Extended Data Table 7. Geneset analysis of de novo genes from schizophrenia exome-sequencing studies.

a. Test of case enrichment of rare variants in cases compared to controls, for genes with one or more de novos in Fromer et al., Xu et al. and/or Girard et al. The P-values in bold are significant at P^corrected < 0.05, correcting for all 3×3×6 = 54 tests reported. b. Genes nominally significant (no correction) that had an observed de novo in one of the schizophrenia studies.

a
Set	N genes	Disruptive			Nonsyn. (strict)			Nonsyn. (broad)
		Singletons	MAF < 0.1%	MAF < 0.5%	Singletons	MAF < 0.1%	MAF < 0.5%	Singletons	MAF < 0.1%	MAF < 0.5%
Fromer et al. (disruptive)	63	0.1484	0.0075	0.0034	0.7401	0.7324	0.6264	0.3347	0.1660	0.2536
Fromer et al. (nonsyn)	464	0.0004	0.0003	0.0016	0.0341	0.0057	0.0892	0.4688	0.4842	0.6547
Girard & Xu (disruptive)	24	0.0342	0.0082	0.0082	0.0423	0.0412	0.0602	0.0774	0.1106	0.0891
Girard & Xu (nonsyn)	151	0.6916	0.4124	0.4186	0.1510	0.1326	0.1285	0.2258	0.3420	0.1790
Combined SCZ (disruptive)	87	0.0319	0.0007	0.0003	0.3355	0.3162	0.2692	0.1325	0.0757	0.1016
Combined SCZ (nonsyn)	611	0.0053	0.0011	0.0055	0.0192	0.0024	0.0379	0.3408	0.4064	0.4472

b
Gene	De novo study (type)	Test	N	A/U	P	Gene name
ALDH1L2	Fromer et al. (Nonsyn)	disruptive	6	10/3	0.028	aldehyde dehydrogenase 1 family, member L2
CACNA1S	Fromer et al. (Nonsyn)	ns-strict	23	28/15	0.031	calcium channel, voltage-dependent, Ltype, alpha 1S subunit
DLG1	Fromer et al. (Nonsyn)	ns-strict	4	5/0	0.021	discs, large homolog 1 (Drosophila)
IGSF22	Fromer et al. (Nonsyn)	disruptive	5	5/0	0.043	immunoglobulin superfamily, member 22
JARID2	Fromer et al. (Nonsyn)	ns-strict	5	5/0	0.041	jumonji, AT rich interactive domain 2
LAMA4	Fromer et al. (Nonsyn)	ns-strict	8	12/4	0.041	laminin, alpha 4
NBEA	Fromer et al. (Nonsyn)	ns-strict	5	5/0	0.025	neurobeachin
POLL	Fromer et al. (Nonsyn)	disruptive	4	4/0	0.042	polymerase (DNA directed), lambda
PTK2B	Fromer et al. (Nonsyn)	ns-strict	4	4/0	0.044	PTK2B protein tyrosine kinase 2 beta
SHKBP1	Fromer et al. (Nonsyn)	ns-strict	9	15/4	0.018	SH3KBP1 binding protein 1
SULF2	Fromer et al. (Nonsyn)	ns-strict	5	7/0	0.007	sulfatase 2
SYNGAP1	Xu et al. (2012) (LoF)	ns-strict	4	4/0	0.043	synaptic Ras GTPase activating protein 1
SZT2	Xu et al. (2012) (LoF)	ns-strict	22	18/9	0.049	seizure threshold 2 homolog (mouse)
TANC1	Fromer et al. (Nonsyn)	ns-strict	14	17/4	0.002	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1
TEP1	Xu et al. (2012) (Nonsyn)	ns-strict	26	25/14	0.048	telomerase-associated protein 1
UFL1	Fromer et al. (LoF)	ns-strict	4	7/0	0.008	UFM1-specific ligase 1
UFL1	Fromer et al. (LoF)	disruptive	2	5/0	0.029	UFM1-specific ligase 1