Table 3.
Genes with known function identified in breakpoint regions
| Cytogenetic Band | Case | Molecular Breakpoint | Breakpoint region | Deleted region | Number of known genes | TSG/Oncogenes |
|---|---|---|---|---|---|---|
| 1p34.2 | 2 | RP11-318G20_RP11-632A13 | chr1:40,270,704-40,309,712 | 1 | ||
| 1q32.1 | 1 | RP11-1089F13_RP11-145I13 | chr1:203,989,316-205,431,690 | 26 | IKBKE, RASSF5, IL10, IL24 | |
| 2q37.1 | 4 | RP11-332L11_RP11-94I20 | chr2:234,593,254-234,594,028 | 0 | ||
| 3p21.31 | 5 | RP11-804H15_RP11-3B7 | chr3:49,112,155-49,222,551 | 8 | ||
| 3p21.31 | 6 | RP11-352L13_RP11-419G15 | chr3:48,468,265-48,572,806 | 4 | ||
| 3p21.31 | 7 | RP11-316 M24 | chr3:48,859,939-48,965,972 | 4 | ||
| 4p16.2 | 11 | 4ptel_RP11-341O1 | chr4:0-4,673,371 | 68 | GAK | |
| 4p16.3 | 8 | RP11-919N24 | chr4:2,317,528-2,486,782 | 2 | ||
| 4q12 | 10 | RP11-167A8_RP11-622J1 | chr4:58,389,737-58,916,984 | 0 | ||
| 6p12.3 | 12 | RP11-446F17_RP1-142O9 | chr6: 46,562,151-46,812,151 | 14 | ||
| 6p21.31 | 13 | RP11-666K4_RP11-652G7 | chr6:36,174,067-36,267,130 | chr6:46,715,042-49,457,682 | 2 | |
| 6p22.1 | 41 | RP11-635O11 | chr6:27,960,335-28,145,568 | 5 | ||
| 6q14.1 | 14 | RP11-1063N1_RP11-422O8 | chr6:83,875,190-83,886,368 | 1 | ||
| 7p14.3 | 15 | RP11-803J20_RP11-350H1 | chr7:32,469,044-33,359,385 | 10 | ||
| 7q22.2 | 37 | RP11-251G23 | chr7:104,957,075-105,071,488 | 3 | RINT1 | |
| 8p12 | 38 | RP11-346L1_RP11-113G10 | chr8:37,687,186-37,715,876 | 1 | ||
| 9p22.3 | 46 | RP11-307K19_RP11-518K17 | chr9:15,455,865-15,456,627 | 1 | ||
| 9p24.1 | 50 | RP11-1084A8 | chr9:6,611,140-6,861,140 | 2 | KDM4C | |
| 9q22.31 | 17 | RP11-412A12 | chr9:93,553,640-93,708,694 | 1 | ||
| 10p11.22 | 39 | RP11-241I20 | chr10:32,303,829-32,447,252 | 1 | ||
| 11p15.4 | 46 | RP11-120E20 | chr11:3,573,461-3,758,006 | 5 | ART1, NUP98 | |
| 11q12.1 | 50 | RP11-624G17 | chr11:56,953,550-57,164,109 | 10 | ||
| 11q13.1 | 19 | RP11-665N17_RP11-821O7 | chr11:64,481,470-65,571,636 | 57 | FAU, SYVN1, RELA, CFL1, CST6 | |
| 11q14.2 | 48 | RP11-185J12_RP11-417F7 | chr11: 85,874,712-124,646,245 | 297 | TSG11, CADM1, FAT3, MLL, ATM, YAP1, ZBTB16, THY1, SDHD, ARHGEF12, BTG4, PPP2R1B, NOX4, POU2F3, TBRG1, TAGLN, CBL | |
| 11q21 | 20 | RP11-8N17 | chr11:95,755,457-95,909,884 | 2 | ||
| 12p13.32 | 43 | RP11-319E16 | chr12:5,163,930-5,344,301 | 0 | ||
| 12q13.13 | 41 | RP11-199A1_RP11-714I16 | chr12:50,423,209-50,425,214 | 1 | ||
| 12q13.2 | 22 | RP11-559I11_RP11-973D8 | chr12:54,583,954-54,618,511 | 2 | ||
| 12q23.3 | 21 | RP11-643D8_RP11-711H11 | chr12:103,271,502-103,364,761 | 0 | ||
| 12q24.21 | 24 | RP11-812F13_RP11-379F8 | chr12:114,705,782-115,018,181 | 1 | ||
| 12q24.31 | 23 | RP11-197N18_RP11-338K17 | chr12:121,978,125-122,877,008 | 19 | ||
| 13q14.12 | 25 | RP11-106H11_RP11-24B19 | chr13:45,658,774-50,678,660 | 33 | RB1, ARL11, TRIM13, FAM10A4 | |
| 14q11.2 | 18 | RP11-749G5_RP11-298I3 | chr14:22,375,744-22,435,254 | 3 | ||
| 14q24.2 | 27 | RP11-667E7 | chr14:71,230,541-71,415,068 | 1 | ||
| 14q32.31 | 49 | RP11-350L3_RP11-114H15 | chr14:101,273,490-101,716,645 | HSP90AA1 | ||
| 15q22.2 | 27 | RP11-74K1 | chr15:58,530,516-58,531,032 | 1 | ||
| 15q24.1 | 40 | RP11-247C2 | chr15:72,158,366-72,251,969 | 3 | ||
| 15q24.1 | 49 | RP11-247C2 | chr15:72,158,366-72,251,969 | 3 | ||
| 15q24.3 | 28 | RP11-20 M10 | chr15:75,965,658-76,128,067 | 3 | ||
| 16p11.2 | 29 | RP11-779B17 | chr16:31,786,062-31,995,517 | 1 | ||
| 16q24.3 | 30 | RP11-79A1 | chr16:88,125,792-88,522,693 | 9 | ||
| 17p13.1 | 30 | RP11-89D11 | chr17:7,436,436-7,603,767 | 18 | TP53 | |
| 17p13.3 | 33 | RP5-1029F21 | chr17:343,377-440,727 | 1 | VPS53 | |
| 17q21.2 | 31 | RP11-156A24 | chr17:36,841,610-37,007,910 | 9 | ||
| 17q25.3 | 32 | RP11-46E14 | chr17:75,316,874-75,477,363 | 4 | ||
| 19q13.32 | 34 | RP11-846 M4 | chr19:51,889,293-52,103,962 | 6 | ||
| 20q13.33 | 42 | RP4-591C20_RP11-266K16 | chr20:62,100,354-62,267,316 | 9 | ||
| 21q22.13 | 35 | RP11-777J19_RP11-105O24 | chr21:37,641,259-37,872,927 | 1 | ||
| Xq13.1 | 36 | RP11-69L22_RP11-237F13 | chrX:68,857,148-68,969,387 | 1 |
The number of the genes with known function mapping in the breakpoint regions or located inside the deleted regions was reported for each case. Known oncogenes and TSGs have been identified according to the NCBI.