Table 3.

Contribution of De Novo Mutations to ASD Risk

Category of de novo mutation	Mutations per sample				Percent of mutations contributing to ASD risk (95% CI)
	Probands			Siblings	Probands
	All	Male	Female	All	All	Male	Female
Deletions	0.03	0.03	0.06	0.01	69.1% (43.2%–85.4%)	64.6% (38.7%–83.2%)	83.7% (66.2%–91.9%)

Duplications	0.03	0.03	0.03	0.01	70.8% (48.3%–86.8%)	70.8% (55.3%–88.6%)	70.9% (0.0%–88.2%)

All CNVs	0.06	0.05	0.09	0.02	69.9% (55.1%–79.6%)	67.7% (49.2%–79.1%)	79.7% (56.9%–88.5%)

Nonsense	0.06	0.06	0.05	0.03	52.9% (33.8%–68.7%)	53.9% (34.6%–66.4%)	44.5% (0.0%–70.4%)

Splice Site	0.02	0.02	0.06	0.01	52.4% (18.9%–73.7%)	39.6% (0.0%–72.3%)	80.8% (57%–91.6%)

Frameshift	0.08	0.08	0.10	0.05	38.9% (14.8%–51.2%)	37.4% (21.1%–52.9%)	47.8% (4.9%–65.6%)

All LoF	0.17	0.16	0.21	0.09	45.9% (31.8%–55.5%)	43.9% (31.4%–53.8%)	56.6% (41.1%–67.7%)

All LoFs and CNVs	0.22	0.21	0.29	0.11	52.2% (45.2%–59.7%)	50.0% (41.0%–58.9%)	63.4% (49.4%–71.8%)

Category of de novo mutation	Percent of cohort with a mutation				Percent of cases with a mutation contributing to ASD risk (95% CI)
	Probands			Siblings	Probands
	All	Male	Female	All	All	Male	Female
Deletions	3.1%	2.7%	6.0%	1.0%	2.2% (1.1%–3.2%)	1.8% (0.8%–2.5%)	5.0% (2.3%–8.4%)

Duplications	2.7%	2.7%	2.8%	0.8%	1.9% (1.2%–2.6%)	1.9% (1.0%–3.0%)	2.0% (0.2%–4.3%)

All CNVs	5.8%	5.3%	8.7%	1.7%	4.1% (2.6–5.7%)	3.6% (2.3%–4.9%)	7.0% (3.2%–11.4%)

Nonsense	5.9%	6.0%	5.0%	2.8%	3.1% (1.4–4.4%)	3.2% (1.8%–4.9%)	2.2% (0.0%–6.2%)

Splice Site	2.4%	1.9%	6.0%	1.1%	1.3% (0.5–2.3%)	0.7% (0.0%–1.5%)	4.8% (1.5%–8.8%)

Frameshift	7.8%	7.7%	8.7%	4.8%	3.0% (1.2–4.8%)	2.9% (1.2%–4.4%)	3.9% (0.2%–7.5%)

All LoF	15.4%	14.9%	18.8%	8.5%	6.9% (4.9–8.9%)	6.4% (3.9%–8.8%)	10.3% (6.3%–16.2%)

All LoFs and CNVs	20.6%	19.7%	26.6%	10.1%	10.5% (7.8–13.1%)	9.6% (6.8%–12.0%)	16.6% (11.4%–22.6%)