Total submissions: 6
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Counsyl | RCV000411170 | SCV000486131 | likely pathogenic | Rhizomelic chondrodysplasia punctata type 1 | 2016-04-05 | criteria provided, single submitter | clinical testing | |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000411170 | SCV000919982 | pathogenic | Rhizomelic chondrodysplasia punctata type 1 | 2018-05-24 | criteria provided, single submitter | clinical testing | Variant summary: PEX7 c.345T>G (p.Tyr115X) 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. One functional study confirmed that this variant is triggering nonsense-mediated decay with lack of a full length transcript (Braverman_2002). The variant allele was found at a frequency of 4.1e-05 in 246196 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in PEX7 causing Rhizomelic Chondrodysplasia Punctata Type 1 (4.1e-05 vs 1.90e-03), allowing no conclusion about variant significance. The variant, c.345T>G, has been reported in the literature in individuals affected with Rhizomelic Chondrodysplasia Punctata Type 1 (Motley_PEX7_AMJHumGenet_2002) and the subphenotype adult Refsum disease (ARD) when found in compound heterozygosity with IVS3-10A>G (Braverman_2002). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classifies the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. |
Invitae | RCV000008228 | SCV001388016 | pathogenic | Peroxisome biogenesis disorder 9B | 2023-10-26 | criteria provided, single submitter | clinical testing | This sequence change creates a premature translational stop signal (p.Tyr115*) 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 (rs121909154, gnomAD 0.009%). This premature translational stop signal has been observed in individual(s) with rhizomelic chondrodysplasia punctata type 1 (PMID: 11781871). ClinVar contains an entry for this variant (Variation ID: 7786). For these reasons, this variant has been classified as Pathogenic. |
Baylor Genetics | RCV000008228 | SCV004203909 | pathogenic | Peroxisome biogenesis disorder 9B | 2023-05-28 | criteria provided, single submitter | clinical testing | |
OMIM | RCV000008228 | SCV000028435 | pathogenic | Peroxisome biogenesis disorder 9B | 2007-02-27 | no assertion criteria provided | literature only | |
Natera, |
RCV001826453 | SCV002077240 | pathogenic | Rhizomelic chondrodysplasia punctata | 2020-11-19 | no assertion criteria provided | clinical testing |