. 2013 Jun 27;22(22):4485–4501. doi: 10.1093/hmg/ddt297

Table 4.

Putative candidate genes for schizophrenia overlapped by very rare (<500 kb) CNVs

Candidate gene	Cytoband	Gene size (nt)	Case #	CNV start	CNV size (bp)	CN	Exonic
Very rare CNVs overlapping the same CNS-related gene in two or more unrelated schizophrenia cases
CAMTA1	1p36.31	984 383	67	7 063 417	33 667	Loss	•
CAMTA1	1p36.31	984 383	68	7 545 052	44 523	Loss
DNM3	1q24.3	571 237	87	170 223 915	47 814	Loss	•
DNM3	1q24.3	571 237	168	170 450 307	4136	Loss
HIST3H3	1q42.13	481	69	226 634 235	54 736	Gain	•
HIST3H3	1q42.13	481	70	226 673 588	109 976	Gain	•
COMMD1	2p15	230 403	66	62 049 330	36 475	Loss	•
COMMD1	2p15	230 403	32	62 106 806	24 384	Loss
LIMS1	2q13	152 892	71	108 619 802	61 009	Loss	•
LIMS1	2q13	152 892	72	108 619 802	61 583	Loss	•
DPP6	7q36.2	679 607	2	153 637 309	9260	Loss
			73	153 737 928	6935	Loss
			74	154 060 964	31 082	Loss	•
PPP3CC	8p21.3	100 043	75	22 265 902	166 778	Gain	•
PPP3CC	8p21.3	100 043	76	22 265 902	166 778	Gain	•
JAK2^a,b	9p24.1	142 939	7	4 527 834	486 659	Loss	•
JAK2^a,b	9p24.1	142 939	77	5 014 345	82 361	Gain	•
ERC1	12p13.33	504 696	78	865 867	157 163	Gain	•
ERC1	12p13.33	504 696	50	1 255 099	369 587	Loss	•
SOX5^a	12p12.1	1 030 150	79	23 826 011	11 461	Loss
			80	23 828 090	9382	Loss
			81	24 063 813	25 105	Loss
			82	24 561 569	35 937	Loss
DNM1L	12p11.21	66 448	83	32 679 398	45 218	Gain	•
DNM1L	12p11.21	66 448	84	32 679 398	47 929	Gain	•
RBFOX1^a	16p13.2	1 694 209	54	6 171 253	32 382	Loss
			85	6 754 460	50 650	Loss	•
			86	6 766 601	9285	Loss
			87	6 973 749	104 964	Loss	•
			62	6 992 360	143 753	Loss	•
PRKCA^a	17q24.2	507 937	61	61 941 341	277 949	Loss	•
PRKCA^a	17q24.2	507 937	88	62 145 527	7081	Loss
DOK6	18q22.2	448 040	89	65 614 643	10 824	Loss
DOK6	18q22.2	448 040	90	65 639 534	10 209	Loss
PTPRT^b	20q12	1 117 166	91	40 639 325	86 602	Loss
			92	40 778 749	187 266	Gain	•
			93	40 887 741	7643	Loss
Very rare CNVs overlapping promising candidate genes for schizophrenia found in a single schizophrenia case
PTGER3^b	1p31.2	195 456	141	71 150 238	44 186	Loss	•
USH2A^b	1q41	800 503	104	213 914 685	64 806	Loss	•
DISC1	1q42.2	414 458	38	230 150 208	121 262	Loss	•
NRXN1^a,b	2p16.3	1 114 032	170	503 371 141	18 515	Loss
GRM7^a,b	3p26.1	880 417	146	7 058 814	35 895	Loss
GRK4	4p16.3	77 132	100	2 994 521	31 371	Loss	•
DOK7^a	4p16.2	31 177	169	3 439 241	13 595	Gain	•
FGF2	4q26	71 528	198	123 980 237	58 004	Loss	•
GRM4	6p21.31	111 816	95	34 175 770	43 039	Gain	•
RUNX2	6p21	222 766	231	45 129 193	298 662	Loss	•
GABRR1	6q15	40 274	182	89 894 102	52 079	Loss	•
CALN1^a	7q11.22	632 885	223	71 331 369	131 729	Loss	•
CACNA2D1^b	7q21.11	493 614	166	81 829 583	187 332	Gain	•
SEMA3A	7q21.11	236 559	195	83 380 795	87 642	Gain	•
RELN	7q22.1	517 733	131	103 178 239	90 728	Loss	•
SLC1A1^a,b	9p24	97 043	7	4 527 834	486 659	Loss	•
ABLIM1	10q25	253 546	200	116 351 384	17 427	Loss	•
RHOG	11p15.4	14 006	188	3 817 748	11 292	Loss	•
MTNR1B	11q21	13 160	240	92 336 224	10 613	Loss	•
WNT5B	12p13.3	30 157	50	1 255 099	369 587	Loss	•
ATN1^c	12p13.31	17 859	208	6 837 052	74 565	Loss	•
ENO2^c	12p13.31	9 246	208	6 837 052	74 565	Loss	•
GRIN2A^b	16p13.2	429 347	32	9 982 679	10 953	Loss
PTPRM^a,b	18p11.2	839 546	119	7 899 131	55 764	Loss	•
PIK3C3^b	18q12.3	126 250	132	37 880 681	27 546	Loss	•
AP3D1^a	19p13.3	50 564	195	2 015 619	180 285	Loss	•
JAK3	19p13.11	23 251	271	17 754 374	68 190	Gain	•
GRIK1	21q21.3	403 029	166	30 082 515	11 811	Loss
S100B	21q22.3	6505	181	46 843 667	16 998	Loss	•

Candidate gene, selected based on the reported neuropsychiatric/neurodevelopmental phenotype identified from systematic searches of human (e.g. Online Mendelian Inheritance in Man; http://www.omim.org/) and model organism (e.g. Mouse Genome Informatics; http://www.informatics.jax.org/) databases; Cytoband, cytogenetic location of candidate gene; Gene size, in nucleotides; Case #, subjects from the discovery sample (n = 454) with schizophrenia; CNV start, hg18 (NCBI Build 36.1, March 2006); CNV size, in base pairs; CN, type of copy number aberration; Exonic, CNV overlaps exon(s) of candidate gene (•).

^aGene implicated in a previous CNV study of schizophrenia: JAK2 (32), SOX5 (36), RBFOX1 (11), PRKCA (32), NRXN1 (9,10,36,67,68), GRM7 (11,36), DOK7 (32), CALN1 (68), SLC1A1 (11,68), PTPRM (36) and AP3D1 (11).

^bGene implicated in a next-generation sequencing study of schizophrenia: JAK2 (34), PTPRT (34), PTGER3 (34), USH2A (34), NRXN1 (34), GRM7 (34), CACNA2D1 (34), SLC1A1 (34), GRIN2A (34), PTPRM (35) and PIK3C3 (34).

^cGenes overlapped by the same CNV.