Extended Data Table 1c.

Enrichment of de novo mutations (as calculated by dnenrich, see Supplementary Text) including all individuals, after excluding individuals with the lowest scholastic achievement (a school grade of 3), or excluding those with a ‘pathogenic’ CNV (see above) or a polygenic score in the top 50% of the distribution (see above). These secondary exclusion analyses were performed on those gene sets identified as significant in the analyses of the full set. p<0.05 are marked in bold.

		All probands				Exclude probands with lowest school grade (3)				Exclude probands with a ‘pathogenic’ CNV or with a polygenic score in the top 5% among probands
		NS (482)		LoF (64)		NS (398)		LoF (49)		NS (423)		LoF (54)
Gene set	# of genes	p	# mut	p	# mut	p	# mut	p	# mut	p	# mut	p	# mut
PSD	681	0.019	34	0.091	6	0.0033	32	0.031	6	0.039	29	0.047	6
ARC complex	28	0.00048	6	0.005	2	0.0002	6	0.0036	2	0.0019	5	0.0048	2
NMDAR complex	60	0.025	6	0.035	2	0.036	5	0.02	2	0.045	5	0.026	2
FMRP targets	784	0.0094	64	0.37	7	0.0041	56	0.28	6	0.031	54	0.55	5
actin filament bundle assembly	34	6.57E-06	8	1	0	0.0023	5	1	0	0.0005	6	1	0
autism LoF genes	128	0.015	11	0.00072	4	0.41	6	0.52	1	0.025	9	0.0013	3
ID LoF genes	30	0.27	1	0.019	1	1	0	1	0	0.22	1	0.016	1