Table 2.

Overall burden of de novo heterozygous variants.

Gene sets	Variant class	Obs_Num	Obs_Rate	Exp_Num	Exp_Rate	Enrichment	p value
All genes	Synonymous	15	0.333	13.7	0.304	1.1	0.68
	Missense	39	0.867	30.2	0.671	1.29	0.12
	D-mis	19	0.422	12.1	0.269	1.57	0.06
	LGD	3	0.066	4.04	0.089	0.743	0.81
Constrained genes	Synonymous	8	0.178	4.98	0.111	1.61	0.17
	Missense	16	0.356	11.06	0.246	1.45	0.13
	D-mis	12	0.267	4.71	0.105	2.55	0.003
SOX2 or EFTUD2 targets	Synonymous	8	0.178	4.84	0.108	1.65	0.16
	Missense	19	0.422	10.76	0.24	1.77	2.2e−16
	D-mis	15	0.333	4.49	0.099	3.34	6.6e−05

LGD likely gene disrupting, including frameshift, stop gain, and variants at canonical splice site, D-mis predicted deleterious missense variants.

Exp_Rate and Obs_Rate are respectively the expected and observed fraction of genes with a specific type of de novo mutation. Exp_Num and Obs_Num are the expected and observed number of genes with a specific type of de novo mutation, respectively. Constrained genes are defined by ExAC_pLI > 0.5.