Table 1. New CNVs and Smallest Region of Overlap.

Region	Chr	Start (hg18 Mbp)	End (hg18 Mbp)	Typea	State	Casesb	Controlsb	Inheritancec		Window q-valued	Simulated p-valuee
								de novo	Inherited
1q24 (FMO Deletions and DNM3)17	1	167.00	172.00	MB	Deletion	12	0		2	0.0324	0.011
2q33.1 (SATB2)22,25	2	199.87	200.22	MB	Deletion	13	0	1		0.0211	0.0002
2p16.1 (NRXN1)18,28	2	50.00	51.11	MB	Deletion	30	9	4	8	focal	0.00005
2p15-16.1 proximal (PEX13 to AHSA2)	2	59.50	63.00	MB	Duplication	9	0	1		0.285	0.00001
3p25.3 (JAGN1 to TATDN2)	3	9.50	11.00	MB	Duplication	10	0	1	3	0.036	0.00103
3p11.2 (CHMP2B to POU1F1)	3	87.32	87.64	MB	Deletion	9	0		3	0.0489	0.000075
3q13 (GAP43)19,29	3	116.72	117.13	MB	Deletion	9	0	4		0.0489	0.0003
3q28-29 (FGF12)	3	193.00	194.50	MB	Deletion	13	1		3	focal	0.00005
4q21 (BMP3)	4	81.00	83.50	MB	Deletion	11	0	2		0.0324	0.00025
5q14 (MEF2C)21,27	5	88.00	88.26	MB	Deletion	10	0	2		focal	0.00005
9p13	9	32.00	39.00	MB	Duplication	18	0	2	2f	0.00216	-
10q1123	10	49.06	52.06	HS, MB	Duplication	10	0		5	0.036	-
10q23.1 (SFTPD to GLUD1, NRG3 inclusive)24,55	10	81.68	88.93	HS, MB	Deletion	11	0	5		0.0211	-
12p13 (SCNN1A to PIANP)20	12	6.34	6.68	MB	Duplication	23	1	3	1f	0.00115	-

^aHotspot (HS) or multiple breakpoint (MB) locus.

^bDue to complex CNV structure the case–control counts are representative of the region but may vary throughout.

^cDe novo counts also include cases from Hehir-Kwa et al.⁵⁶

^dWindow q-value is the weighted median for unique segments in the critical region

^eReported as the median simulation p-value for all genes in the region (Supplementary Table 4).

^fCarrier of a balanced translocation.