1. Leveraging protein structural information to improve variant effect prediction.
- Author
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Gerasimavicius L, Teichmann SA, and Marsh JA
- Abstract
Despite massive sequencing efforts, understanding the difference between human pathogenic and benign variants remains a challenge. Computational variant effect predictors (VEPs) have emerged as essential tools for assessing the impact of genetic variants, although their performance varies. Initially, sequence-based methods dominated the field, but recent advances, particularly in protein structure prediction technologies like AlphaFold, have led to an increased utilization of structural information by VEPs aimed at scoring human missense variants. This review highlights the progress in integrating structural information into VEPs, showcasing novel models such as AlphaMissense, PrimateAI-3D, and CPT-1 that demonstrate improved variant evaluation. Structural data offers more interpretability, especially for non-loss-of-function variants, and provides insights into complex variant interactions in vivo. As the field advances, utilizing biomolecular complex structures will be pivotal for future VEP development, with recent breakthroughs in protein-ligand and protein-nucleic acid complex prediction offering new avenues., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Joseph Marsh reports financial support was provided by UK Research and Innovation Medical Research Council. Sarah Teichmann reports a relationship with Sanofi that includes: board membership. Sarah Teichmann reports a relationship with GlaxoSmithKline Inc that includes: board membership and employment. Sarah Teichmann reports a relationship with Foresite Labs that includes: board membership. Sarah Teichmann reports a relationship with QIAGEN GmbH that includes: board membership. Sarah Teichmann reports a relationship with Transition Bio, Inc. that includes: equity or stocks. Sarah Teichmann reports a relationship with Ensocell that includes:. Sarah Teichmann reports a relationship with 10x Genomics, Inc. that includes: board membership. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2025 The Author(s). Published by Elsevier Ltd.. All rights reserved.)
- Published
- 2025
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