ClinVar Miner

Submissions for variant NM_173500.4(TTBK2):c.1499G>T (p.Arg500Leu)

dbSNP: rs56039839
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001115318 SCV001273287 likely benign Spinocerebellar ataxia type 11 2018-03-06 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002556262 SCV002955705 uncertain significance not provided 2022-07-23 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with TTBK2-related conditions. This variant is present in population databases (rs56039839, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. This sequence change replaces arginine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 500 of the TTBK2 protein (p.Arg500Leu). ClinVar contains an entry for this variant (Variation ID: 884308). 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0").

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