In silico versus functional characterization of genetic variants: lessons from muscle channelopathies

Accurate determination of the pathogenicity of missense genetic variants of uncertain significance is a huge challenge for implementing genetic data in clinical practice. In silico predictive tools are used to score variants' pathogenicity. However, their value in clinical settings is often unclear, as they have not usually been validated against robust functional assays. We compared nine widely used in silico predictive tools, including more recently developed tools (EVE and REVEL) with detailed cell-based electrophysiology, for 126 CLCN1 variants discovered in patients with the skeletal muscle channelopathy myotonia congenita. We found poor accuracy for most tools. The highest accuracy was obtained with MutationTaster (84.58%) and REVEL (82.54%). Both of these scores showed poor specificity, although specificity was better using EVE. Combining methods based on concordance improved performance overall but still lacked specificity. Our calculated statistics for the predictive tools were different to reported values for other genes in the literature, suggesting that the utility of the tools varies between genes. Overall, current predictive tools for this chloride channel are not reliable for clinical use, and tools with better specificity are urgently required. Improving the accuracy of predictive tools is a wider issue and a huge challenge for effective clinical implementation of genetic data. Vivekanandam et al. show that in silico predictive tools for determining pathogenicity of genetic variants in skeletal muscle channelopathies have poor specificity compared to functional prediction. Improved in silico predictive tools are needed.

Automated summary

Accurately determining the pathogenicity of uncertain missense genetic variants is a challenge for clinical use of genetic data. In this study, nine in silico predictive tools were compared with cell-based electrophysiology for CLCN1 variants related to myotonia congenita. Most tools showed poor accuracy, with MutationTaster and REVEL having the highest accuracy but poor specificity. Combining methods improved overall performance but lacked specificity. The current predictive tools for this chloride channel are unreliable, and better tools are urgently needed. Improving predictive tool accuracy is a wider challenge for genetic data implementation.