60KE SAVs predicted to have more effect than cross-species variants. SNAP2 predicts the effect of single amino acid sequence variants (SAVs) upon protein function: the higher the score, the more reliable the prediction (horizontal x-axis, toward right); the more negative, the stronger the prediction that the variant is neutral (horizontal x-axis, toward left). The top panel (A) gives cumulative percentages, i.e. the percentage of SAVs in a data set predicted above a certain value, e.g. for SNAP2-score ≥+75, about 6% of all 60KE SAVs are predicted to have an effect; at the same threshold about half of all disease-causing SAVs are predicted to affect function. For 60KE, denisova and chimp, 99.7% confidence intervals (SNAP2-score ±3 standard error of mean) are indicated by dotted lines (indistinguishable for 60KE, barely distinguishable for chimp, clearly visible for denisova). Lower panel (B) gives cumulative accuracy (red: effect-SAVs correctly predicted to have effects, green: neutral-SAVs correctly predicted); here the values accumulate from the extremes to 0, i.e. left-to-right for neutral (green −100 to 0) and right-to-left for effect (red +100 to 0); estimates from cross-validation using only molecular function21. For instance, at SNAP2-scores ≥+75 about 88% of all effect-SAVs are correctly predicted. On the other hand, variations between homologs in human and other species (human-denisova, human-chimp, human-mouse, and human-fly) were predicted to be much more neutral (all curves shifted toward lower left corner of neutral variants).