ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.3031G>A (p.Val1011Met) (rs141650598)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000298949 SCV000342312 likely benign not specified 2018-02-13 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000345924 SCV000470501 uncertain significance Peroxisome biogenesis disorder 1A (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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV000766589 SCV000576500 uncertain significance not provided 2017-05-02 criteria provided, single submitter clinical testing The V1011M variant in the PEX1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The V1011M variant is observed in 47/16422 (0.29%) alleles from individuals of South Asian background, including 1 homozygous individual, in the ExAC dataset (Lek et al., 2016). The V1011M variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret V1011M as a variant of uncertain significance.
Invitae RCV001277301 SCV001024312 benign Zellweger syndrome 2020-12-04 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000766589 SCV001144901 benign not provided 2019-03-21 criteria provided, single submitter clinical testing
Pars Genome Lab RCV000345924 SCV001652857 likely benign Peroxisome biogenesis disorder 1A (Zellweger) 2021-05-18 criteria provided, single submitter clinical testing
Natera, Inc. RCV001277301 SCV001464242 benign Zellweger syndrome 2020-06-01 no assertion criteria provided clinical testing

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