We evaluated the enrichment and depletion of pLOF variants (allele frequency < 0.5%) in gene sets (that is, terms) from Gene Ontology (GO)87,88. For each gene annotated with a particular GO term, we computed the number of pLOF variants per protein-coding base pair, L, and proportion of singletons, S. We then tested for lower or higher mean L and S in a GO term using bootstrapping (1,000,000 samples) with adjustment for the gene length of the protein-coding sequence (CDS): (1) sort all genes by their CDS length in ascending order and divide them into equal-size bins (1,000 genes each); (2) count how many genes from a GO term are in each bin; (3) from each bin, sample with replacement the same number of genes and compute the average L and S; (4) count how many times sampled L and S were lower or higher than observed values. The P values were computed as the proportion of bootstrap samples that exceeded the observed values. The fold change of average L and S was computed as a ratio of observed values to
