Top 21 significant genes arising from both the permutation-based test and the DNV rate-based test.

Cases/Controls: Number of cases and controls carrying CNV deletions overlapping the gene in the CNV analysis. Pcnv: p-value from the CNV permutation test. nsDNV: Number of constrained non-synonymous variations in the de novo analysis. Pdnv: p-value from the DNV analysis. Significant: The analysis where the gene was significant (dnv: DNV analysis, cnv: CNV analysis, both: Both analysis, none: Non-significant neither DNV nor CNV analysis). metaP: combined p-value (Pdnv and Pcnv) using the Fisher method. Pihw: Bonferroni corrected p-value using independent hypothesis weighting (IHW) and LOEUF metric as covariate. LOEUF: o/e LOF ratio upper bound fraction from gnomAD. *All the 21 genes were significant after combining their p-values and applying Bonferroni correction. 1Evidence is from mouse models [24,62].