Extended Data Table 6c.

Linear modeling of variant GERP and per-gene GERP was employed to test whether the differences observed in (a) were driven by those observed in (b). The coefficients and p-value of the variant GERP score (from the joint linear models) are shown, where, for example, “ID > Current study” indicates a test of whether the conservation at sites of de novo mutations in ID is greater than that of mutations in SZ (from the current study), after correcting for the fact that the mutations in ID hit genes with greater overall conservation (b). p<0.05 are marked in bold.

Comparison	Coefficient	P-value
ID > ASD	0.052	0.270
ID > Current study	0.102	0.044
ASD > Current study	0.039	0.079

Logistic regression model for (X > Y): type ~ gene_gerp + variant_gerp