ClinVar Miner

Submissions for variant NM_020956.2(PRX):c.*3701C>T (rs147826200)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001086843 SCV000255226 likely benign Charcot-Marie-Tooth disease type 4 2019-12-31 criteria provided, single submitter clinical testing
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia RCV000202796 SCV000258270 uncertain significance not specified 2015-07-01 criteria provided, single submitter clinical testing
GeneDx RCV000202796 SCV000515632 likely benign not specified 2016-07-01 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.
Athena Diagnostics Inc RCV000757695 SCV000614810 likely benign not provided 2018-10-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000757695 SCV000886017 uncertain significance not provided 2017-10-03 criteria provided, single submitter clinical testing The PRX c.3496C>T; p.Pro1166Ser variant (rs147826200), to our knowledge, is not reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the genome Aggregation Database (gnomAD) with an non-Finnish European population frequency of 0.15% (identified on 194 out of 125,772 chromosomes) and is classified as likely benign/uncertain significance in ClinVar (ID:216835). The proline at position 1166 is moderately conserved, considering 11 species, and computational analyses of the effects of the p.Pro1166Ser variant on protein structure and function do not predict a deleterious effect (SIFT: tolerated, MutationTaster: polymorphism, PolyPhen-2: benign). Based on the available information, the clinical significance of the p.Pro1166Ser variant cannot be determined with certainty.
Illumina Clinical Services Laboratory,Illumina RCV001135981 SCV001295793 uncertain significance 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, 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.
Molecular Genetics Laboratory,London Health Sciences Centre RCV001172771 SCV001335839 likely benign Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing

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