Genes affected by CNV

Gene name	Cumulative scoring evidence^a	Genetic linkage and association evidence^b	Gene-based evidence (P values from PGC GWAS)^c	Physical interaction evidence (Interactor)^d	Endeavour P value^e	Total score^f
NRXN1	18.4	0	1 (0.042)	0	N/A	19.4
CHRNA7	13.9	1	0 (0.28)	0	1.53×10^-4	14.9
BCL9	9.5	3^g	0 (0.92)	1 (TCF4)	4.16×10^-3	13.5
CYFIP1	11.8	0	0 (0.27)	1 (SYN2)	3.28×10^-1	12.8
GJA8	11.8	1	0 (0.73)	0	6.70×10^-3	12.8
NDE1	10.7	0	1 (0.038)	1 (KIF2A)	4.64×10^-1	12.7
SNAP29	10.1	1	0 (0.70)	1 (STX1A)	N/A	12.1
GJA5	11.7	0	0 (0.35)	0	2.03×10^-1	11.7
NTAN1	10.7	0	0 (0.18)	0	4.70×10^-1	10.7
PRKAB2	9.5	0	0 (0.94)	1 (NQO2)	7.38×10^-1	10.5
VIPR2	9.4	0	0 (0.90)	1 (ADCYAP1)	1.35×10^-2	10.4
PARK2	9.3	0	0 (0.54)	1 (SYT11, GRIN2B, YWHAH)	2.55×10^-1	10.3
COMT	9.2	1	0 (0.10)	0	1.23×10^-3	10.2
DLG2	6.7	0	2 (0.00717)	1 (GRIN2B, GRIN1, NOS1, ERBB4, GRID1)	4.48×10^-2	9.7
FMO5	9.5	0	0 (0.89)	0	3.35×10^-1	9.5
NIPA1	9.5	0	0 (0.58)	0	4.66×10^-2	9.5
ACP6	9.5	0	0 (0.83)	0	1.15×10^-1	9.5
TUBGCP5	9.5	0	0 (0.23)	0	4.73×10^-1	9.5
MYH11	8.4	0	0 (0.089)	1 (SLC1A2, SYNGR1)	1.14×10^-1	9.4
A2BP1	9.0	0	0 (0.071)	0	N/A	9.0
KLHL22	8.8	0	0 (0.86)	0	2.78×10^-1	8.8
RTN4R	6.6	1	0 (0.11)	1 (RTN4)	3.71×10^-3	8.6
ABCC1	8.4	0	0 (0.43)	0	3.74×10^-1	8.4
PRODH	6.9	1	0 (0.74)	0	3.10×10^-3	7.9
ZDHHC8	6.6	1	0 (0.96)	0	1.24×10^-4	7.6
CRKL	6.6	0	0 (0.16)	1 (ERBB3, ERBB4, NPAS3, ANK3)	4.38×10^-2	7.6
THAP7	6.6	0	1 (0.033)	0	8.51×10^-2	7.6
DGCR6L	6.6	0	0 (0.25)	1 (DTNBP1)	6.79×10^-1	7.6
Gene name	Cumulative scoring evidence^a	Genetic linkage and association evidence^b	Gene-based evidence (P values from PGC GWAS)^c	Physical interaction evidence (Interactor)^d	Endeavour P value^e	Total score^f

Note:

^aCumulative scoring evidence is based on the frequency of their disruption in 32 eligible studies. In addition, study type (GWAS or regional CNV study) and sample size were also taken into account and weighted accordingly. ^bGenetic linkage and association evidence indicates whether the prioritized genes was reported to be associated with schizophrenia in previous genetic linkage or association studies. ^cPGC GWAS evidence is based on gene-based P value calculated from Schizophrenia PGC data. ^dPhysical interaction evidence indicates whether proteins encoded by the prioritized genes interact with proteins encoded by known schizophrenia risk genes. ^eP value is obtained by Endeavor prioritization tool. ^fTotal score shows the overall points of the prioritized genes. ^gBCL9 is significantly associated with schizophrenia in a GWAS study. N/A, not available.
for more information, please refer here.
Data source: Luo et al. Systematic prioritization and integrative analysis of copy number variations in schizophrenia reveal key schizophrenia susceptibility genes. Schizophrenia Bulletin, 40(6): 1285-1299(2014).