ClinVar Miner

Submissions for variant NM_000288.4(PEX7):c.618G>A (p.Trp206Ter)

gnomAD frequency: 0.00004  dbSNP: rs61753245
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 8
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169479 SCV000220925 likely pathogenic Rhizomelic chondrodysplasia punctata type 1 2014-11-26 criteria provided, single submitter literature only
GeneDx RCV000578930 SCV000680694 pathogenic not provided 2025-02-20 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25525159, 34229749, 22057399, 31964843, 21465523, 12325024)
Athena Diagnostics RCV000578930 SCV001144912 likely pathogenic not provided 2018-10-31 criteria provided, single submitter clinical testing The variant creates a premature nonsense codon, and is therefore predicted to significantly disrupt the protein structure. The best available variant frequency is uninformative because it is below the disease allele frequency.
Baylor Genetics RCV000169479 SCV001162999 pathogenic Rhizomelic chondrodysplasia punctata type 1 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000169479 SCV001482184 pathogenic Rhizomelic chondrodysplasia punctata type 1 2021-02-21 criteria provided, single submitter clinical testing Variant summary: PEX7 c.618G>A (p.Trp206X) 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 allele was found at a frequency of 1.2e-05 in 251332 control chromosomes. c.618G>A has been reported in the literature in at-least one individual affected with Rhizomelic Chondrodysplasia Punctata Type 1 and subsequently cited by others (example, Braverman_2002, Dranchak_2011). At least one publication reports experimental evidence supporting the presence of a truncated form of this protein in transfected cells that did not demonstrate measurable nonsense supression in the presence of PTC124 (ataluren) (Dranchak_2011). 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 citing overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV001380052 SCV001577986 pathogenic Peroxisome biogenesis disorder 9B 2024-08-07 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Trp206*) 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 (rs61753245, gnomAD 0.01%). This premature translational stop signal has been observed in individual(s) with clinical features of rhizomelic chondrodysplasia punctata (PMID: 12325024). ClinVar contains an entry for this variant (Variation ID: 189076). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV000578930 SCV003811365 likely pathogenic not provided 2022-07-23 criteria provided, single submitter clinical testing
Baylor Genetics RCV001380052 SCV004203905 pathogenic Peroxisome biogenesis disorder 9B 2024-02-06 criteria provided, single submitter clinical testing

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.