ClinVar Miner

Submissions for variant NM_000287.4(PEX6):c.210G>A (p.Gly70=) (rs398123304)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000078570 SCV000110426 benign not specified 2016-06-19 criteria provided, single submitter clinical testing
Invitae RCV001083809 SCV000761085 benign Peroxisome biogenesis disorders, Zellweger syndrome spectrum 2020-12-06 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000078570 SCV000917991 benign not specified 2018-04-27 criteria provided, single submitter clinical testing Variant summary: PEX6 c.210G>A alters a non-conserved nucleotide resulting in a synonymous change. 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 0.0064 in 122756 control chromosomes in the gnomAD database, including 5 homozygotes. The observed variant frequency is approximately 3.28 fold of the estimated maximal expected allele frequency for a pathogenic variant in PEX6 causing Zellweger Syndrome phenotype (0.0019), strongly suggesting that the variant is benign. The variant, c.210G>A, has been reported in the literature in individuals affected with Zellweger Syndrome (Ebberink_2010, Yik_2009) but were classified as neutral. These report(s) do not provide unequivocal conclusions about association of the variant with Zellweger Syndrome . To our knowledge, no experimental evidence demonstrating an impact on protein function has 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 benign.
Athena Diagnostics Inc RCV000676100 SCV001144907 benign not provided 2019-02-15 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001163760 SCV001325830 benign Peroxisome biogenesis disorder 4a (zellweger) 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
GeneDx RCV000676100 SCV001752004 likely benign not provided 2019-04-12 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000676100 SCV000801842 likely benign not provided 2015-12-16 no assertion criteria provided clinical testing
Natera, Inc. RCV001276626 SCV001463078 benign Zellweger syndrome 2020-09-16 no assertion criteria provided clinical testing

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