ClinVar Miner

Submissions for variant NM_000287.4(PEX6):c.2814G>A (p.Glu938=) (rs1129186)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000078573 SCV000110429 benign not specified 2016-02-25 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000078573 SCV000303467 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000292393 SCV000463341 benign Peroxisome biogenesis disorder 4a (zellweger) 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Integrated Genetics/Laboratory Corporation of America RCV000590232 SCV000696487 benign not provided 2016-10-10 criteria provided, single submitter clinical testing Variant summary: The PEX6 c.2814G>A (p.Glu938Glu) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools predict no significant impact on normal splicing and ESE finder predicts that this variant may alter ESE binding. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 58981/120096 (15519 homozygotes, 1/2), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic PEX6 variant of 1/516 (0.0019365), suggesting this variant is likely a benign polymorphism. In addition, multiple reputable clinical diagnostic laboratories/databases cite the variant as "benign." Therefore, the variant of interest has been classified as Benign.
GeneDx RCV000590232 SCV000968191 benign not provided 2018-06-13 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic RCV000590232 SCV000801827 benign not provided 2015-10-21 no assertion criteria provided clinical testing

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