Mutation rate heterogeneity biases variant effect prediction and reveals genuine mutational robustness.

Mutation rate heterogeneity causes systematic bias in variant effect predictions and uncovers biological mutational robustness in proteins.

• Why it matters: Accurate interpretation of genetic variation is crucial for understanding disease and evolution, but current predictors often conflate mutation rates with functional importance, risking misclassification.
• What they did: The study analyzed mutation patterns and conservation metrics, demonstrating that most variant effect predictors and conservation scores are biased by underlying mutation rate differences, with phyloP scores correlating strongly with mutation rates even at neutral sites.
• The result: Variants at low-mutation-rate sites are overpredicted as damaging, while those at high-mutation-rate sites are underpredicted, emphasizing the need to incorporate mutation probabilities into prediction models and revealing that amino acid substitutions more likely to occur tend to be less destabilizing, indicating mutational robustness.