ClinVar Miner

Submissions for variant NM_016156.5(MTMR2):c.16A>T (p.Ser6Cys) (rs377006678)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000535242 SCV000657876 uncertain significance Charcot-Marie-Tooth disease type 4 2019-12-18 criteria provided, single submitter clinical testing This sequence change replaces serine with cysteine at codon 6 of the MTMR2 protein (p.Ser6Cys). The serine residue is moderately conserved and there is a moderate physicochemical difference between serine and cysteine. This variant is present in population databases (rs377006678, ExAC 0.4%). This variant has not been reported in the literature in individuals with MTMR2-related disease. ClinVar contains an entry for this variant (Variation ID: 476870). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Athena Diagnostics Inc RCV000992370 SCV001144597 uncertain significance not provided 2019-05-09 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001110931 SCV001268423 benign Charcot-Marie-Tooth disease, type 4B1 2018-03-26 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.
Molecular Genetics Laboratory,London Health Sciences Centre RCV001172717 SCV001335783 uncertain significance Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing

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