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Association Linkage Expression Literature GO_Annotation Gene Network miRNA Targets

Association Linkage Expression Literature GO_Annotation Gene Network miRNA Targets Datasets Gene Ranking

Table 1. Genome-wide association study findings for schizophrenia

Authors	Ancestry	Discovery	Replication	Combined	Locus	SNP	Position (Mb)	Allele	Freq.	Odds ratio (95% CI)	P-value	Closest gene
Purcell [1]	EU	ISC 3322/3587	MGS/SG+ 4686/15490	ISC/MGS/SG+ 8008/19077	6p22.1	rs13194053	27.3	C	0.16	0.82 (NR)	9.54 × 10^-9	HIST1H2BJ
Shi [2]	EU AA	MGS 2681/2653 1286/973	ISC/SG+ 5327/16424 --	MGS/ISC/SG+ 8008/19077 --	6p22.1	rs13194053	27.3	C	0.16	0.88 (NR)	9.54 × 10^-9	HIST1H2BJ
Stefansson [3]	EU	SG+ 2663/13498	1: SG-fu 4999/15555 2:MGS/ISC 5283/5538	1: SG+/SG-fu 7662/29053 2: SG+/SG-fu/ISC/MGS 12945/34591	6p21.3-22.1	rs6932590	27.4	T	0.78	1.16 (1.11-1.21)	1.4 × 10^-12	PRSS16
					11q24.2	rs12807809	124.1	T	0.83	1.15 (1.10-1.20)	2.4 × 10^-9	NRGN
					18q21.2	rs9960767	51.3	C	0.05	1.23 (1.15-1.32)	4.1 × 10^-9	TCF4
Rietschel [4]	EU	1169/3714	2569/4088	3738/7802	11p11.2	rs11819869	46.5	T	0.16	1.25 (NR)	3.89 × 10^-9	AMBRA1
Ripke [5]	EU	PGC-SCZ 9394/12462	PGC-SCZ 8442/21397	PGC-SCZ 17836/33859	1p21.3	rs1625579	98.3	T	0.80	1.12 (1.09-1.16)	1.59 × 10^-11	MIR137
					2q32.3	rs17662626	193.7	A	0.91	1.20 (1.13-1.26)	4.65 × 10^-8	PCGEM1
					6p21.3-22.1	rs2021722	30.3	C	0.78	1.15 (1.11-1.19)	2.18 × 10^-12	TRIM26
					8p23.2	rs10503253	4.2	A	0.19	1.11 (1.07-1.15)	4.14 × 10^-8	CSMD1
					8q21.3	rs7004633	89.8	G	0.18	1.16 (1.11-1.21)	1.45 × 10^-8	MMP16
					10q24.32	rs7914558	104.8	G	0.59	1.10 (1.07-1.13)	1.82 × 10^-9	CNNM2
					10q24.33	rs11191580	104.9	T	0.91	1.15 (1.10-1.20)	1.11 × 10^-8	NT5C2
					11q24.2	rs548181	125.0	G	0.88	1.20 (1.13-1.26)	2.91 × 10^-8	STT3A
					18q21.2	rs12966547	50.9	G	0.58	1.09 (1.06-1.12)	2.60 × 10^-10	CCDC68
					18q21.2	rs17512836	51.3	C	0.02	1.40 (1.28-1.52)	2.35 × 10^-8	TCF4
Shi [6]	HC	BIOX 3750/6468	BIOX 4383/4539	BIOX 8133/11007	1q24.2	rs10489202	166.2	A	0.14	1.19 (1.09-1.29)	9.50 × 10^-9	BRP44
					8p12	rs16887244	38.2	G	0.32	0.83 (0.78–0.89)	1.27 × 10^-10	LSM1
					8p12	rs1488935	38.3	T	0.32	0.87 (0.82–0.93)	5.06 × 10^-9	WHSC1L1
Steinberg [7]	EU	SG+/ISC/MGS 7946/19036	9246/22356 1014/1144	18206/42536	2p15.1	rs2312147	58.1	C	0.61	1.09 (1.06–1.12)	1.9 × 10^-9	VRK2
Steinberg [7]	EU	SG+/ISC/MGS 7946/19036	9246/22356 1014/1144	18206/42536	18q21.2	rs4309482	50.9	A	0.58	1.09 (1.06–1.12)	7.8 × 10^-9	TCF4
Yue [8]	HC	746/1599	4027/5603	4773/7207	6p21-22.1	rs1635	28.3	T	0.33	0.78 (0.73–0.82)	6.91 × 10^-12	NKAPL
Yue [8]	HC	746/1599	4027/5603	4773/7207	11p11.2	rs11038167	44.8	A	0.40	1.29 (1.23–1.36)	1.09 × 10^-11	TSPAN18
Schizophrenia and bipolar disorder
O’Donovan [9]	EU	SCZ: 479/2937	SCZ: 6666/9897 BP: 1865/—	9173/12834	2q32.1	rs1344706	185.5	T	0.59	1.12 (NR)	9.96 × 10^-9	ZNF804A
Ripke [10]	EU			PGC-SCZ/BP 16374/14044	3p21.1	rs2239547	52.8	T	0.72	1.12 (1.08–1.16)	7.83 × 10^-9	ITIH3/4
					10q21.2	rs10994359	61.9	C	0.06	1.22 (1.15–1.29)	2.5 × 10^-8	ANK3
					12p13.3	rs4765905	2.2	C	0.33	1.11 (1.07–1.15)	7.0 × 10^-9	CACNA1C

Table 2. Replicated CNVs in schizophrenia

Locus	CNV	Position (Mb)	Size (Mb)	Genes	CNV frequency (with/without)		OR (95% CI)	P-value	Studies	Other disorders
Locus	CNV	Position (Mb)	Size (Mb)	Genes	Cases	Controls	OR (95% CI)	P-value	Studies	Other disorders
1q21.1	Del	144.6–146.3	1.67	11	0.00176 (20/11372)	0.00021 (10/47311)	8.3 (3.7–19.9)	2.2 × 10^-8	Studies	ASD, MR
2p16.3	Ex del	49.9–51.5	0.02–0.42	1 (NRXN1)	0.00182 (23/12627)	0.00022 (10/45284)	8.2 (3.8–19.4)	5.5 × 10^-9	Studies	ASD, MR
3q29	Del	197.2–198.8	0.84–1.6	19	0.00080 (6/7539)	0.00003 (1/39747)	17.0 (1.4–1198.4)	9.7 × 10^-3	Studies	ASD, MR
3q29	Dup	196.8–196.9	0.05	2	0.00121 (10/8280)	<0.00013 (0/7431)	∞ (1.6–∞)	1.0 × 10^-2	Studies
7q36.3	Ex dup	158.5–158.8	0.12–0.36	1 (VIPR2)	0.00191 (14/7322)	0.00047 (7/14814)	4.0 (1.5–11.9)	2.0 × 10^-3	Studies
15q11.2	Del	20.3–20.8	0.5	4	0.00551 (26/4692)	0.00192 (79/41115)	2.7 (1.5–4.9)	6.0 × 10^-4	Studies	ASD, PWS/AS
15q13.3	Del	28.7–30.3	1.5	8	0.00193 (21/10866)	0.00020 (9/45913)	9.9 (4.3–24.4)	2.0 × 10^-9	Studies	ASD, MR, IGE
15q11.2-13.1	Mat dup	20.3–26.4	4.1–9.0	13-24	0.00053 (4/7578)	0.00007 (3/41367)	7.3 (1.2–50.0)	1.0 × 10^-2	Studies	ASD, MR, IGE
16p11.2	Dup	29.4–30.1	0.7	26	0.00313 (31/9859)	0.00027 (8/29589)	11.6 (5.6–29.3)	1.5 × 10^-12	Studies	ASD, MR, DD
17p12	Del	14.1–15.4	0.93–1.31	15	0.00151 (8/5292)	0.00015 (6/39213)	9.9 (3.4–28.5)	5.0 × 10^-5	Studies	HN
22q11.2	Del	17.1–20.2	1.4–2.5	29–43	0.00307 (35/11365)	<0.00002 (0/45361)	∞ (35.9–∞)	<1.0 × 10^-16	Studies	VCFS

Table 3. de novo mutations found in schizophrenia (Gauthier et al. [11])

Individual	Chr.	Position (hg19)	Gene	Reference allele	Mutant allele	Mutation	Nucleotide substitution	Amino acid substitution	PhyloP	Grantham score	PolyPhen	SIFT prediction
SCZ0101	19	36,673,714	ZNF565	T	C	Missense	Transition	p.His385Arg	4.28987	Conservative	Possibly damaging	Damaging
SCZ0101	21	16,338,349	NRIP1	T	G	Missense	Transversion	p.Lys722Thr	1.81401	Moderately conservative	Probably damaging	Damaging
SCZ0201	12	57,579,450	LRP1	C	A	Nonsense	Transversion	p.Tyr2200X	1.52978	–	–	–
SCZ0201	17	79,637,360	CCDC137	A	G	Missense	Transition	p.Tyr125Cys	3.55235	Radical	Probably damaging	Damaging
SCZ0401	3	122,146,472	KPNA1	C	A	Nonsense	Transversion	p.Glu448X	5.78062	–	–	–
SCZ0401	19	52,826,001	ZNF480	C	T	Nonsense	Transition	p.Arg480X	–2.01835	–	–	–
SCZ0601	14	103,806,120	EIF5	A	G	Missense	Transition	p.Iso351Val	2.10831	Conservative	Benign	Tolerated
SCZ0901	3	46,717,166	ALS2CL	G	A	Nonsense	Transition	p.Arg733X	0.727551	–	–	–
SCZ1001	12	6,707,226	CHD4	G	A	Missense	Transition	p.Arg576Trp	2.53121	Moderately radical	Probably damaging	Damaging
SCZ1001	12	121,882,033	KDM2B	C	T	Missense	Transition	p.Gly745Ser	6.313	Moderately conservative	Probably damaging	Damaging
SCZ1001	18	6,974,966	LAMA1	T	C	Missense	Transition	p.Thr2187Ala	–0.76152	Moderately conservative	Benign	Tolerated
SCZ1101	11	104,825,480	CASP4	T	C	Missense	Transition	p.Glu39Lys	–1.1914	Moderately conservative	Possibly damaging	Tolerated
SCZ1401	1	1,153,867	SDF4	C	T	Missense	Transition	p.Asp295Asn	1.88812	Conservative	Benign	Damaging
SCZ1401	3	138,461,543	PIK3CB	T	C	Missense	Transition	p.Iso160Val	1.18761	Conservative	Benign	Tolerated
SCZ1401	12	123,804,988	SBNO1	G	C	Missense	Transversion	p.Asn886Lys	–0.120827	Moderately conservative	Probably damaging	Tolerated

Table 4. de novo mutations found in schizophrenia (Xu et al. [12])

Gene	Mutation type	NS or S	PolyPhen-2	Grantham score	phyloP score	Chr. (position)	Nucleotide change	Amino acid change	Diagnosis	Sex	Trio ID
PLCL2	SNV	NS	Probably damaging	112	4.99	3 (17,051,253)	TGT-aGT	p.Cys30Ser	SCZ	M	trio_002
WDR11	SNV	NS	Probably damaging	29	6.30	10 (122,664,879)	CGC-CaC	p.Arg1081His	SCZ	M	trio_011
DPYD	SNV	NS	Probably damaging	125	3.89	1 (97,981,407)	GGA-aGA	p.Gly539Arg	SCZ	M	trio_016
OR4C46	SNV	NS	Probably damaging	125	1.61	11 (51,515,885)	GGA-aGA	p.Gly202Arg	SCZ	F	trio_019
UGT1A3	SNV	NS	Probably damaging	15	0.53	2 (234,637,866)	TTG-aTG	p.Leu32Met	SCZ	F	trio_023
FAM3D	SNV	NS	Probably damaging	194	1.18	3 (58,622,886)	TAC-TgC	p.Tyr147Cys	SCZ	M	trio_024
KLF12	SNV	NS	Probably damaging	112	6.02	13 (74,289,537)	TCT-TgT	p.Ser45Cys	SCZ	M	trio_033
ADCY7	SNV	NS	Probably damaging	56	4.93	16 (50,349,011)	AGC-gGC	p.Ser1020Gly	SCZ	M	trio_038
GPR153	SNV	NS	Probably damaging	89	5.80	1 (6,314,661)	ACC-AtC	p.Thr102Ile	SCZAFF-dpr	M	trio_040
PML	SNV	NS	Probably damaging	81	2.93	15 (74,290,439)	ACG-AtG	p.Thr75Met	SCZAFF-dpr	M	trio_044
SLC26A8	SNV	NS	Probably damaging	56	1.87	6 (35,927,251)	GAG-aAG	p.Glu512Lys	SCZAFF-bp	F	trio_077
CCDC108	SNV	NS	Probably damaging	46	2.43	2 (219,900,235)	AAT-AgT	p.Asn105Ser	SCZ	F	trio_080
TRAK1	SNV	NS	Probably damaging	29	4.80	3 (42,261,055)	CAT-CgT	p.His678Arg	SCZ	F	trio_083
FASTKD5	SNV	NS	Probably damaging	60	5.61	20 (3,128,479)	GCA-GgA	p.Ala413Gly	SCZ	M	trio_089
DGCR2	SNV	NS	Probably damaging	103	6.24	22 (19,028,681)	CCT-CgT	p.Pro429Arg	SCZ	M	trio_091
ACOT6	SNV	NS	Possibly damaging	194	–0.08	14 (74,086,428)	TAT-TgT	p.Tyr170Cys	SCZ	F	trio_047
PITPNM1	SNV	NS/splice	Probably damaging	101	0.30	11 (67,267,884)	CGG-tGG	p.Arg217Trp	SCZ	M	trio_039
NPRL2	SNV	NS/splice	Possibly damaging	56	6.11	3 (50,385,987)	GGC-aGC	p.Gly231Ser	SCZ	F	trio_023
MAGEC1	SNV	NS	Unknown	58	0.37	X (140,993,957)	ACT-AgT	p.Thr256Ser	SCZ	M	trio_003
TRRAP	SNV	NS	Unknown	21	5.12	7 (98,498,329)	ATC-tTC	p.Ile295Phe	SCZ	M	trio_033
COL3A1	SNV	NS/splice	Unknown	155	2.54	2 (189,851,792)	TCT-TtT	p.Ser152Phe	SCZ	M	trio_089
GIF	SNV	NS	Benign	29	0.83	11 (59,603,474)	GTA-aTA	p.Val294Ile	SCZAFF-dpr	F	trio_001
TEKT5	SNV	NS	Benign	89	0.25	16 (10,783,119)	ATC-AcC	p.Ile237Thr	SCZ	M	trio_011
THBS1	SNV	NS	Benign	56	5.66	15 (39,881,442)	GAG-aAG	p.Glu605Lys	SCZ	M	trio_015
PAG1	SNV	NS	Benign	29	0.15	8 (81,905,378)	GTC-aTC	p.Val29Ile	SCZ	M	trio_020
RGS12	SNV	NS	Benign	98	0.06	4 (3,429,844)	CCA-CtA	p.Pro518Leu	SCZAFF-dpr	M	trio_040
SAP30BP	SNV	NS	Benign	56	5.37	17 (73,702,542)	GGC-aGC	p.Gly274Ser	SCZ	F	trio_047
ZNF530	SNV	NS	Benign	46	–0.04	19 (58,118,122)	AGT-AaT	p.Ser410Asn	SCZAFF-bp	F	trio_077
MTOR	SNV	NS	Benign	46	2.82	1 (11,293,489)	AAT-AgT	p.Asn796Ser	SCZ	F	trio_080
INPP5A	SNV	NS	Benign	64	2.62	10 (134,463,942)	GCG-GtG	p.Ala80Val	SCZAFF-bp	F	trio_093
EDEM2	SNV	NS	Benign	83	3.39	20 (33,703,457)	TAC-cAC	p.Tyr469His	SCZ	M	trio_095
CELF2	SNV	S/splice	Coding-synon	–	3.06	10 (11,356,223)	GGT-GGc	p.Gly345Gly	SCZ	M	trio_016
SLC26A7	SNV	S	Coding-synon	–	0.03	8 (92,346,630)	CAG-CAa	p.Gln250Gln	SCZ	M	trio_094
VPS35	SNV	Splice	–	–	–	16 (46,705,610)	C/T	–	SCZ	M	trio_002
ADAMTS3	SNV	Splice	–	–	–	4 (73,185,683)	G/A	–	SCZ	F	trio_023
GPR115	DNV	NS	Probably damaging	99	3.35	6 (47,682,855)	CTC-aaC	p.Leu625Asn	SCZ	F	trio_080
SPATA5	Indel	Amino acid deletion	Damaging	215	–	4 (123,855,728)	TTCTT-caa-CAACA	–	SCZ	F	trio_023
RB1CC1	Indel	Frameshift deletion	Damaging	215	–	8 (53,568,705)	ACTGT-tc-TCTGT	–	SCZ	M	trio_026
LAMA2	Indel	Frameshift deletion	Damaging	215	–	6 (129,835,668)	GGTGG-aagccca-AAGCC	–	SCZ	M	trio_092
ESAM	Indel	Frameshift deletion	Damaging	215	–	11 (124,626,163)	tggac-AGCG-agcgg	–	SCZ	M	trio_042
NS, non-synonymous; S, synonymous; SNV, single nucleotide variant; DNV, dinucleotide variant; chr., chromosome; SCZ, schizophrenia; SCZAFF-dpr, schizoaffective disorder depressed subtype; SCZAFF-bp, schizoaffective disorder bipolar subtype; M, male; F, female.

Table 5. De novo mutations found in schizophrenia (Awadalla et al. [13])

Gene	Sample and Ref.	Diagnosis	Mutation Type	Mutation Location	Chr.	Position	Nucleotide Change and Genomic Context	Amino Acid and/or Structural Change	MAPP p Value
NRXN1	S02959	Schizophrenia	INDEL	CODING	2	50002821	CAGCACACGG(-/ACGG)GTATGGTCGT	G1402DfsX29	–
MAP2K1	S00237	Schizophrenia	INTRONIC	INTRONIC	15	64561310	CTTCTTGTAC(G/T)GTCAGGGAGA	Within intron	–
SHANK3	S00161	Childhood-onset Schizophrenia	MISSENSE	CODING	22	49484091	GCATGACACA(C/T)GGCCTGGTGA	R536W	0.051
GRIN2B	S05650	Paranoid Schizophrenia	MISSENSE	CODING	12	13611351	CTTCTACATG(T/G)TGGGGGCGGC	L825V	<0.001
SHANK3	S00285	Schizoaffective, mild mental retardation	NONSENSE	CODING	22	49506476	TGCCCGAGAG(C/T)GAGCTCTGGC	R1117X	–
KIF17	S00215	Schizophrenia	NONSENSE	CODING	1	20886681	GGAGCAGATA(C/A)TTCCTGGATG	Y575X	–
BSN	S00237	Schizophrenia	SILENT	CODING	3	49666988	GCACTGCAGT(G/C)GTAGACCTCC	V1665V	–
ATP2B4	S00182	Disorganized Schizophrenia	SILENT	CODING	1	201935404	TCATCCGAAA(C/T)GGTCAACTCA	N195N	–
SHANK3	S04261	QNTS, unknown	MISSENSE	CODING	22	49507364	GCCACCAGTG(C/T)CTCCCAAGCC	P1429S	0.107