Table 1. 5′ and 3′ breakpoint locations from gross gene deletions and detection of long inverted repeats*.
| GENE/DELETION SIZE | BREAKPOINT LOCATION/NCBI ACCESSION NUMBER | 5′LIR/3′LIR | GENE/DELETION SIZE | BREAKPOINT LOCATION/NCBI ACCESSION NUMBER | 5′LIR/3′LIR |
|---|---|---|---|---|---|
| 1-BRCA1/14 kb | (3′) 16223-30238 (5′)/NT_010755.15 | +/+ | 32-PTEN/662 kb | (5′) 475951-1138023 (3′)/NT_030059.12 | +/− |
| 2-BRCA1/3.8 kb | (3′) 59697-63533 (5′)/NT_010755.15 | +/+ | 33-PTEN/13.6 kb | (5′) 607242-620845 (3′)/NT_030059.12 | +/− |
| 3-BRCA1/36.3 kb | (5′) 29197-65577 (3′)/L78833.1 | +/+ | 34-PTEN/300 kb | (5′) 612328-912640 (3′)/NT_030059.12 | −/− |
| 4-BRCA1/19.8 kb | (5′) 51483-71369 (3′)/L78833.1 | +/+ | 35-MEN1/67.7 kb | (3′) 131486-199212 (5′)/AC000134.14 | +/+ |
| 5-BRCA1/18.3 kb | (5′) 56990-75331 (3′)/L78833.1 | +/+ | 36-BTK/5.9 kb | (5′) 62499-68391 (3′)/U78027.1 | +/+ |
| 6-BRCA1/4.8 kb | (5′) 62115-66940 (3′)/L78833.1 | +/+ | 37-HBB/9.1 kb | (5′) 53257-62324 (3′)/U01317.1 | +/− |
| 7-BRCA2/5.1 kb | (5′) 3806-8872 (3′)/NC_000013.9 | +/+ | 38-ATM/3.4 kb | (5′) 73863-77312 (3′)/U82828.1 | +/+ |
| 8-BRCA2/14.3 kb | (5′) 12323-26644 (3′)/AY436640.1 | +/− | 39-MSH2/36.6 kb | (5′) 99957-136583 (3′)/AC079775.6 | +/+ |
| 9-BRCA2/7.9 kb | (5′) 27566-35513 (3′)/AY436640.1 | −/+ | 40-MSH2/2.2 kb | (5′) 104712-106890 (3′)/AC079775.6 | +/+ |
| 10-BRCA2/10.8 kb | (5′) 45138-55975 (3′)/AY436640.1 | +/+ | 41-MSH2/15.4 kb | (5′) 105900-121280 (3′)/AC079775.6 | +/+ |
| 11-BRCA2/4.9 kb | (5′) 56447-61399 (3′)/AY436640.1 | +/+ | 42-MSH2/6.7 kb | (5′) 124511-131175 (3′)/AC079775.6 | +/+ |
| 12-CDKN/33.8 kb 2A/2B | (3′) 176468-210312 (5′)/NT_008413.17 | −/+ | 43-MLH1/6.1 kb | (3′) 86839-92892 (5′)/AC006583.31 | +/+ |
| 13-NF1/99.6 kb | (5′) 238391-338000 (3′)/NT_010799.14 | −/+ | 44-MLH1/3.5 kb | (3′) 93192-96718 (5′)/AC006583.31 | −/+ |
| 14-NF1/12 kb | (5′) 347607-359613 (3′)/NT_010799.14 | +/− | 45-MLH1/14.3 kb | (5′) 145570-159901 (3′)/AC011816.17 | +/+ |
| 15-RB1/52.3 kb | (5′) 305422-357770 (3′)/NT_024524.13 | −/− | 46-MLH1/12.7 kb | (5′) 147927-160607 (3′)/AC011816.17 | +/+ |
| 16-RB1/178 kb | (5′) 312336-490300 (3′)/NT_024524.13 | +/− | 47-MSH6/11.3 kb | (5′) 5698337-5709648 (3′)/NT_034483.3 | +/+ |
| 17-RB1/201.9 kb | (5′) 356866-558723 (3′)/NT_024524.13 | +/− | 48-MSH6/21.7 kb | (5′) 5699487-5721160 (3′)/NT_034483.3 | +/+ |
| 18-RB1/40 kb | (5′) 365612-405655 (3′)/NT_024524.13 | −/+ | 49-PMS2/1.1 kb | (5′) 53291-54449 (3′)/AC005995.3 | +/+ |
| 19-RB1/3.9 kb | (5′) 378370-382275 (3′)/NT_024524.13 | +/− | 50-HEXA/7.9 kb | (3′) 449987-457933 (5′)/NT_010194.16 | −/+ |
| 20-RB1/2.4 kb | (5′) 462638-465032 (3′)/NT_024524.13 | +/− | 51-HPRT1/13.3 kb | (5′) 297453-310733 (3′)/NT_011786.15 | +/+ |
| 21-APC/435 kb | (5′) 384224-819689 (3′)/NT_034772.5 | −/+ | 52-HPRT1/159 bp | (5′) 314410-314569 (3′)/NT_011786.15 | −/− |
| 22-APC/737 kb | (5′) 529476-1266975 (3′)/NT_034772.5 | −/− | 53-LDLR/7.1 kb | (5′) 191462-198534 (3′)/NT_011295.10 | +/+ |
| 23-TSC2/8.4 kb | (5′) 417616-426044 (3′)/NT_037887.4 | +/− | 54-PAX6/1002 kb | (3′) 750100-1752166 (5′)/NT_009237.17 | −/+ |
| 24-TSC2/10.1 kb | (5′) 432071-442186 (3′)/NT_037887.4 | +/− | 55-PAX6/836 kb | (3′) 905528-1741689 (5′)/NT_009237.17 | −/− |
| 25-TSC2/916 bp | (5′) 437300-438216 (3′)/NT_037887.4 | +/+ | 56-IGHM/732 kb | (3′) 204471-936631 (5′)/NT_026437.11 | −/− |
| 26-TSC1/7.6 kb | (3′) 177985-185621 (5′)/NT_035014.4 | −/+ | 57-PKLR/1.1 kb | (5′) 9489-10630 (3′)/AY316591.1 | +/− |
| 27-ADA/3.2 kb | (3′) 500551-503808 (5′)/NT_011362.9 | +/+ | 58-LHCGR/6.1 kb | (5′) 63641-69726 (3′)/NG_008193.1 | −/+ |
| 28-WT1/7.3 kb | (3′) 32504-39823 (5′)/NC_000011.8 | −/+ | 59-F 8/19.9 kb | (5′) 105125-125067 (3′)/AY769950.1 | +/− |
| 29-DMD/7.8 kb | (3′) 152815-160602 (5′)/NT_011757.15 | +/− | 60-F 8/29.2 kb | (5′) 29349-58524 (3′)/AY769950.1 | −/− |
| 30-DMD/3.8 kb | (3′) 155384-159231 (5′)/NT_011757.15 | −/+ | 61-STS/40.1 kb | (5′) 32594-72652 (3′)/NT_011757.15 | −/− |
| 31-PTEN/453 kb | (5′) 452645-905607 (3′)/NT_030059.12 | +/+ | 62-WAS/1.9 kb | (5′) 2932-4803 (3′)/AF115549.2 | +/+ |
| 63-VWF/61 kb | (5′) 20561-81606 (3′)/NG_009072.1 | +/+ | 87-CFTR/1.5 kb | (5′) 184647-186177 (3′)/NC_000007.12 | −/− |
| 64-VWF/2.3 kb | (5′) 146608-148929 (3′)/NG_009072.1 | −/+ | 88-CFTR/21.1 kb | (5′) 18350-39431 (3′)/NC_000007.12 | +/+ |
| 65-VPS13B/1.8 kb | (5′) 8039-9822 (3′)/NG_007098.2 | +/+ | 89-CHRNE/1.3 kb | (3′) 1335845-1337134(5′)/NT_010823.11 | +/− |
| 66-SMN1/6.7 kb | (5′) 23935-30628 (3′)/NG_008691.1 | +/+ | 90-COL17A1/21 kb | (5′) 11200-32195 (3′)/NG_007069.1 | −/− |
| 67-SLC3A1/30.3 kb | (5′) 101289-131606 (3′)/AC013717.8 | +/+ | 91-CYBB/25.3 kb | (5′) 37250-62577 (3′)/NT_079573.3 | −/− |
| 68-SERPING/2.9 kb | (5′) 4337-7226 (3′)/X54486.1 | +/+ | 92-FANCA/2.1 kb | (3′) 20800-22859 (5′)/NT_010542.15 | +/+ |
| 69-SDHC/8.4 kb | (5′) 85491-93861 (3′)/AL592295.25 | +/+ | 93-FANCA/44.1 kb | (3′) 32415-76544 (5′)/NT_010542.15 | +/+ |
| 70-SALL4/8.9 kb | (3′) 23922-32811 (5′)/AL034420.16 | +/− | 94-FBN1/6.4 kb | (5′) 187965-194400 (3′)/NG_008805.1 | −/− |
| 71-PROS1/4.4 kb | (3′) 89888-94322 (5′)/NC_000003.10 | +/+ | 95-FBN1/7.1 kb | (5′) 197759-204893 (3′)/NG_008805.1 | −/+ |
| 72-PREPL/23.9 kb | (3′) 120275-144148 (5′)/AC013717.8 | −/+ | 96-FERMT1/3.9 kb | (5′) 70250-74168 (3′)/AL118505.17 | +/+ |
| 73-PREPL/38.1 kb | (3′) 123903-162024 (5′)/AC013717.8 | +/+ | 97-FGA/15.2 kb | (3′) 47644-62873 (5′)/AC107385.4 | −/− |
| 74-PKHD1/7.3 kb | (5′) 332887-340206 (3′)/AY129465.1 | −/− | 98-FOXL2/8.2 kb | (3′) 60868-69094 (5′)/AC092947.12 | −/− |
| 75-PKHD1/13.2 kb | (5′) 337078-350281 (3′)/AY129465.1 | −/+ | 99-GAA/8.3 kb | (5′) 97036-105323 (3′)/NT_024871.11 | −/− |
| 76-PKD1/2.9 kb | (5′) 18177-21076 (3′)/L39891.1 | −/− | 100-GBE1/105.7 kb | (3′) 119019-224705 (5′)/NC_000003.10 | −/+ |
| 77-PINK1/4.6 kb | (5′) 18515-23118 (3′)/NG_008164.1 | +/+ | 101-GHR/4.1 kb | (5′) 437912-442010 (3′)/NT_006576.15 | −/− |
| 78-PARK2/156 kb | (5′) 484956-641159 (3′)/NG_008289.1 | +/− | 102-GLA/4.5 kb | (3′) 30733-35251 (5′)/NT_011651.16 | +/+ |
| 79-OCA2/122.6 kb | (3′) 131887-254458 (5′)/NW_925783.1 | +/− | 103-GLA/4.6 kb | (3′) 36143-40797 (5′)/NT_011651.16 | +/+ |
| 80-NSD1/23.9 kb | (5′) 15361-39242 (3′)/NT_023133.12 | +/+ | 104-GLI3/176 kb | (3′)15719-53929(5′)/AC005026.2-AC005158.3 | +/− |
| 81-NSD1/8 kb | (5′) 170994-178991 (3′)/NT_023133.12 | +/+ | 105-GLI3/151 kb | (3′) 64730-77461 (5′)/AC005026.2-AC005158.3 | −/− |
| 82-MLC1/2.1 kb | (5′) 9586-11738 (3′)/NG_009162.1 | +/+ | 106-GLI3/1.01 Mb | (3′)154476-127754(5′)/AC012596.4- AC099798.4 | −/− |
| 83-ATP7A/15.2 kb | (3′) 12883-28093 (5′)/Z94801.1 | −/+ | 107-GLI3/728 kb | (3′) 149442-238453 (5′)/AC012596.4-AC005158.3 | +/− |
| 84-ATP7A/13.7 kb | (3′) 19564-33298 (5′)/Z94801.1 | +/+ | 108-GLI3/6.0 Mb | (3′) 7206-147487 (5′)/AC004844.1-AC005483.1 | −/+ |
| 85-ATP7A/13.7 kb | (3′) 31126-44864 (5′)/Z94801.1 | +/+ | 109-HBA1/11.2 kb | (5′) (31695-31724)-(42846-42867) (3′)/NG_000006.1 | +/+ |
| 86-AVPR2/21.5 kb | (5′) 54052-75566 (3′)/U52112.2 | +/− |
*5′ and 3′ deletion breakpoint sequences were obtained from HGMD and GRaBD. DNA sequences of gene contigs were downloaded from NCBI. DNA sequences of 5′ and 3′ breakpoints and related gene contigs were compared using NCBI-Blast, and breakpoint locations of gross gene deletions determined. LIRs within genomic regions that included gene breakpoint sequences were investigated. Abbreviations: Bp, base pair; GRaBD, gross rearrangement breakpoint database; HGMD, human gene mutation database; kb, kilobase; LIR, long inverted repeat; Mb, megabase.