ClinVar Miner

Submissions for variant NM_000287.4(PEX6):c.1947del (p.Ile650fs) (rs267608227)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000665650 SCV000789804 pathogenic Peroxisome biogenesis disorder 4a (zellweger); Peroxisome biogenesis disorder 4B 2017-02-21 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000734107 SCV000862220 pathogenic not provided 2018-06-29 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000586808 SCV000696485 pathogenic Peroxisome biogenesis disorders, Zellweger syndrome spectrum 2016-09-09 criteria provided, single submitter clinical testing Variant summary: The PEX6 c.1947delG (p.Ile650Serfs) variant results in a premature termination codon, predicted to cause a truncated or absent PEX6 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. One in silico tool predicts a damaging outcome for this variant. This variant was found in 4/121404 control chromosomes at a frequency of 0.0000329, which does not exceed the estimated maximal expected allele frequency of a pathogenic PEX6 variant (0.0019365). The variant has been reported in affected individuals in the literature in the homozygous and heterozygous state. Taken together, this variant is classified as pathogenic.
Invitae RCV000586808 SCV000963976 pathogenic Peroxisome biogenesis disorders, Zellweger syndrome spectrum 2018-08-06 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Ile650Serfs*10) in the PEX6 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs267608227, ExAC 0.01%). This variant has been observed in several individuals affected with Zellweger syndrome (PMID: 19877282, 19142205). ClinVar contains an entry for this variant (Variation ID: 495796). Loss-of-function variants in PEX6 are known to be pathogenic (PMID: 8670792, 19877282, 21031596). For these reasons, this variant has been classified as Pathogenic.

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