ClinVar Miner

Submissions for variant NM_000288.4(PEX7):c.641T>C (p.Leu214Pro)

dbSNP: rs1554333880
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000502761 SCV000596395 likely pathogenic Rhizomelic chondrodysplasia punctata type 1 2016-10-11 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001865618 SCV002280927 uncertain significance Peroxisome biogenesis disorder 9B 2021-09-17 criteria provided, single submitter clinical testing This sequence change replaces leucine with proline at codon 214 of the PEX7 protein (p.Leu214Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PEX7-related conditions. ClinVar contains an entry for this variant (Variation ID: 436287). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004767315 SCV005381520 uncertain significance not specified 2024-08-12 criteria provided, single submitter clinical testing Variant summary: PEX7 c.641T>C (p.Leu214Pro) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251378 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.641T>C in individuals affected with Rhizomelic Chondrodysplasia Punctata Type 1 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 436287). Based on the evidence outlined above, the variant was classified as uncertain significance.

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