Extended Data Table 2. Genes overlapped by two nonsynonymous de novo mutations in schizophrenia probands.

Genes hit by nonsynonymous (NS) mutations in two different probands with schizophrenia (N=18) are listed, with the expected functional impact of those mutations and the nominal p-value for genic recurrence (calculated by dnenrich); for the single instance of two loss-of-function (LoF) alleles in a single gene (TAF13), the p-value for LoF recurrence is given in parentheses; this is bolded since it is significant after Bonferroni correction for multiple testing of all genes (see Supplementary Text). Also shown are the case/control counts from the parallel exome sequencing study¹⁵ and the corresponding nominal p-value for association with schizophrenia.

18 genes with recurrent nonsynonymous de novos mutations (p = 0.0314)
Gene	De novo mutations	Nominal p-value for recurrence of NS (LoF) de novos	Case/control counts of rare (MAF < 0.001) LoF mutations in Purcell, et al.15	Nominal case/control p-value
AKD1	frameshift, missense	0.0024	2/8	1
BAIAP2	codon-deletion, missense	0.00042	1/0	0.53
C7orf60	missense (x2)	0.00013	0/0	1
CD14	missense (x2)	0.00021	0/0	1
HSPA8	frameshift, missense	0.00035	0/0	1
HUWE1	missense (x2)	0.014	0/0	1
KIAA1244	missense (x2)	0.0041	0/0	1
KIF18A	missense (x2)	0.00063	1/0	0.52
LPHN2	missense, nonsense	0.0014	0/0	1
MUC6	missense (x2)	0.0059	3/5	1
NIPAL3	missense, nonsense	0.00017	0/0	1
NLRC5	missense (x2)	0.0025	3/4	1
PHC2	missense (x2)	0.00072	0/0	1
PHF7	missense, nonsense	9.80E-05	0/0	1
PIK3C2B	frameshift, missense	0.0024	3/0	0.11
PSPC1	missense, nonsense	0.00034	0/0	1
RYR3	missense (x2)	0.018	4/1	0.22
TAF13	frameshift, nonsense	1.5e-05 (1.2e-06)	1/0	0.53