Extended Data Table 1.

CNVs hitting TADA genes.

Gene	ASD subject		Unaffected parent2			Unaffected	Odds4 Ratio
	Unknown Inheritance	Inherited	Tr-ASD3	NT3	Tr-not-ASD3
q-value < 0.1
ANK2	1						∞
ASXL3	1						∞
VIL1		1	1				1.49
0.1 ≤ q-value < 0.3: Evidence for role in ASD
UTP6	1						∞
DNAH10		1	1				1.49
ATP1B1	1						∞
GGNBP2	1						∞
NRXN1		2	1				2.99
WHSC1	1						∞
HDLBP 5	1	2	1		1	1	2.24
CERS4		1	1				1.49
SHANK3	4						∞
IQGAP2	1						∞
0.1 ≤ q-value < 0.3: Evidence against role in ASD
EP400						1	0
SLCO1B1 5,6	1	1	1	1		1	0.996
SLCO1B3 6		1	1	2		1	0.37
KDM6B						1	0

Count of deletion copy number variants, inferred from sequence, for ASD subjects and those unaffected by ASD. Number of subjects and family status: 849 ASD without family information; 1467 ASD subjects in families; 2766 unaffected parents; 319 unaffected siblings of ASD subjects; 373 unaffected subjects without family information.

²No parents in this count were affected; 7 parents in the study were affected, none carried a CNV reported in the table and these subjects did not enter the calculation.

³Tr-ASD = transmitted to ASD subject from carrier parent; NT=parent a carrier but CNV not transmitted to affected child; Tr-not-ASD = parent transmits a CNV to an unaffected child.

⁴To compute the odds ratio we count the number ‘a’ of affected carriers, ‘b’ unaffected carriers (including parents), ‘c’ affected subjects who do not have the CNV, and ‘d’ unaffected non-carriers. The odds ratio = (ad)/(bc).

⁵One parent transmits the CNV to an affected and unaffected offspring; to obtain the total count of controls with a CNV, subtract one.

⁶Genes are adjacent in the genome (see Extended Data Fig. 4). For 3 subjects both genes are hit by the same CNV (1 ASD and 2 unaffected subjects).