single submitter research

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