ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.3303_3304dup (p.Cys1102fs)

dbSNP: rs886043558
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000328396 SCV000340692 pathogenic not provided 2016-03-30 criteria provided, single submitter clinical testing
Baylor Genetics RCV001004314 SCV001163195 likely pathogenic Peroxisome biogenesis disorder 1A (Zellweger); Peroxisome biogenesis disorder 1B criteria provided, single submitter clinical testing
GeneDx RCV000328396 SCV001168949 pathogenic not provided 2018-11-08 criteria provided, single submitter clinical testing The c.3303_3304dupAT variant in the PEX1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.3303_3304dupAT variant causes a frameshift starting with codon Cysteine 1102, changes this amino acid to a Tyrosine residue, and creates a premature Stop codon at position 4 of the new reading frame, denoted p.Cys1102TyrfsX4. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.3303_3304dupAT variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.3303_3304dupAT as a pathogenic variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV001214049 SCV001385712 pathogenic Zellweger spectrum disorders 2023-12-11 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Cys1102Tyrfs*4) 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 variant has not been reported in the literature in individuals affected with PEX1-related conditions. ClinVar contains an entry for this variant (Variation ID: 287046). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003475913 SCV004203385 likely pathogenic Heimler syndrome 1 2024-03-27 criteria provided, single submitter clinical testing

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