ClinVar Miner

Submissions for variant NM_001136473.1(LITAF):c.302A>G (p.Lys101Arg) (rs201283647)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000463036 SCV000541547 uncertain significance Charcot-Marie-Tooth disease, type 1C 2019-12-27 criteria provided, single submitter clinical testing This sequence change replaces lysine with arginine at codon 101 of the LITAF protein (p.Lys101Arg). The lysine residue is moderately conserved and there is a small physicochemical difference between lysine and arginine. This variant is present in population databases (rs201283647, ExAC 0.04%), and has an allele count higher than expected for a pathogenic variant (PMID: 28166811). This variant has been reported in an individual affected with peripheral neuropathy (PMID: 26392352). ClinVar contains an entry for this variant (Variation ID: 404114). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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.
GeneDx RCV000829946 SCV000971678 likely benign not provided 2018-05-09 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.
Molecular Genetics Laboratory,London Health Sciences Centre RCV001173622 SCV001336723 uncertain significance Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing

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