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Abstract Background Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, or non-synonymous Single Nucleotide Variants – missense SNVs or nsSNVs) for particular proteins. We assembled SAV annotations from 22 different DMS experiments and normalized the effect scores to evaluate variant effect prediction methods. Three trained on traditional variant effect data (PolyPhen-2, SIFT, SNAP2), a regression method optimized on DMS data (Envision), and a naïve prediction using conservation information from homologs. Results On a set of 32,981 SAVs, all methods captured some aspects of the experimental effect scores, albeit not the same. Traditional methods such as SNAP2 correlated slightly more with measurements and better classified binary states (effect or neutral). Envision appeared to better estimate the precise degree of effect. Most surprising was that the simple naïve conservation approach using PSI-BLAST in many cases outperformed other methods. All methods captured beneficial effects (gain-of-function) significantly worse than deleterious (loss-of-function). For the few proteins with multiple independent experimental measurements, experiments differed substantially, but agreed more with each other than with predictions. Conclusions DMS provides a new powerful experimental means of understanding the dynamics of the protein sequence space. As always, promising new beginnings have to overcome challenges. While our results demonstrated that DMS will be crucial to improve variant effect prediction methods, data diversity hindered simplification and generalization.

Background: Deep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs; also referred to as missense mutations, or non-synonymous Single Nucleotide Variants – missense SNVs or nsSNVs) for particular proteins. We assembled SAV annotations from 22 different DMS experiments and normalized the effect scores to evaluate variant effect prediction methods. Three trained on traditional variant effect data (PolyPhen-2, SIFT, SNAP2), a regression method optimized on DMS data (Envision), and a naïve prediction using conservation information from homologs. Results: On a set of 32,981 SAVs, all methods captured some aspects of the experimental effect scores, albeit not the same. Traditional methods such as SNAP2 correlated slightly more with measurements and better classified binary states (effect or neutral). Envision appeared to better estimate the precise degree of effect. Most surprising was that the simple naïve conservation approach using PSI-BLAST in many cases outperformed other methods. All methods captured beneficial effects (gain-of-function) significantly worse than deleterious (loss-of-function). For the few proteins with multiple independent experimental measurements, experiments differed substantially, but agreed more with each other than with predictions. Conclusions: DMS provides a new powerful experimental means of understanding the dynamics of the protein sequence space. As always, promising new beginnings have to overcome challenges. While our results demonstrated that DMS will be crucial to improve variant effect prediction methods, data diversity hindered simplification and generalization. [ABSTRACT FROM AUTHOR]