ClinVar Miner

Submissions for variant NM_024577.3(SH3TC2):c.79A>G (p.Thr27Ala) (rs141649676)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000441918 SCV000514619 likely benign not specified 2018-01-08 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.
Inherited Neuropathy Consortium RCV000789695 SCV000929071 uncertain significance Charcot-Marie-Tooth disease no assertion criteria provided literature only
Invitae RCV000205289 SCV000260732 uncertain significance Charcot-Marie-Tooth disease type 4 2018-05-23 criteria provided, single submitter clinical testing This sequence change replaces threonine with alanine at codon 27 of the SH3TC2 protein (p.Thr27Ala). The threonine residue is weakly conserved and there is a small physicochemical difference between threonine and alanine. This variant is present in population databases (rs141649676, ExAC 0.2%). This variant has been reported in an individual affected with hereditary motor neuropathy (HMN) (PMID: 26392352). ClinVar contains an entry for this variant (Variation ID: 220296). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: (SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). The alanine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies. In summary, this variant is a rare missense change that is not predicted to affect protein function, and is found in the population at an appreciable frequency. This variant is not anticipated to cause disease; however, the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance.

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