Table 3.
Candidate genes included in CNVs from schizophrenia cases and controls
| Gene | Name | Schizophrenia cases |
Controls | ||||
|---|---|---|---|---|---|---|---|
| ID | Coordinates (hg19) | Size (bp) | CNV | Notes | |||
| AP3B2 | AP-3 complex subunit β2 | 1828 | chr15:83220050-83338322 | 118,272 | dup | Includes 2 genes, AP3B2 could be disrupted | — |
| CLTCL1 | Clathrin, heavy polypeptide-like 1 | 379 | chr22:18862611-21597066 | 2,734,455 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — |
| 269 | chr22:18862611-21462530 | 2,599,919 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 1133 | chr22:18884862-21597066 | 2,712,204 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 994 | chr22:18884862-21462530 | 2,577,668 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 494 | chr22:18884862-21462530 | 2,577,668 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 357 | chr22:18884862-21462530 | 2,577,668 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 960 | chr22:18732920-20311918 | 1,578,998 | del | Recurrent deletion (22q11.21 BP: A-B), includes 44 genes | — | ||
| 777 | chr22:18862611-20309394 | 1,446,783 | del | Recurrent deletion (22q11.21 BP: A-B), includes 44 genes | — | ||
| 986 | chr22:18876429-20311918 | 1,435,489 | del | Recurrent deletion (22q11.21 BP: A-B), includes 44 genes | — | ||
| 857 | chr22:18876429-20397857 | 1,521,428 | del | Recurrent deletion (22q11.21 BP: A-B), includes 44 genes | — | ||
| 252 | chr22:18884862-20310127 | 1,425,265 | del | Recurrent deletion (22q11.21 BP: A-B), includes 44 genes | — | ||
| COG4 | Conserved oligomeric Golgi complex subunit 4 | 163 | chr16:70211445-71804074 | 1,592,629 | del | Includes 31 genes | — |
| EXOC3 | Exocyst complex component 3 | 1999 | chr5:19569-3546658 | 3,527,089 | del | Includes 35 genes | — |
| EXOC4 | Exocyst complex component 4 | 2749 | chr7:132446243-132977338 | 531,096 | dup | Includes 2 genes, EXOC4 could be disrupted | 5352 |
| KCNQ5 | Potassium voltage-gated channel, KQT-like | 2114 | chr6:73835991-74134200 | 298,209 | dup | Includes 8 genes, KCNQ5 could be disrupted | — |
| MAP4 | Microtubule-associated protein 4 | 3517 | chr3:48108692-48370770 | 262,078 | dup | Includes 7 genes, MAP4 could be disrupted | — |
| PRDX1 | Peroxiredoxin-1 | 3219 | chr1:45891857-46066609 | 174,752 | dup | Includes 6 genes, PRDX1 is completely duplicated | — |
| SNAP29 | Synaptosomal-associated protein 29 | 1057 | chr22:20705854-21462530 | 756,676 | del | Recurrent deletion (22q11.21 BP: B-D), includes 21 genes | — |
| 1309 | chr22:20716937-21465836 | 748,899 | del | Recurrent deletion (22q11.21 BP: B-D), includes 21 genes | — | ||
| 379 | chr22:18862611-21597066 | 2,734,455 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 269 | chr22:18862611-21462530 | 2,599,919 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 1133 | chr22:18884862-21597066 | 2,712,204 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 994 | chr22:18884862-21462530 | 2,577,668 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 494 | chr22:18884862-21462530 | 2,577,668 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| 357 | chr22:18884862-21462530 | 2,577,668 | del | Recurrent deletion (22q11.21 BP: A-D), includes >50 genes | — | ||
| SNAPIN | SNARE-associated protein Snapin | 2324 | chr1:153482037-153634059 | 152,022 | dup | Includes 11 genes, SNAPIN could be disrupted | 6079 |
| 2476 | chr1:153618767-153727633 | 108,866 | dup | Includes 5 genes, SNAPIN is completely duplicated | 6079 | ||
The table shows schizophrenia candidate genes identified in our study that are included in CNV regions from 3391 patients with schizophrenia and 3181 controls reported by the International Schizophrenia Consortium (2008). Chromosomal location, size, and rearrangement type are listed for each CNV. Genomic coordinates are provided in the most recent genome build (GRCh37/hg19). bp, base pairs; dup, duplication; del, deletion; BP, break point; —, absent. Patient ID numbers in bold are the same cases with a hemideletion of both SNAP29 and CLTCL1.