ClinVar Miner

Submissions for variant NM_000288.4(PEX7):c.429del (p.Val144fs)

gnomAD frequency: 0.00001  dbSNP: rs61753248
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000670475 SCV000795330 likely pathogenic Rhizomelic chondrodysplasia punctata type 1 2017-11-03 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000809601 SCV000949760 pathogenic Peroxisome biogenesis disorder 9B 2025-01-06 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Val144Leufs*37) in the PEX7 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX7 are known to be pathogenic (PMID: 12325024, 12522768, 20301447). This variant is present in population databases (rs61753248, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with rhizomelic chondrodysplasia punctata (PMID: 12325024). ClinVar contains an entry for this variant (Variation ID: 554785). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000670475 SCV003844607 likely pathogenic Rhizomelic chondrodysplasia punctata type 1 2023-02-13 criteria provided, single submitter clinical testing Variant summary: PEX7 c.429delT (p.Val144LeufsX37) 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 classified as pathogenic by our laboratory. The variant was absent in 251234 control chromosomes (gnomAD). c.429delT has been reported in the literature in individuals affected with Rhizomelic Chondrodysplasia Punctata Type 1 (example: Braverman_2002). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Baylor Genetics RCV000809601 SCV004203899 pathogenic Peroxisome biogenesis disorder 9B 2024-03-20 criteria provided, single submitter clinical testing
Natera, Inc. RCV001275004 SCV001459667 pathogenic Rhizomelic chondrodysplasia punctata 2020-09-16 no assertion criteria provided clinical testing

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