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. Author manuscript; available in PMC: 2015 Nov 1.
Published in final edited form as: Hum Mutat. 2014 Nov;35(11):1342–1353. doi: 10.1002/humu.22680

Table 3.

Exact Breakpoint Coordinates and Characteristics of Deletions Determined by Cloning and Sequencing in FA Families

FAM ID No.Δ FA
Gene		 Δ Start Δ End Δ size
(bps)		 Cen Rep Cen Rep Start Cen Rep End +/− Tel
Rep		 Tel Rep Start Tel Rep End +/− Overlap
or
Insertion bps* 		Potential
Mechanism		 Alu
-
Alu 		Δ Exons
2 1 A 88,172,538 88,337,600 165,063 AluSx 88,172,387 88,172,690 + AluSp 88,337,451 88,337,757 + 11 NAHR Y 37–43
4 1 A 88,224,066 88,408,991 184,926 NR AluSx 88,408,947 88,409,245 − 3 alt-EJ N 3–43
7 1 A 88,250,100 88,425,360 175,261 AluY 88,250,056 88,250,345 − AluY 88,425,297 88,425,605 − 27 NAHR Y 1–43
8 1 A 88,257,445 88,409,236 151,792 AluSp 88,257,167 88,257,453 − AluSx 88,408,947 88,409,245 − 26 NAHR Y 3–43
10 1 A 88,285,490 88,362,122 76,633 NR NR 2 alt-EJ N 27–43
11 1 A 88,302,909 88,483,387 180,479 NR NR 4 alt-EJ N 1–43
13 1 A 88,322,270 88,505,839 183,570 AluSx 88,322,116 88,322,301 − AluY 88,505,703 88,506,000 − 24 NAHR Y 1–43
14 1 A 88,327,695 88,377,962 50,268 NR AluSp 88,377,678 88,377,968 − 2 alt-EJ N 16–43
15 1 A 88,329,020 88,355,305 26,286 AluSx 88,328,786 88,329,049 + AluY 88,355,047 88,355,357 + 11 NAHR Y 30–43
17 1 A 88,331,201 88,352,999 21,799 AluSg 88,331,149 88,331,450 + AluY 88,352,948 88,353,258 + 4 NAHR Y 30–43
18 1 A 88,331,357 88,351,875 20,519 AluSg 88,331,149 88,331,450 + AluSx 88,351,789 88,352,065 − 2 alt-EJ YO 31–43
19 1 A 88,331,930 88,415,141 83,212 NR AluSx 88,415,082 88,415,384 − 2 alt-EJ N 1–43
21 1 A 88,336,484 88,414,112 77,629 AluY 88,336,437 88,336,568 + AluSx 88,414,066 88,414,360 + 36 NAHR Y 1–37
23_d1 2 HE A 88,341,384 88,375,356 33,973 AluSg 88,341,341 88,341,647 + AluY 88,375,302 88,375,614 + 21 NAHR Y 18–33
24 2 HO A 88,344,051 88,347,742 3,692 AluJ FLAM 88,343,990 88,344,068 + AluSx 88,347,682 88,347,981 + 31 NAHR Y 31
25 1 A 88,344,194 88,355,131 10,938 AluY 88,344,109 88,344,414 + AluY 88,355,047 88,355,357 + 7 NAHR Y 30–31
26 2 HO A 88,344,637 88,404,186 59,550 AluSq 88,344,416 88,344,697 + AluSx 88,403,786 88,403,949 + 17 NAHR Y 6–31
27 1 A 88,345,159 88,389,286 44,128 AluJb 88,345,131 88,345,394 + AluSx 88,389,257 88,389,566 + 10 NAHR Y 12–31
28_d1 2 HE A 88,345,766 88,460,603 114,838 AluY 88,345,678 88,345,977 − AluY 88,460,509 88,460,817 − 45 NAHR Y 1–31
29 1 A 88,347,917 88,433,278 85,362 AluSx 88,347,682 88,347,981 + AluY 88,432,969 88,433,298 + 11 NAHR Y 1–30
30 1 A 88,348,428 88,353,975 5,548 AluSq 88,348,275 88,348,577 − NR graphic file with name nihms626669t1.jpg FoSTeS/MMBIR N 30
31 1 A 88,351,156 88,359,359 8,204 AluSx 88,350,890 88,351,168 − NR ins. 29bps FoSTeS/MMBIR N 28–30
32 1 A 88,355,680 88,365,679 10,000 AluJb 88,355,542 88,355,833 − FANCA exon23 88,365,587 88,365,723 2 alt-EJ N 23–29
33 1 A 88,356,841 88,368,468 11,628 AluY 88,356,875 88,357,188 + AluY 88,368,358 88,368,663 + 21 NAHR Y 22–28
34 1 A 88,356,984 88,370,562 13,579 AluY 88,356,875 88,357,188 + AluY 88,370,455 88,370,769 + 44 NAHR Y 21–28
35 1 A 88,356,998 88,373,127 16,130 AluY 88,356,875 88,357,188 + AluYINS AluYINS 88,373,127 + graphic file with name nihms626669t2.jpg FoSTeS/MMBIR Y 19–28
36 1 A 88,357,692 88,376,135 18,444 AluSg 88,357,566 88,357,859 + AluY 88,376,003 88,376,138 + 4 NAHR Y 18–28
37 1 A 88,357,692 88,376,135 18,444 AluSg 88,357,566 88,357,859 + AluY 88,376,003 88,376,138 + 4 NAHR Y 18–28
38 1 A 88,357,692 88,376,135 18,444 AluSg 88,357,566 88,357,859 + AluY 88,376,003 88,376,138 + 4 NAHR Y 18–28
39 1 A 88,357,733 88,365,259 7,527 AluSg 88,357,566 88,357,859 + AluJb 88,365,086 88,365,390 + 20 NAHR Y 18–24
40 1 A 88,357,923 88,376,192 18,270 AluSq 88,357,872 88,358,166 + AluY 88,376,003 88,376,138 + 12 NAHR Y 18–28
44 1 A 88,366,653 88,394,866 28,214 AluSx 88,366,445 88,366,750 + AluSx 88,394,658 88,394,971 + 10 NAHR Y 9–22
45 1 A 88,366,653 88,394,866 28,214 AluSx 88,366,445 88,366,750 + AluSx 88,394,658 88,394,971 + 10 NAHR Y 9–22
46_d1 2 HE A 88,368,466 88,404,057 35,592 AluY 88,368,358 88,368,663 + AluY 88,403,951 88,404,249 + 28 NAHR Y 6–21
47_d1 2 HE A 88,368,481 88,393,743 25,263 AluY 88,368,358 88,368,663 + AluY 88,393,654 88,393,920 + 14 NAHR Y 9–21
48 1 A 88,368,519 88,384,182 15,664 AluY 88,368,358 88,368,663 + AluSx 88,384,029 88,384,350 + 8 NAHR Y 15–21
49 1 A 88,368,578 88,375,523 6,946 AluY 88,368,358 88,368,663 + AluY 88,375,302 88,375,614 + 14 NAHR Y 18–21
50 1 A 88,368,840 88,373,628 4,789 AluSx 88,368,721 88,369,009 + NR 2 alt-EJ N 18–21
51 1 A 88,368,840 88,373,628 4,789 AluSx 88,368,721 88,369,009 + NR 2 alt-EJ N 18–21
52 1 A 88,372,488 88,396,714 24,227 AluSg x 88,372,403 88,372,566 + LINE 88,396,612 88,397,058 + none NHEJ N 9–20
53 1 A 88,375,333 88,377,211 1,879 AluY 88,375,302 88,375,614 + AluY 88,377,178 88,377,485 + 13 NAHR Y 16–17
54 1 A 88,375,502 88,389,110 13,609 AluY 88,375,302 88,375,614 + AluSx 88,388,912 88,389,192 + 22 NAHR Y 12–17
55 1 A 88,376,050 88,377,224 1,175 AluY 88,375,627 88,375,930 + AluY 88,377,178 88,377,485 + 22 NAHR Y 16–17
56 1 A 88,376,126 88,377,300 1,175 AluY 88,376,139 88,376,434 + AluY 88,377,178 88,377,485 + 14 NAHR Y 16–17
57 1 A 88,376,281 88,382,229 5,949 AluY 88,376,139 88,376,434 + AluSc 88,382,090 88,382,369 + 10 NAHR Y 15–17
46_d2 2 HE A 88,383,475 88,391,064 7,590 AluJo 88,383,349 88,383,647 − AluY 88,390,786 88,391,090 + ins. 2bps NHEJ YO 11–14
63_d2 2 HE A 88,383,475 88,391,064 7,590 AluJo 88,383,349 88,383,647 − AluY 88,390,786 88,391,090 + ins. 2bps NHEJ YO 11–14
58 1 A 88,383,475 88,391,064 7,590 AluJo 88,383,349 88,383,647 − AluY 88,390,786 88,391,090 + ins. 2bps NHEJ YO 11–14
59 1 A 88,383,475 88,391,064 7,590 AluJo 88,383,349 88,383,647 − AluY 88,390,786 88,391,090 + ins. 2bps NHEJ YO 11–14
60 1 A 88,383,475 88,391,064 7,590 AluJo 88,383,349 88,383,647 − AluY 88,390,786 88,391,090 + ins. 2bps NHEJ YO 11–14
47_d2 2 HE A 88,384,547 88,394,863 10,317 AluSg 88,384,358 88,384,675 + AluSx 88,394,658 88,394,971 + 23 NAHR Y 9–14
28_d2 2 HE A 88,390,697 88,406,009 15,313 AluSg 88,390,650 88,390,785 + AluY 88,405,963 88,406,268 + 8 NAHR Y 4–10
67 1 A 88,393,778 88,401,667 7,890 AluY 88,393,654 88,393,920 + AluY 88,401,513 88,401,817 + 12 NAHR Y 7–8
68 1 A 88,394,840 88,404,129 9,290 AluSx 88,394,658 88,394,971 + AluY 88,403,951 88,404,249 + 20 NAHR Y 6–8
71 1 A 88,399,194 88,406,309 7,116 FANCA exon7 88,399,189 88,399,301 − AluSp 88,406,274 88,406,579 + 1 NHEJ N 4–7
73 1 A 88,399,898 88,409,021 9,124 AluSq 88,399,826 88,400,121 − AluSx 88,408,947 88,409,245 − 5 NAHR Y 3–6
74 2 HO A 88,400,101 88,419,559 19,459 AluSq 88,399,826 88,400,121 − AluY 88,419,273 88,419,580 − 26 NAHR Y 1–6
75 1 A 88,401,663 88,433,153 31,491 AluY 88,401,513 88,401,817 + AluY 88,432,969 88,433,298 + 13 NAHR Y 1–6
76 1 A 88,401,663 88,433,153 31,491 AluY 88,401,513 88,401,817 + AluY 88,432,969 88,433,298 + 13 NAHR Y 1–6
77 1 A 88,401,663 88,433,153 31,491 AluY 88,401,513 88,401,817 + AluY 88,432,969 88,433,298 + 13 NAHR Y 1–6
78 1 A 88,401,663 88,433,153 31,491 AluY 88,401,513 88,401,817 + AluY 88,432,969 88,433,298 + 13 NAHR Y 1–6
79 1 A 88,401,663 88,433,153 31,491 AluY 88,401,513 88,401,817 + AluY 88,432,969 88,433,298 + 13 NAHR Y 1–6
80 1 A 88,402,939 88,435,730 32,792 AluY 88,402,820 88,403,114 − AluSp 88,435,611 88,435,932 − 13 NAHR Y 1–5
81 2 HO A 88,403,094 88,418,774 15,681 AluY 88,402,820 88,403,114 − AluSg 88,418,482 88,418,795 − 27 NAHR Y 1–5
82 1 A 88,403,094 88,418,774 15,681 AluY 88,402,820 88,403,114 − AluSg 88,418,482 88,418,795 − 27 NAHR Y 1–5
83 1 A 88,403,104 88,418,467 15,364 AluY 88,402,820 88,403,114 − AluSc 88,418,349 88,418,478 − 46 NAHR Y 1–5
87 1 A 88,406,084 88,408,690 2,607 AluY 88,405,963 88,406,268 + AluSg 88,408,570 88,408,879 + 22 NAHR Y 3
23_d2 2 HE A 88,406,326 88,414,712 8,387 AluSp 88,406,274 88,406,579 + AluSq2 88,414,671 88,414,970 + 31 NAHR Y 1–3
90 1 C 97,046,452 97,050,240 3,789 NR AluY 97,046,501 97,046,811 + ins. 18bps FoSTeS/MMBIR N 3
91 1 C 97,046,452 97,050,240 3,789 NR AluY 97,046,501 97,046,811 + ins. 18bps FoSTeS/MMBIR N 3
92 1 C 97,046,452 97,050,240 3,789 NR AluY 97,046,501 97,046,811 + ins. 18bps FoSTeS/MMBIR N 3
93 1 C 97,046,452 97,050,240 3,789 NR AluY 97,046,501 97,046,811 + ins. 18bps FoSTeS/MMBIR N 3
94 1 C 97,046,452 97,050,240 3,789 NR AluY 97,046,501 97,046,811 + ins. 18bps FoSTeS/MMBIR N 3
95 1 C 97,115,943 97,125,170 9,228 NR MLT1J MaLR 97,125,086 97,125,394 + graphic file with name nihms626669t3.jpg NHEJ N 1

Foot notes in Table 2 also apply here. Cen and Tel represent centromeric and telomeric ends of a deletion. The ΔStart is the Cen breakpoint and contains any overlap sequence.

The ΔEnd coordinate is the Tel breakpoint and contains none of the overlap sequence.

Strand (+/−) indicates the orientation of the repeat element. YO =yes in opposite orientation. Identical deletions are shaded in gray.

*

The precise sequence of the Overlap or Insertion bps is provided in Table S4

The Criteria for “potential mechanism” are as described in Yang et al., (2013, Cell)

The deletion coordinates are according to the NCBI36/hg18 build.