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Table 2 Known de novo pathogenic retrotransposon insertions associated with deletions ≥ 100 bp in the human genome

From: SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints

Gene Chromosomal location Disease Retrotransposon (length) Length of the deletion Reference
HLA-A 6p22.1 Leukemiaa SVA_F1 (2 kb) ~14 kb [76]
ABCD1 Xq28 Adrenoleukodystrophy AluYb9 (98 bp) 4,726 bp [77]
SERPINC1 1q25.1 Antithrombin deficiency type 1 Alu (6 bp)b 1,444 bp [78]
LPL 8p21.3 Lipoprotein lipase deficiency AluYb9 (150 bp) 2.2 kb [79]
CHD7 8q12.2 CHARGE syndrome AluYa5/8 (75 bp) 10 kb [80]
PMM2 16p13.2 Congenital disorders of glycosylation type-Ia AluYb8 (263 bp) 28 kb [81]
APC 5q22.2 Familial adenomatous polyposis AluYb9 (93 bp) 1,599 bp [82]
EYA1 8q13.3 Branchio-oto-renal syndrome L1 Hs (3,756 bp) 17 kb [83]
PDHX 11p13 Pyruvate dehydrogenase complex deficiency L1 Hs (6,086 bp) 46 kb [84]
BRCA1 17q21.31 Hereditary breast/ovarian cancer AluY (~190 bp) 23,363 bp [85]
  1. aThe germline SVA insertion-associated deletion was identified in three unrelated Japanese families. Of the individuals harboring the SVA insertion-associated deletion, one individual in each family presented with leukemia.
  2. bThe affected family members harbored an intragenic 1,444 bp deletion and an insertion of a polyT tract of 40 nucleotides followed by a 6 bp sequence (5′-GAGACG-3′). This 6 bp sequence, located at the 3′end of the insertion, was homologous to the consensus sequence of the free right Alu monomer (FRAM).