ClinVar Miner

Submissions for variant NM_020956.2(PRX):c.*4152C>T (rs142762689)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000767048 SCV000293538 uncertain significance not provided 2017-03-02 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the PRX gene. The A1316V variant has been reported previously in a patient with chemotherapy-induced peripheral neuropathy (CIPN); however, a second PRX variant was not identified in this individual (Beutler et al., 2014). The authors suggested that variants in the PRX gene may contribute to susceptibility to CIPN (Beutler et al., 2014). The A1316V variant is observed in 31/5286 (0.6%) alleles from individuals of African background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The A1316V 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. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Illumina Clinical Services Laboratory,Illumina RCV001094578 SCV000413201 likely benign Charcot-Marie-Tooth disease, demyelinating, type 4F 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Athena Diagnostics Inc RCV000236760 SCV000614813 likely benign not specified 2017-06-30 criteria provided, single submitter clinical testing
Invitae RCV000559953 SCV000658021 likely benign Charcot-Marie-Tooth disease type 4 2019-12-31 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000236760 SCV000859022 likely benign not specified 2018-01-02 criteria provided, single submitter clinical testing
Molecular Genetics Laboratory,London Health Sciences Centre RCV001173096 SCV001336172 likely benign Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing

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