Submissions for variant NM_000287.4(PEX6):c.2816C>A (p.Pro939Gln)

gnomAD frequency: 0.40479  dbSNP: rs1129187

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000078574	SCV000110430	benign	not specified	2016-02-25	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000078574	SCV000303468	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000407233	SCV000463340	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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000586703	SCV000696488	benign	not provided	2016-10-10	criteria provided, single submitter	clinical testing	Variant summary: The PEX6 c.2816C>A (p.Pro939Gln) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 46985/120122 control chromosomes (9823 homozygotes) at a frequency of 0.391144, which is approximately 202 times the estimated maximal expected allele frequency of a pathogenic PEX6 variant (0.0019365), evidence that this variant is a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
GeneDx	RCV000586703	SCV000968192	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.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001520392	SCV001729481	benign	Peroxisome biogenesis disorder	2025-02-04	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001543723	SCV001762556	benign	Heimler syndrome 2	2021-07-10	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000407233	SCV001762557	benign	Peroxisome biogenesis disorder 4A (Zellweger)	2021-07-10	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001543724	SCV001762558	benign	Peroxisome biogenesis disorder 4B	2021-07-10	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000586703	SCV000801826	benign	not provided	2015-10-21	no assertion criteria provided	clinical testing
Natera, Inc.	RCV001274620	SCV001458945	benign	Zellweger spectrum disorders	2020-09-16	no assertion criteria provided	clinical testing