Deep indel mutagenesis reveals the impact of insertions and deletions on protein stability and function
Amino acid insertions and deletions (indels) are an abundant class of genetic variants.   However, compared to substitutions, the effects of indels are not well understood and poorly predicted.  Here we address this shortcoming by performing deep indel mutagenesis (DIM) of structurally diverse proteins. Indel tolerance is strikingly different to substitution tolerance and varies extensively both between different proteins and within different regions of the same protein. Although state of the art variant effect predictors perform poorly on indels, we show that both experimentally-measured and computationally-predicted substitution scores can be repurposed as good indel variant effect predictors by incorporating information on protein secondary structures. Quantifying the effects of indels on protein-protein interactions reveals that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide. Overall design: DNA-seq of PCR amplicon