ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.2584-20T>A

gnomAD frequency: 0.02687  dbSNP: rs111535201
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000078923 SCV000110783 benign not specified 2013-11-20 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000078923 SCV001362555 benign not specified 2019-02-07 criteria provided, single submitter clinical testing Variant summary: PEX1 c.2584-20T>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.027 in 271588 control chromosomes in the gnomAD database, including 122 homozygotes. The observed variant frequency is approximately 7-folds higher than the estimated maximal expected allele frequency for a pathogenic variant in PEX1 causing Zellweger Syndrome phenotype (0.0039), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.2584-20T>A in individuals affected with Zellweger Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV001515888 SCV001724063 benign Zellweger spectrum disorders 2025-01-27 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001532815 SCV001748549 benign Peroxisome biogenesis disorder 1A (Zellweger) 2021-07-01 criteria provided, single submitter clinical testing
GeneDx RCV001562513 SCV001785289 likely benign not provided 2019-08-23 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001562513 SCV005221039 likely benign not provided criteria provided, single submitter not provided
Natera, Inc. RCV001515888 SCV002076856 benign Zellweger spectrum disorders 2018-04-13 no assertion criteria provided clinical testing

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