Submissions for variant NM_002617.4(PEX10):c.868dup (p.His290fs)

Total submissions: 2

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV003123553	SCV003801287	likely pathogenic	Peroxisome biogenesis disorder	2023-01-23	criteria provided, single submitter	clinical testing	Variant summary: PEX10 c.928dupC (p.His310ProfsX49) causes a frameshift which results in an extension of the protein. The variant was absent in 250140 control chromosomes. To our knowledge, no occurrence of c.928dupC in individuals affected with Zellweger Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. However, multiple other protein-extending variants have been classified as pathogenic by our lab and others in ClinVar (e.g. c.874_875delCT, p.Leu292fsX55+; c.764dupA, p.Leu256AlafsX92+). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Invitae	RCV003649424	SCV004453445	pathogenic	Peroxisome biogenesis disorder, complementation group 7	2023-04-20	criteria provided, single submitter	clinical testing	For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the PEX10 protein in which other variant(s) (p.Arg331Gln) have been determined to be pathogenic (PMID: 20695019, 27230853). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 2429314). This variant has not been reported in the literature in individuals affected with PEX10-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change results in a frameshift in the PEX10 gene (p.His310Profs*49). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 37 amino acid(s) of the PEX10 protein and extend the protein by 11 additional amino acid residues.