ClinVar Miner

Submissions for variant NM_000287.4(PEX6):c.517del (p.Ser173fs) (rs61753212)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000673874 SCV000799126 pathogenic Peroxisome biogenesis disorder 4a (zellweger); Peroxisome biogenesis disorder 4B 2018-04-11 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV001193475 SCV001362343 pathogenic Peroxisome biogenesis disorders, Zellweger syndrome spectrum 2019-04-08 criteria provided, single submitter clinical testing Variant summary: PEX6 c.517delA (p.Ser173AlafsX33) 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 (e.g. c.1314_1321del/p.Glu439fsX3, c.1947delG/p.Ile650fsX10). The variant allele was found at a frequency of 1e-05 in 192728 control chromosomes (gnomAD). c.517delA has been reported in the literature in at least two unrelated, compound heterozygous individuals affected with Zellweger Syndrome (Steinberg 2004, 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. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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