ClinVar Miner

Submissions for variant NM_004813.4(PEX16):c.956_958del (p.Pro319del)

dbSNP: rs754790425
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000484315 SCV000573947 likely pathogenic not provided 2017-03-06 criteria provided, single submitter clinical testing The c.956_958delCGC variant in the PEX16 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.956_958delCGC variant causes an in-frame deletion of one amnio acid, Proline 319, denoted p.Pro319del. The c.956_958delCGC variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This deletion occurs at a position that is conserved across species. In silico analysis predicts this deletion is probably damaging to the protein structure/function. We interpret c.956_958delCGC as a likely pathogenic variant.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003235242 SCV003933788 uncertain significance not specified 2023-05-30 criteria provided, single submitter clinical testing Variant summary: PEX16 c.956_958delCGC (p.Pro319del) results in an in-frame deletion that is predicted to remove one amino acid from the encoded protein. The variant allele was found at a frequency of 4e-06 in 250804 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.956_958delCGC has been reported in the literature in the compound heterozygous state in an individual affected with a Peroxisome Biogenesis Disorder on the Zellweger Syndrome Spectrum with a mild phenotype (Cheung_2022). This report does not provide unequivocal conclusions about association of the variant with Peroxisome Biogenesis Disorders, Zellweger Syndrome Spectrum. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 35106698). One clinical diagnostic laboratory has submitted a clinical-significance assessment for this variant to ClinVar after 2014 and classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance.

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