ClinVar Miner

Submissions for variant NM_002617.4(PEX10):c.835G>T (p.Glu279Ter)

dbSNP: rs62641225
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000289565 SCV000333750 pathogenic not provided 2015-08-12 criteria provided, single submitter clinical testing
Invitae RCV001381855 SCV001580413 pathogenic Peroxisome biogenesis disorder, complementation group 7 2023-07-19 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 282334). For these reasons, this variant has been classified as Pathogenic. This variant is also known as E279X. This premature translational stop signal has been observed in individual(s) with a Zellweger syndrome spectrum disorder (PMID: 15542397). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Glu299*) in the PEX10 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX10 are known to be pathogenic (PMID: 9683594, 10862081, 21031596).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003155147 SCV003844296 likely pathogenic Peroxisome biogenesis disorder 2023-02-27 criteria provided, single submitter clinical testing Variant summary: PEX10 c.895G>T (p.Glu299X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant was absent in 250302 control chromosomes (gnomAD). c.895G>T has been reported in the literature in individuals affected with Zellweger Syndrome (example: Steinberg_2004 and Ebberink_2010 ). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Baylor Genetics RCV003475892 SCV004201388 pathogenic Peroxisome biogenesis disorder 6A (Zellweger) 2023-10-10 criteria provided, single submitter clinical testing
Natera, Inc. RCV001833319 SCV002094105 pathogenic Zellweger spectrum disorders 2021-08-09 no assertion criteria provided clinical testing

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