ClinVar Miner

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

dbSNP: rs774131564
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 6
Download table as spreadsheet
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
Labcorp Genetics (formerly Invitae), Labcorp 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 2024-01-18 criteria provided, single submitter clinical testing
Juno Genomics, Hangzhou Juno Genomics, Inc RCV000490306 SCV005416652 likely pathogenic Rhizomelic chondrodysplasia punctata type 1; Peroxisome biogenesis disorder 9B criteria provided, single submitter clinical testing PVS1+PM2_Supporting

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.