TABLE 3

Polymorphisms identified in the ABCB4 gene

Numbering of nucleotides is according to GenBank accession numbers AC005068.2 (noncoding exons –3 to 1 and coding exons 2 and 3), AC006154.1 (exons 4–12), and AC0005045.2 (exons 13–28). Positions of polymorphisms are counted with respect to the MDR3 translation start site (exon 2) with the A of ATG being +1 and the 5′-following base being –1. The numbers 1 to 42 in the variant ID column indicate all variants included in haplotype analysis and linkage disequilibrium estimation.


Variant ID

5′ Sequence

Genetic Variation

3′ Sequence

Region

Amino Acid Change

CA

KO

JA

Total
n
%
n
%
n
%
n
%
43 TCAATGCAC g.-7676A>T GTCTCACAA PromA 110 0.9 96 0.0 88 0.0 294 0.3
44 CTACCCTCT g.-7554T>C CAATGCCTC PromA 110 0.9 96 0.0 88 0.0 294 0.3
45 GAGTGAAGT g.-7253G>A TAGAAATCT PromA 106 0.0 96 1.0 94 0.0 296 0.3
46 AATTTAGAA g.-7114A>T ACTCAATAG PromA 108 0.0 96 1.0 94 0.0 298 0.3
1 AAGAGGAAA g.-7094G>C TTTCTTGTA PromA 108 13.0 96 30.2 94 24.5 298 22.1
47 CAAGAATTT g.-6816C>T ATTAGGCAA PromA 102 0.0 96 1.0 92 0.0 290 0.3
48 GAGAGAGAG g.-6639A>C GAGCTGAAT PromA 110 0.9 90 0.0 92 0.0 292 0.3
49 GAGAGAGAG g.-6637_-6636 delAG CTGAATCAG PromA 110 0.0 90 1.1 92 0.0 292 0.3
2 GTGCCTTTG g.-6588G>T GTGTGCTGG PromA 110 2.7 88 0.0 92 2.2 290 1.7
3 AAAGAAGAA g.-6540C>T GAAACCAAA PromA 108 14.8 86 26.7 90 27.8 284 22.5
4 TTAGTGACC g.-6325A>G AAAGTTTGG PromA 108 17.6 90 31.1 92 26.1 290 24.5
5 ATTCTTTTT g.-6014G>T TACAAACCC PromA 108 16.7 94 28.7 88 26.1 290 23.4
50 ACTGGTGCT g.-5941G>A TGGGCACTA PromA 108 0.0 94 0.0 88 1.1 290 0.3
6 TGAAGTCAC g.-5859G>A TGGCCAGAG PromA 108 16.7 94 28.7 88 26.1 290 23.4
7 ATGAGATGA g.-5717T>C ATATATGTG PromA 110 0.0 92 1.1 86 3.5 288 1.4
8 CCTTCTTTA g.-5610T>C ATGCCTAAA PromA 110 100.0 96 100.0 94 97.9 300 99.3
9 TAAGTGTGG g.-5570G>C CAGCAATTA PromA 110 12.7 96 29.2 94 24.5 300 21.7
51 TACTCTCAC g.-5509G>A GCTCTTATG PromA 110 0.0 96 1.0 94 0.0 300 0.3
10 CTCTCTTGT g.-5236C>T TGAGTAATA PromA 108 15.7 90 27.8 94 26.6 292 22.9
52 GAGGATAAA g.-2551A>T AAGAAAGAT PromB 126 0.0 88 0.0 90 1.1 304 0.3
11 AGCCTTACA g.-2478T>G CAATGCATA PromB 126 4.8 88 0.0 90 2.2 304 2.6
12 GAAGGAATT g.-1921T>C GGGTTGATT PromB/Exon -3 122 4.9 92 0.0 82 1.2 296 2.4
53 GAAGAGAAT g.-1899C>A CTCATGGTC PromB/Exon -3 122 0.8 92 0.0 82 0.0 296 0.3
13 ATCCTAATA g.-1603A>T CACCCTTAT PromB 128 0.0 94 2.1 86 1.2 308 1.0
14 TTTATAGAT g.-1584C>T CAATGACTG PromB/Exon -2 118 11.0 94 29.8 74 23.0 286 20.3
54 ACACCAGGG g.-1510T>G CCACCCAGC PromB 126 0.0 94 1.1 68 0.0 288 0.3
15 CTTATACCA g.-1484T>C GCTCTGCTT PromB 126 0.0 94 1.1 68 5.9 288 1.7
55 TTTGAAAGT g.-1146C>T TCCGGTTTC PromB 126 0.0 92 1.1 82 0.0 300 0.3
16 TGGTAGGAG g.-1031C>T AGAGACAAT PromB 126 11.1 92 30.4 82 24.4 300 20.7
56 GAGACAATT g.-1020C>G AATACAGAC PromB 126 0.0 92 1.1 82 0.0 300 0.3
17 ATTCAATAC g.-1014A>G GACAGAAGT PromB 126 13.5 92 30.4 82 24.4 300 21.7
18 GAACTGGGG g.-682A>C TGCGGAAGC PromB/Exon -1 124 1.6 70 0.0 64 0.0 258 0.8
19 AGGCTCCAG g.-495C>G CTGATCTCG PromB 126 17.5 86 29.1 84 28.6 296 24.0
20 GCGCCCCGG g.-414C>T GGCAAGAGC PromB 126 4.8 86 3.5 84 6.0 296 4.7
21 GGCAGGCTG g.-395C>G GCCCCTGGC PromB 126 13.5 86 3.5 84 6.0 296 8.4
22 GCCCGCGCC g.-378T>C AGCCTGGGG PromB 126 26.2 86 27.9 84 20.2 296 25.0
57 GCGTTTCCC g.-292G>T GGCCGGACG PromB 128 0.0 96 0.0 92 1.1 316 0.3
58 CCGGACGCG g.-280C>A GTGGGGGGC PromB 126 0.8 86 0.0 84 0.0 296 0.3
59 CCCTGCCAG g.-186A>G CACGCGCGA PromB/Exon 1 128 0.0 96 1.0 92 0.0 316 0.3
23 TGCCCCCGG g.-75G>T CCCCGCGAC PromB 128 0.0 96 0.0 92 1.1 316 0.3
24 TTTATGTCG g.12597C>T TGGGTACCA Exon 4 L59L 126 12.7 96 25.0 94 21.3 316 19.0
60 CAAATTTGT g.12680T>G GATACTGCA Exon 4 V86V 126 0.0 96 0.0 94 1.1 316 0.3
61 ATTTGTTGA g.12683T>G ACTGCAGGA Exon 4 D87E 126 0.0 96 0.0 94 1.1 316 0.3
62 TTCTCCTTT g.12705C>T CAGGTAAGC Exon 4 P95S 126 0.0 96 0.0 94 1.1 316 0.3
63 TAGCTTTCA g.20782T>G ACATTTAAA Intron 4 114 0.0 88 1.1 70 0.0 272 0.4
25 TTTTAAAAA g.20813C>T CTGGCAATG Intron 4 116 3.4 90 1.1 70 0.0 276 1.8
26 TCACCTATT g.21044A>G TTATCATTT Intron 5 122 16.4 52 15.4 46 32.6 220 19.5
27 AAAAGAAAA g.22281_22284delGAAAA AAGAAAAGA Intron 5 126 7.9 88 0.0 84 0.0 298 3.4
28 TGACATCAA g.22490C>T GACACCACT Exon 6 N168N 126 42.9 88 37.5 90 44.4 304 47.7
29 GAACTCAAT g.22509A>G CGCGGCTAA Exon 6 T175A 126 3.2 88 0.0 90 0.0 304 1.3
64 CTCTGCAGC g.23831C>T GTTTGGGCA Exon 7 A232A 128 0.0 94 0.0 90 1.1 312 0.3
65 AAGGGTTGA g.25313C>G CAGAGTGCC Intron 7 124 0.8 96 0.0 90 0.0 310 0.3
30 TGTCCAGAT g.25376A>T CTCTCGGCA Exon 8 I237l 126 15.1 96 27.1 90 27.8 312 22.4
66 GTTAATATA g.28354T>C GCATCATAT Exon 9 Y309Y 128 0.8 96 0.0 92 0.0 316 0.3
67 GCATATGTG g.30584A>G TCTTTGATA Exon 10 I367V 118 0.8 92 0.0 92 0.0 302 0.3
68 TAATATTTA g.31823T>G AGGAATTCC Intron 11 128 0.0 96 0.0 92 1.1 316 0.3
31 ACTTTTTTT g.31941delT CAAATTTCA Intron 11 128 7.0 96 3.1 94 1.1 318 4.1
69 ACCCTGATG g.32140A>G GGGCACAGT Exon 12 E450G 128 0.0 96 1.0 94 0.0 318 0.3
70 ACAAATTTG g.32232C>T GTGTGAATC Intron 12 128 0.0 96 1.0 94 0.0 318 0.3
32 GGCAATGCC g.32277G>T ATGGATAAT Intron 12 124 6.5 96 3.1 94 3.2 314 4.5
33 CAGCTATTA g.35024A>G ATGGTTAAA Intron 12 124 95.2 94 70.2 94 72.3 312 80.8
71 ACAGGTAAA g.35273G>A CCTCTGATA Intron 13 126 0.0 96 0.0 94 1.1 316 0.3
72 AGTGTGCCA g.43862A>G TACTGTAAC Intron 14 122 0.8 88 0.0 72 0.0 282 0.4
34 TGTGCCAAT g.43864A>G CTGTAACCC Intron 14 124 0.0 88 1.1 72 2.8 284 1.1
73 TAGCACACC g.43938G>A ACTGTCTAC Exon 15 R590Q 124 0.8 88 0.0 74 0.0 286 0.3
35 GCTGCCACT g.48606A>G GAATGGCCC Exon 16 R652G 124 7.3 86 2.3 74 1.4 284 4.2
36 GCTACAATT g.48771A>G TTGAAATTC Intron 16 114 5.3 86 2.3 70 1.4 270 3.3
37 TTGCAAACA g.51576C>T CACATAACA Intron 17 122 95.1 70 74.3 80 71.3 272 82.7
38 TTACATAAC g.56969A>G TGGTTTTAG Intron 20 126 6.3 60 3.3 66 1.5 252 4.4
74 ATATTTTAC g.58304T>C GTATTAATG Intron 21 124 0.0 96 0.0 92 1.1 212 0.3
39 CTGTATTAA g.58312T>C GTCTAGAAC Intron 21 122 4.1 96 1.0 92 1.1 310 2.3
75 AAAGGAGGC g.63395delT GAAGAGATG Intron 22 124 0.8 92 0.0 94 0.0 310 0.3
76 AATATTAAG g.63598A>T TTATTCTAT Intron 23 124 0.0 92 1.1 94 0.0 310 0.3
40 ATGGTCAAG g.68988A>G AGCAAAGAA Exon 26 E1099G 112 1.8 92 0.0 84 0.0 288 0.7
41 TATTTATAA g.72169T>C TTGGTTAAC Intron 26 122 91.8 90 65.6 92 75.0 304 78.9
42
GTAACATTT
g.73092T>C
CAAATTTAC
Intron 27

124
7.3
94
1.1
86
1.2
304
3.6
  • n, number of alleles analyzed (number of subjects times 2). %, allele frequencies for Caucasians (CA), Japanese (JA), and Koreans (KO).