Table 1.
Retrotransposition events associated with human disease
| Insertion | Gene | CHR | Reference | Disease | Subfamily | Size | polyA tail length | Truncation | Transduction (bp) | Strand | Exon/Intron/Mechanism | Target-site duplication (TSD) | L1 EN site (5′-TTTT/AA-3′) | Note | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Alu | ABCD1 | X | Kutsche et al. 2002 [255] | ALD | AluYb9 | 98 | 20 | Y/5′TR | N | S | 4.7 kb Deletion | No TSD | ATTT/GT | |
| 2 | Alu | ATP7A | X | Gu et al. 2007 [256] | Menkes Disease | AluYa5a2 | 282 | 89 | N | N | AS | E | AAAAAGGACAGC | TTTT/AT | |
| 3 | Alu | BTK | X | Lester et al. 1997 [257] | XLA | AluY | N/A | N/A | N/A | N | AS | E | N/A | N/A | |
| 4 | Alu | BTK | X | Conley et al. 2005 [258] | XLA | AluY | 281 | 74 | N | N | S | E | AGAAATGTATGAGTAAGT | TTCT/AT | Same insertion site Conley et al. SVA |
| 5 | Alu | CD40LG | X | Apoil et al. 2007 [259] | HIGM | AluYb8 | 292 | 8 | N | N | AS | E | AAAAATTTTC | TTTT/AT | |
| 6 | Alu | CLCN5 | X | Claverie-Martin et. al. 2003 [260] | Dent’s Disease | AluYa5 | 281 | 50 | N | N | S | E | AGAAAATGCTCGAAAGA | TTCT/AT | |
| 7 | Alu | CTRC | 1 | Masson et. al. 2013 [160] | Chronic pancreatitis | Alu | 31 | 11 | Y/5′TR | N | AS | 53.9 kb Deletion | N/A | TCTT/AT | Deletes entire CTRC and ELA2A genes |
| 8 | Alu | PKLR | 1 | Lesmana et. al. 2015 [159] | Severe Hereditary Nonspherocytic Hemolytic Anemia | Yb8 | 288 | 70 | N | N | S | E | AAGATCATCAGCAAA | TCTT/GA | consanguinity, consensus Yb8 |
| 9 | Alu | FVIII | X | Sukarova et. al. 2001 [261] | Hemophilia A | AluYb8 | 290 | 47 | N | N | AS | 3 nt Deletion | No TSD | TTTC/AT | |
| 10 | Alu | FVIII | X | Ganguly et. al. 2003 [262] | Hemophilia A | AluYb9 | 288 | 37 | N | N | AS | I/Splicing | AAAAACCAACAGG | TTTT/AT | Consensus Yb9 |
| 11 | Alu | FVIII | X | Green et. al. 2008 [263] | Hemophilia A | AluYb8 | FL | N/A | N | N | AS | E | N/A | ||
| 12 | Alu | FIX | X | Vidaud et al. 1993 [264] | Hemophilia B | AluYa5a2 | 244 | 78 | Y/5′TR | N | S | E | AAGAATGGCAGATGCGA | TCTT/AA | Same insertion site as Wulff et al. Alu |
| 13 | Alu | FIX | X | Wulff et al. 2000 [265] | Hemophilia B | AluYa5a2 | 237 | 39 | Y/5′TR | N | S | E | AAGAATGGCAGATGC | TCTT/AA | Same insertion site as Vidaud et al. Alu |
| 14 | Alu | FIX | X | Li et al. 2001 [266] | Hemophilia B | AluY | 279 | 40 | Y/5′TR | N | AS | E | AAGAAACTGGTCCC | TCTT/AA | |
| 15 | Alu | GK | X | Zhang et al. 2000 [267] | GKD | AluYc1 | 241 | 74 | Y/5′TR | N | AS | I | AAAAAATAAG | TTTT/AA | |
| 16 | Alu | IL2RG | X | Lester et al. 1997 [257] | XSCID | AluYa5 | N/A | N/A | N/A | N | AS | I | N/A | N/A | |
| 17 | Alu | CRB1 | 1 | den Hollander et al. 1999 [268] | RP | AluY | 244 | 70 | Y/5′TR | N | AS | E | AAGAGTAAAGATGA | TCTT/GA | |
| 18 | Alu | SERPINC1 | 1 | Beauchamp et al. 2000 [269] | Type 1 ATP | Alu | 6 | 40 | Y/5′TR | N | AS | 1.4 kb Deletion | N/A | TTCT/AT | Shortest Alu insertion |
| 19 | Alu | ALMS1 | 2 | Taşkesen et al. 2012 [270] | Alström syndrome | AluYa5 | 257 | 76 | Y/5′TR | N | S | E | AAAAGCCTAGAGAA | TTTT/AA | |
| 20 | Alu | MSH2 | 2 | Kloor et al. 2004 [271] | HNPCC | AluJ | 85 | 40 | Y/5′TR | N | S | E | N/A | N/A | Contains extra 99 nt 3′-of Alu, may be transduction or recombination |
| 21 | Alu | MSH2 | 2 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 22 | Alu | ZFHX1B | 2 | Ishihara et al. 2004 [272] | MWS | AluYa5 | 281 | 93 | N | N | S | E | AAAATTAAAACA | TTTT/AA | |
| 23 | Alu | BCHE | 3 | Muratani et al. 1991 [273] | Cholinesterase deficiency | AluYb9 | 289 | 38 | N | N | S | E | AAAAATATTTTTTCC | TTTT/AA | |
| 24 | Alu | CASR | 3 | Janicic et al. 1995 [274] | FHH and NSHPT | AluYa5 | 280 | 93 | N | N | AS | E | GAAAGCGTGAGCTGC | TTTC/AA | |
| 25 | Alu | HESX1 | 3 | Sobrier et al. 2005 [275] | Anterior Pituitary Aplasia | AluYb8 | 288 | 30 | N | N | S | E | AGAAAATGTCTTTAGA | TTCT/AA | |
| 26 | Alu | OPA1 | 3 | Gallus et al. 2010 [276] | ADOA | AluYb8 | 289 | 25 | N | N | AS | I/Splicing | AAAAATTTTAAAAAGTT | TTTT/AC | |
| 27 | Alu | MLVI2 | 5 | Economou-Pachnis and Tsichlis 1985 [277] | Associated with leukemia | AluYa5 | 280 | 26 | N | N | AS | I | GAAAATGT | TTTC/AT | |
| 28 | Alu | APC | 5 | Halling et al. 1999 [278] | Hereditary desmoid disease | AluYb8 | 278 | 40 | Y/5′TR | N | S | E | AAGAATAATG | TCTT/AA | Same insertion site as Miki et al. L1 |
| 29 | Alu | APC | 5 | Su et al. 2000 [279] | FAP | AluYb9 | 93 | 60 | Y/5′TR | N | AS | I/Splicing | No TSD | TTTT/AA | 1.6 kb intronic deletion |
| 30 | Alu | APC | 5 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 31 | Alu | MAK | 6 | Tucker et al. 2011 [280], Edwin Stone, personal communication | RP | AluYb8 | 281 | 57 | N | N | AS | E | AAAGAAAAAA | CTTT/AA | Identified by exome resequence |
| 32 | Alu | NT5C3 | 7 | Manco et al. 2006 [281], Leticia Ribeiro, personal communication | Chronic hemolytic anemia | Alu Ya5 | 281 | 36 | N | N | S | E | AAGAATGGCAGATGG | TCTT/AA | |
| 33 | Alu | CFTR | 7 | Chen et al. 2008 [282] | Cystic Fibrosis | AluY | 46 | 57 | Y/5′TR | N | AS | E | AAGAATCCCACCTATAAT | TCTT/AA | |
| 34 | Alu | CFTR | 7 | Chen et al. 2008 [282] | Cystic Fibrosis | AluYa5 | 281 | 56 | N | N | S | E | AATAGAAATGATTTTTGTC | TCTC/AT | 3′-Processing of (5′-CTC-3′) |
| 35 | Alu | EYA1 | 8 | Abdelhak et al. 1997 [283] | BOR syndrome | AluYa5 | n/a | 97,31 | N/A | N | AS | E | AAAAAATAAATGTGTG | TTTT/AA | PolyA tail shortening between generations |
| 36 | Alu | LPL | 8 | Okubo et al. 2007 [284] | LPL deficiency | AluYb9 | 150 | 60 | Y/5′TR | N | AS | 2.2 kb Deletion | No TSD | TTTT/AA | |
| 37 | Alu | CHD7 | 8 | Udaka et al. 2007 [285] | CHARGE syndrome | AluYa5/8 | 75 | 100 | Y/5′TR | N | S | 10 kb Deletion | No TSD | ATTT/AA | |
| 38 | Alu | POMT1 | 9 | Bouchet et al. 2007 [286] | Walker Warburg syndrome | AluYa5 | 290 | 53 | N | N | AS | E | AAAAAGAGATGTACTG | TTTT/AC | |
| 39 | Alu | FGFR2 | 10 | Oldridge et al. 1999 [287] | Apert syndrome | AluYa5 | 283 | 69 | N | N | AS | I/Splicing | AGAAAACAAGGGAAGCA | TTCT/AG | |
| 40 | Alu | FGFR2 | 10 | Oldridge et al. 1999 [287] | Apert syndrome | AluYb8 | 288 | 47 | N | N | AS | E | AGAATTACCCGCCAAG | TTCT/AT | |
| 41 | Alu | FGFR2 | 10 | Bochukova et al. 2009 [288] | Apert syndrome | AluYk13 | 214 | 12 | Y/5′TR | N | AS | E | AAAAGTTACATTCCG | TTTT/GA | |
| 42 | Alu | FAS | 10 | Tighe et al. 2002 [289] | ALPS | AluYa5 | 281 | 33 | N | N | AS | I | AGAATATTCTAAATGTG | TTCT/AA | |
| 43 | Alu | SERPING1 | 11 | Stoppa-Lyonnet et al. 1990 [290] | HAE | AluYc1 | 285 | 42 | N | N | S | I | AAAAATACAAAAATTAG | TTTT/AG | |
| 44 | Alu | HMBS | 11 | Mustajoki et al. 1999 [291] | AIP | AluYa5 | 279 | 39 | N | N | AS | E | AAGAATCTTGTCCC | TCTT/GA | |
| 45 | Alu | ATM | 11 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 46 | Alu | GNPTAB | 12 | Tappino et al. 2008 [292] | ML II | AluYa5 | 279 | 17 | N | N | AS | E | AAAAACAACAACTGAG | TTTT/GA | |
| 47 | Alu | BRCA2 | 13 | Miki et al. 1996 [293] | Breast Cancer | AluYc1 | 281 | 62 | N | N | S | E | AATCACAGGC | GATT/AT | |
| 48 | Alu | BRCA2 | 13 | Teugels et al. 2005 [294] | Breast Cancer | AluYa5 | 285 | N/A | N | N | S | E | AAGAATCTGAACAT | TTCT/GC | 3′ Processing 2 nt (5′-CT-3′) |
| 49 | Alu | BRCA2 | 13 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 50 | Alu | BRCA2 | 13 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 51 | Alu | BRCA2 | 13 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 52 | Alu | BRCA2 | 13 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 53 | Alu | BRCA2 | 13 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 54 | Alu | BRCA2 | 13 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 55 | Alu | BRCA2 | 13 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 56 | Alu | BRCA2 | 13 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 57 | Alu | PMM2 | 16 | Schollen et al. 2007 [295] | CDG-Ia | AluYb8 | 263 | 10 | Y/5′TR | N | AS | 28 kb Deletion | No TSD | TTTT/AA | |
| 58 | Alu | PALB2 | 16 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 59 | Alu | BRCA1 | 17 | Peixoto et al. 2013 [161] | Breast and Ovarian Cancer Family | AluYc | 191 | 60 | Y/5′TR | N | AS | 23.3 kb Deletion | No TSD | CTTT/AG | |
| 60 | Alu | BRCA1 | 17 | Teugels et al. 2005 [294] | Breast Cancer | AluS | 286 | N/A | N | N | S | E | GAAAAAGAATCTGCTTT | TTTC/GA | |
| 61 | Alu | BRCA1 | 17 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 62 | Alu | NF1 | 17 | Wallace et al. 1991 [23] | NF1 | AluYa5 | 282 | 40 | N | N | AS | I/Splicing | AAAAAAAAAAACAT | TTTT/AA | First report of de novo Alu insertion |
| 63 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluY | 280 | N/A | N | N | S | I | AAAAAATTCAG | TTTT/AA | Same insertion site as Wimmer et al.a |
| 64 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluY | 281 | N/A | N/A | N | AS | I | N/A | ||
| 65 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYa5 | 282 | 60 | N | N | S | E | ATAAATAGCCTGGA | TTAT/AA | |
| 66 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYa5 | 284 | 120 | N | N | AS | E | AAAAAACTTGCT | TTTT/GA | Same insertion site as Wimmer et al.c |
| 67 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYa5 | 281 | N/A | N | N | AS | E | AAAAAACTTGCTGATGG | TTTT/GA | Same insertion site as Wimmer et al.c |
| 68 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYa5 | 284 | 110 | N | N | AS | E | AATAAAACCTAAAGA | TATT/GA | |
| 69 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYa5 | 279 | N/A | N | N | S | E | AAAAGAAGAACATAT | TTTT/GT | Same insertion site as Wimmer et al.b |
| 70 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYa5 | 264 | 60-85 | Y/5′TR | N | AS | E | AAGAAGTGCGGTACCT | TCTT/GA | |
| 71 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYb8 | 249 | 121 | Y/5′TR | N | S | E | AAAGCAGTGC | CTTT/AT | |
| 72 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYb8 | 288 | N/A | N | N | AS | I | AAAAAAGAGAAAGACAA | TTTT/AA | Same insertion site as Wimmer et al.a |
| 73 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYb8 | 289 | 120 | N | N | AS | E | AACAATGGTCTT | TGTT/AA | |
| 74 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYb8 | 288 | 78-178 | N | N | S | E | AAACAATGATGTTA | TTTC/AA | 3′ Processing of 1 nt (C) |
| 75 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYb8 | 288 | 118 | N | N | S | E | AAAAGAAGAACATAT | TTTT/GT | Same insertion site as Wimmer et al.b |
| 76 | Alu | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | AluYb8 | 268 | 121 | Y/5′TR | N | AS | I | AAAAAACAAACAAACA | TTTT/GT | |
| 77 | L1 | CYBB | X | Meischl et al. 1998 [297], Brouha et al. 2002 [181] | CGD | L1 Ta | 1722 | 101 | Y/5′TR | Y (280) | S | E | AA | TGTT/GA | Maternal Meiosis I |
| 78 | L1 | CYBB | X | Meischl et al. 2000 [298] | CGD | L1 Ta | 836 | 69 | Y/5′TR/INV | N | S | I/Splicing | AGAAATAACTATTTAA | TTCT/AA | |
| 79 | L1 | CHM | X | van den Hurk et al. 2003 [177] | Choroideremia | L1 Ta | 6017 | 71 | FL | Y (119/406) | AS | E | AGAAGATCAATTAG | TTCT/AA | Insertion in Early Development |
| 80 | L1 | DMD | X | Musova et al. 2006 [299] | DMD | L1 Ta | 452 | 41 | Y/5′TR/INV | N | AS | E | AAATATCTTTATATCA | ATTT/AA | |
| 81 | L1 | DMD | X | Narita et al. 1993 [164] | DMD | L1 Ta | 608 | 16 | Y/5′TR | N | AS | E | No TSD | TCTT/AA | 2 nt deletion |
| 82 | L1 | DMD | X | Holmes et al. 1994 [176] | DMD | L1 Ta | 1400 | 38 | Y/5′TR/INV | Y(489) | S | E | AAATCATCTGCTGCT | ATTT/AA | First Report of L1 3′TR |
| 83 | L1 | DMD | X | Yoshida et al. 1998 [300] | XLDCM | L1 Ta | 530 | 73 | Y/5′TR | N | AS | 5′-UTR/Loss of mRNA | AAAAAAAACCTGGTAAA | TTTT/AT | Tissue specific loss of mRNA |
| 84 | L1 | DMD | X | E Bakker & G van Omenn, personal communication | DMD | N/A | 878 | N/A | Y/5′TR | N | S | N/A | N/A | N/A | |
| 85 | L1 | DMD | X | Awano et al. 2010 [301], Solyom et al. 2011 [302] | DMD | L1 Ta | 212 | 118 | Y/5′TR | Y (212) | AS | E | GAA | TTTC/AA | Orphan 3′-transduction |
| 86 | L1 | FVIII | X | Kazazian et al. 1988 [22] | Hemophilia A | L1 Ta | 3800 | 54 | Y/5′TR | N | S | E | AAAGACAAACAAAAC | CTTT/AA | First report of de novo L1 insertion |
| 87 | L1 | FVIII | X | Kazazian et al. 1988 [22] | Hemophilia A | L1 preTa | 2300 | 77 | Y/5′TR/INV | N | AS | E | AATGTTTCCTTCTTTTC | CATT/AA | |
| 88 | L1 | FIX | X | Li et al. 2001 [266] | Hemophilia B | L1 Ta | 463 | 68 | Y/5′TR | N | S | E | AAAAATAGTGCTGATA | TTTT/AC | |
| 89 | L1 | FIX | X | Mukherjee et al. 2004 [303] | Hemophilia B | L1 Ta | 163 | 125 | Y/5′TR | N | S | E | GAAAAATGGATTGT | TTTC/AT | |
| 90 | L1 | RP2 | X | Schwahn et al. 1998 [304] | XLRP | L1 Ta | 6000 | 64 | FL | N | S | I/Loss of mRNA | AAGACTGTAAGGTG | TCTT/AA | Interrupted polyA |
| 91 | L1 | RPS6KA3 | X | Martinez-Garay et al. 2003 [305] | Coffin-Lowry syndrome | L1 Hs | 2800 | Yes | Y/5′TR/INV | N | AS | E | AAGAAAACCTGCATTT | TCTT/AG | |
| 92 | L1 | ABDH5 | 3 | Samuelov et al. 2011 [306], Eli Sprecher, personal communication | CDS | N/A | FL | N/A | N | N/A | N | I/Splicing | N/A | N/A | |
| 93 | L1 | MLH1 | 3 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 94 | L1 | MLH1 | 3 | Qian et al. 2015 [158] | Hereditary Cancer | N/A | N/A | N/A | N/A | N/A | N/A | E | N/A | N/A | Pan-cancer panel testing |
| 95 | L1 | APC | 5 | Miki et al. 1992 [200] | Colon cancer | L1Ta | 520 | 222 | Y/5′TR/INV | N | S | E | AAGAATAATG | TCTT/AA | Somatic Insertion/same insertion site as Halling et al. Alu |
| 96 | L1 | EYA1 | 8 | Morisada et al. 2010 [247] | BOR syndrome | L1 Hs | 3756 | None | Y/3′TR | N | AS | 17 kb Deletion | No TSD | TCTC/AG | Internal Priming |
| 97 | L1 | FKTN | 9 | Kondo-Iida et al. 1999 [307] | FCMD | L1Ta | 1200 | 59 | Y/5′TR | N | S | I/Splicing/6 nt Deletion | No TSD | TTTT/AA | |
| 98 | L1 | SETX | 9 | Bernard et al. 2009 [308], Christine Zühlke, personal communication | AOA2 | L1 Hs | 1300 | 42 | Y/5′TR/INV | N | S | E | GGAAGAATGTGAACTGGCTA | TTCC/AG | 3′-processing 2 nt (5′-CC-3′) |
| 99 | L1 | PTEN | 10 | Helman et al. 2014 [201] | endometrial carcinoma | L1 Hs | 90 | 22 | Y/5′TR | N | S | E | AAAGAATCATCTGGATTATAG | CTTT/AA | Somatic Insertion |
| 100 | L1 | HBB | 11 | Divoky et al. 1996 [309] | β-thalassemia | L1 Ta | 6000 | 107 | FL | N | AS | I | AAAATAAAAGCAGA | TTTT/AT | |
| 101 | L1 | PDHX | 11 | Mine et al. 2007 [310] | PDHc deficiency | L1 Hs | 6086 | 67 | FL | N | S | 46 kb Deletion | No TSD | TTTT/AT | |
| 102 | L1 | SLCO1B3 | 12 | Kagawa et al. 2015 [157] | Rotor syndrome | L1 Ta-1d | 5989 | 100 | Near FL | N | S | I/Splicing | AAGAATTAATAGTGACAGT | TCTT/AC | 0.054 Japanese Allele Frequency, may be “Hot L1” |
| 103 | L1 | RB1 | 13 | Rodriguez-Martin et al.2016 [202] | Familial Retinoblastoma | L1 Ta-1d | 6044 | 33 | FL | N | S | I/Splicing | AAATTATCTGTTTC | ATTT/AA | N/A |
| 104 | L1 | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | L1 preTa | 1800 | N/A | Y/5′TR | N | S | E | AAAAACGAAACTGTGT | TTTT/AT | Untemplated 3′- T? |
| 105 | L1 | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | L1 Ta | 6000 | N/A | FL | N | S | E | AAAAATCGAGGG | TTTT/AA | Untemplated 3′- T? |
| 106 | L1 | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | N/A | 2200 | N/A | Y/5′TR/INV | N | AS | I/Splicing | AAGAAAATGGT | TCTT/AA | |
| 107 | SVA | BTK | X | Rohrer et al. 1999 [311], Conley et al. 2005 [258] | XLA | N/A | 251 | 92 | Y/5′TR | N | S | E | AGAAATGTATGAGTAA | TTCT/AT | Same insertion site as Conley et. al. Alu |
| 108 | SVA | TAF1 | X | Makino et al. 2007 [312] | XDP | F | 2627 | 62 | FL | N | AS | I | AAAAAAAAAAAATGAAATAG | TCCT/AT | 3′-Processing 3 nt (5′-CCT-3′) |
| 109 | SVA | FIX | X | Nakamura et.al. 2015 [156] | Hemophilia B | F | 2524 | 28 | FL | N | AS | E | AAATGGCACTAGAA | TTCC/AT | 3′-Processing 1 nt (5′-C-3′) |
| 110 | SVA | LDRAP1 | 1 | Wilund et al. 2002 [313] | ARH | E | 2600 | 57 | FL | N | S | I/Splicing | GAAACCTGTTTTCTC | TTTC/AA | |
| 111 | SVA | SPTA1 | 1 | Hassoun et al. 1994 [314], Ostertag et al. 2003 [24] | HE and HPP | E | 632 | 50 | Y/5′TR/INV | Y (183/599) | S | E | GAAATTTGAAGACTTCCAAGT | TTTC/AA | Orphan 3′-transduction |
| 112 | SVA | CASP8 | 2 | Stacey et al. 2016 [203] | Breast Cancer Susceptibility | E | 2782 | N/A | FL | N | AS | I/Decreased RNA | AAGAATTTGA | TCTT/AT | Protective against prostate cancer; active locus? |
| 113 | SVA | A4GNT | 3 | Nazaryan et al. 2015 [155] | Chromothripsis | E | 502 | None | Y/5′TR (VNTR) | N | AS | I | N/A | TTTT/GA | First report of large scale rearrangement and an insertion. Implicates retrotransposition in germline chromothripsis. |
| 114 | SVA | HLA-A | 6 | Takasu et al. 2007 [315] | Leukemia | F1 | 2000 | 45 | FL | N/A | AS | 14 kb Deletion | N/A | CCTT/AG | Novel SVA subfamily (F1) |
| 115 | SVA | PMS2 | 7 | van der Klift et al. 2012 [154] | Lynch syndrome | F | 2200 | 64 | Y/5′TR (VNTR) | N | S | I/Splicing | AAGAATGTGCCATGTGA | TCTT/AA | SVA exonization |
| 116 | SVA | FKTN | 9 | Kobayashi et al. 1998 [162] | FCMD | E | 3023 | 32 | FL | N | S | 3′UTR/Splicing | AAGAAAAAAAAAATTGT | TCTT/AA | |
| 117 | SVA | PNPLA2 | 11 | Akman et al. 2010 [316] | NLSDM | E | 1800 | 44 | Y/5′TR | N | S | E | AAAGAGGCCCGG | CTTT/AG | |
| 118 | SVA | SUZ1P | 17 | Vogt et al. 2014 [153] | NF1 | F1 | 1700 | 23 | Y/5′TR (VNTR) | Y (282/160) | AS | I/Deletion of NF1 | N/A | TTTT/AC | Largest reported insertion associated deletion (~1 Mb), somatic |
| 119 | SVA | SUZ1P | 17 | Vogt et al. 2014 [153] | NF1 | F | 1300 | 40 | Y/5′TR (VNTR) | N | AS | I/Deletion of NF1 | N/A | CTTT/AC | 867 kb deletion, somatic |
| 120 | Processed Pseudogene | CYBB | X | de Boer et al. 2014 [152] | CGD | N/A | 5739 | 100 | FL | No | AS | I/Splicing | AAAACTCAAAGACTC | TTTT/AA | First reported de novo processed pseudogene (TMF1) |
| 121 | pA | COL4A6 | X | Segal et al. 1999 [317] | Alport syndrome | N/A | N/A | 70 | N/A | N/A | AS | 13.4 kb Deletion | No TSD | TTCT/AT | |
| 122 | pA | AGA | 4 | Jalanko et al. 1995 [318] | AGU | N/A | N/A | 37 | N/A | N/A | AS | 2 kb Deletion | No TSD | TTCT/AA | |
| 123 | pA | BRCA2 | 13 | Wang et al. 2001 [319] | Breast Cancer | N/A | N/A | 35 | N/A | N/A | S | 6.2 kb Deletion | No TSD | TTCT/AA | |
| 124 | pA | NF1 | 17 | Wimmer et al. 2011 [296] | NF1 | N/A | 130 | 120 | N/A | N/A | AS | E | AAGAAA | TCTTNAA |
Data for this table were compiled from the primary references listed and reports prior to 2009 are reviewed in the following: Ostertag and Kazazian 2001 [35], Chen et al. 2006 [150], Belancio et al. 2008 [151], Hancks and Kazazian 2012 [86]
A few insertions were left off the list as they were common polymorphisms or did not cause disease. The following websites and databases were used in the analysis: http://www.repeatmasker.org/, Repbase (http://www.girinst.org/), http://dbrip.brocku.ca/, The following symbols, a,b,c, indicate same insertion site in Wimmer et al. [296]
Abbreviations: TR truncation, INV inversion, E exon, FL full-length, I intron
Disease acronyms: ADOA Autosomal dominant optic atrophy, AGU Aspartylglucosaminuria, AIP Acute intermittent porphyria, ALD Adrenoleukodystrophy, ALPS Autoimmune lymphoproliferative syndrome, AOA2 Ataxia with oculomotor apraxia 2, ARH Autosomal recessive hypercholesterolemia, BOR Branchio-oto-renal syndrome, CDG-Ia Congenital disorders of glycosylation type Ia, CDS Chanarin-Dorfman syndrome, CGD Chronic granulomatous disease, DMD Duchenne muscular dystrophy, FAP Familial adenomatous polyposis, FCMD Fukuyama-type congenital muscular dystrophy, FHH and NSHPT Familial hypocalciuric hypercalcemia and neonatal severe hyperparathyroidism, GKD Glycerol kinase deficiency, HAE Hereditary form of angioedema, HE and HPP Hereditary elliptocytosis and hereditary pyropoikilocytosis, HIGM Hyper-immunoglobulin M syndrome, HNPCC Hereditary non-polyposis colorectal cancer syndrome, LPL Lipoprotein lipase, MLII Mucolipidosis Type II, MWS Mowat-Wilson syndrome, NF1 Neurofibromatosis Type I, PDHc Pyruvate dehydrogenase complex deficiency, NLSDM Neutral lipid storage disease with subclinical myopathy, RP Retinitis pigmentosa, Type 1 ATP Type 1 antithrombin deficiency, XDP X-linked dystonia-parkinsonism, XLA X-linked agammaglobulinemia, XLDCM X-linked dilated cardiomyopathy, XLRP X-linked retinitis pigmentosa, XSCID X-linked severe combined immunodeficiency