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Assessing predictions on fitness effects of missense variants in calmodulin

Zhang, Jing and Kinch, Lisa N and Cong, Qian and Katsonis, Panagiotis and Lichtarge, Olivier and Savojardo, Castrense and Babbi, Giulia and Martelli, Pier Luigi and Capriotti, Emidio and Casadio, Rita and Garg, Aditi and Pal, Debnath and Weile, Jochen and Sun, Song and Verby, Marta and Roth, Frederick P and Grishin, Nick (2019) Assessing predictions on fitness effects of missense variants in calmodulin. In: HUMAN MUTATION, 40 (9, SI). pp. 1463-1473.

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Official URL: https://dx.doi.org/10.1002/humu.23857


This paper reports the evaluation of predictions for the ``CALM1'' challenge in the fifth round of the Critical Assessment of Genome Interpretation held in 2018. In the challenge, the participants were asked to predict effects on yeast growth caused by missense variants of human calmodulin, a highly conserved protein in eukaryotic cells sensing calcium concentration. The performance of predictors implementing different algorithms and methods is similar. Most predictors are able to identify the deleterious or tolerated variants with modest accuracy, with a baseline predictor based purely on sequence conservation slightly outperforming the submitted predictions. Nevertheless, we think that the accuracy of predictions remains far from satisfactory, and the field awaits substantial improvements. The most poorly predicted variants in this round surround functional CALM1 sites that bind calcium or peptide, which suggests that better incorporation of structural analysis may help improve predictions.

Item Type: Journal Article
Publisher: WILEY
Additional Information: Copyright of this article belongs to WILEY
Keywords: CAGI; calmodulin; disease; missense variants; predictors
Department/Centre: Division of Interdisciplinary Sciences > Computational and Data Sciences
Date Deposited: 17 Dec 2019 11:58
Last Modified: 17 Dec 2019 11:58
URI: http://eprints.iisc.ac.in/id/eprint/63857

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