ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.1085C>T (p.Ser362Leu)

gnomAD frequency: 0.00057  dbSNP: rs138758170
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000942051 SCV001087963 benign Zellweger spectrum disorders 2024-01-25 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001255595 SCV001432102 likely benign not specified 2020-08-17 criteria provided, single submitter clinical testing Variant summary: PEX1 c.1085C>T (p.Ser362Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00092 in 282642 control chromosomes, predominantly at a frequency of 0.0069 within the Finnish European subpopulation in the gnomAD database, including 2 homozygotes. The observed variant frequency within the Finnish European control individuals in the gnomAD database is approximately 1.8-fold of the estimated maximal expected allele frequency for a pathogenic variant in PEX1 causing Zellweger Syndrome phenotype (0.0039), strongly suggesting that the variant is a benign polymorphism. To our knowledge, no occurrence of c.1085C>T in individuals affected with Zellweger Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as benign. Based on the evidence outlined above, the variant was classified as likely benign.
PreventionGenetics, part of Exact Sciences RCV003970626 SCV004789602 likely benign PEX1-related disorder 2020-03-03 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV000942051 SCV002079318 likely benign Zellweger spectrum disorders 2018-06-19 no assertion criteria provided clinical testing

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