ClinVar Miner

Submissions for variant NM_000288.4(PEX7):c.183del (p.Phe61fs)

dbSNP: rs774131564
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center RCV000490306 SCV000267444 likely pathogenic Rhizomelic chondrodysplasia punctata type 1; Peroxisome biogenesis disorder 9B 2016-03-18 criteria provided, single submitter reference population
Baylor Genetics RCV001004176 SCV001162993 pathogenic Rhizomelic chondrodysplasia punctata type 1 criteria provided, single submitter clinical testing
Invitae RCV001043666 SCV001207424 pathogenic Peroxisome biogenesis disorder 9B 2023-12-15 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Phe61Leufs*13) 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 (rs774131564, gnomAD 0.08%). This variant has not been reported in the literature in individuals affected with PEX7-related conditions. ClinVar contains an entry for this variant (Variation ID: 225436). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001004176 SCV003934430 pathogenic Rhizomelic chondrodysplasia punctata type 1 2023-05-06 criteria provided, single submitter clinical testing Variant summary: PEX7 c.183delT (p.Phe61LeufsX13) results in a premature termination codon, predicted to cause absence of the protein due to nonsense mediated decay, which is a commonly known mechanism for disease. Variants downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 5.2e-05 in 251456 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in PEX7 causing Rhizomelic Chondrodysplasia Punctata Type 1 (5.2e-05 vs 0.0019), allowing no conclusion about variant significance. c.183delT has been reported in the literature in individuals affected with Rhizomelic Chondrodysplasia Punctata Type 1 (example, Luisman_2021 citing van den Brink_2004). The following publications have been ascertained in the context of this evaluation (PMID: 34229749, 34671977). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Baylor Genetics RCV001043666 SCV004203893 pathogenic Peroxisome biogenesis disorder 9B 2023-10-07 criteria provided, single submitter clinical testing

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