Table 3.

Autism Candidate Genes Enriched for Exon-Disrupting CNVs in Cases versus Controls

Candidate Gene(s)	Autism Cases (n = 2,588)			Controls (n = 580)			WTCCC Controls (n = 2,090)			Enriched Event	p Valuea
	Deletions	Duplications	Total	Deletions	Duplications	Total	Deletions	Duplications	Total
A2BP1	6	0	6	0	0	0	6	0	6	del	0.591
ANO5	0	1	1	1	0	0	0	0	0	dup	n/a
CACNA2D3	1	0	1	0	0	0	0	0	0	del	n/a
CADPS2	0	1	1	0	0	0	0	0	0	dup	n/a
CNR1	0	7	7	0	1	1	0	0	0	dup	0.032
CNTNAP2	1	1	2	0	0	0	0	0	0	del/dup	0.242
CTNNA3b	21	1	22	4	0	4	8	0	8	del/dup	0.050
CTNND2b	1	0	1	0	0	0	0	0	0	del	n/a
DIAPH3	1	0	1	0	0	0	2	0	2	del	0.869
DISC1	2	5	7	0	3	0	0	0	0	del	0.242
DNAH5	0	1	1	0	0	0	0	0	0	dup	n/a
DOCK1b	2	0	2	0	0	0	0	0	0	del	0.242
DPP10	0	5	5	0	0	0	0	0	0	dup	0.029
DPP6	1	4	5	0	1	1	0	0	0	del/dup	0.102
EML1	0	4	4	0	0	0	0	1	1	dup	0.178
EPHA6	0	1	1	0	0	0	0	0	0	dup	n/a
ERBB4	1	0	1	0	0	0	0	0	0	del	n/a
F13A1b	0	1	1	0	0	0	0	0	0	dup	n/a
FHITc	2	1	3	0	0	0	2	0	2	del/dup	0.485
FOXP1	2	0	2	0	0	0	0	0	0	del	0.242
GABRB3b	0	1	1	0	0	0	0	0	0	dup	n/a
GALNT13	1	0	1	0	0	0	1	0	1	del	0.742
GIMAP8	1	0	1	0	0	0	0	0	0	del	n/a
GPC6	1	0	1	0	0	0	0	0	0	del	n/a
GRID2b	1	1	2	0	0	0	0	0	0	del/dup	0.242
GRIN2A	0	1	1	0	0	0	0	0	0	dup	n/a
HYDINc	1	2	3	0	0	0	0	0	0	del/dup	0.119
IARSb	0	2	2	0	0	0	0	0	0	dup	0.242
ICA1, NXPH1	0	3	3	0	0	0	0	0	0	dup	0.119
IQGAP2	1	0	1	0	0	0	0	0	0	del	n/a
KANK1	2	6	8	0	1	1	0	2	2	del/dup	0.103
KHDRBS2	0	3	3	0	0	0	1	2	3	dup	0.641
KIAA1586	3	5	8	1	0	1	1	0	1	del/dup	0.049
MBD5b	2	1	3	0	0	0	1	0	1	del	0.301
MCC	2	0	2	0	1	0	1	1	1	del	0.488
MCPH1	2	2	4	0	0	0	0	0	0	del/dup	0.059
MCPH1, DLGAP2	1	0	1	0	0	0	0	0	0	del	n/a
MET	0	1	1	0	0	0	0	0	0	dup	n/a
MKL2	0	1	1	0	0	0	0	0	0	dup	n/a
MLL3b	1	1	1	0	1	0	0	0	0	del	n/a
MLL5	0	1	1	0	0	0	0	0	0	dup	n/a
MPHOSPH8b	0	3	3	0	0	0	0	0	0	dup	0.119
NLGN1	0	1	1	0	0	0	0	0	0	dup	n/a
NRXN1c	7	0	7	0	0	0	1	0	1	del	0.032
NRXN3	1	0	1	0	0	0	0	0	0	del	n/a
NTRK3	1	0	1	0	0	0	0	0	0	del	n/a
NXPH1	1	0	1	0	0	0	0	0	0	del	n/a
PARK2b	12	12	24	1	2	3	4	3	7	del/dup	0.009
PCDH9	0	1	1	0	0	0	0	0	0	dup	n/a
PDE4A	0	1	1	0	0	0	0	0	0	dup	n/a
PLCB1	2	4	6	0	0	0	0	2	2	del/dup	0.134
POGZ	0	1	1	0	0	0	0	0	0	dup	n/a
RGS7	0	1	1	0	0	0	0	1	1	dup	0.742
ROBO1b	1	1	2	0	0	0	0	0	0	del/dup	0.242
RSRC1	0	1	1	0	0	0	0	0	0	dup	n/a
SEMA5A	1	0	1	0	0	0	1	1	2	del	0.869
SLC1A1	0	2	2	0	0	0	0	0	0	dup	0.242
TBC1D4	1	0	1	0	0	0	0	0	0	del	n/a
THSD7A	0	1	1	0	0	0	0	2	2	dup	0.869
ZMYND11b	0	2	2	0	0	0	0	0	0	dup	0.242

^ap value determined by a Fisher’s exact test.

^bCandidate genes with private de novo events.

^cCandidate genes with recurrent de novo events. See Table S11 for a complete list of CNVs.