ABCMdb

ABCB2 p.Ile393Val

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Publications

PMID: 11829140 [PubMed] Saito S et al: "Three hundred twenty-six genetic variations in genes encoding nine members of ATP-binding cassette, subfamily B (ABCB/MDR/TAP), in the Japanese population."

No. Sentence Comment

34 Table 1A. Summary of genetic variations detected in the ABCB1 gene No. Location Positiona Genetic variation NCBI SNP ID 1 5Ј Flanking -196 T/C 2 5Ј Flanking -16 T/C 3 Intron 1 71660 A/C 4 Intron 1 80091 A/C 5 Intron 1 103126 T/C 6 Intron 1 103148 C/T 7 Intron 1 108428 A/G 8 Intron 1 112042 A/Gd 9 Exon 2 202 T/C(5ЈUTR)b,d 10 Intron 2 491 G/del 11 Intron 4 36 C/T 12 Intron 5 1596 T/C 13 Intron 7 139 T/Cb,c rs1202168 14 Intron 7 251 G/A rs1202169 15 Intron 8 1789 C/T 16 Intron 9 7225 A/G rs1922240 17 Exon 13 12 T/C(Gly412Gly)b,c,d rs2032588 18 Intron 14 24 T/C 19 Intron 14 81 C/T 20 Intron 15 38 A/G 21 Intron 17 73 A/G 22 Intron 17 472 T/Ab,c 23 Intron 18 564 G/A 24 Intron 18 2062 C/T 25 Intron 18 2293 A/G 26 Intron 20 557 G/A 27 Intron 21 24 G/A 28 Intron 21 2725 A/G 29 Intron 21 4725 A/G 30 Exon 22 196 G/T/A(893Ala/Ser/Thr)c,d rs2032582 31 Intron 22 49 T/C rs2032583 32 Intron 22 8507 T/C 33 Intron 22 8537 T/A 34 Intron 22 8565 T/C 35 Intron 22 8952 G/A 36 Intron 22 9520 A/G 37 Intron 22 9836 C/T 38 Intron 24 377 C/A 39 Intron 24 1493 A/del 40 Intron 24 1495 A/T 41 Intron 25 342 C/T 42 Intron 26 134 C/G 43 Intron 26 1043 G/A rs1922243 44 Intron 26 1272 A/G 45 Intron 26 1394 A/G 46 Intron 26 1987-1988 AAAG/ins 47 Exon 27 153 C/T(Ile1145Ile)b,c,d rs1045642 48 Intron 27 59 G/T 49 Intron 27 80 T/C 50 Intron 28 1220 A/G rs1186746 51 Intron 28 1266 G/T rs1186745 52 Exon 29 400 A/G(3ЈUTR)d rs3842 53 3Ј Flanking 264 G/A rs1055302 ABCB1, ATP-binding cassette, subfamily B, member 1; NCBI, National Center for Biotechnology Information; SNP, single-nucleotide polymorphism; UTR, untranslated region; del, deletion; ins, insertion a For SNPs in the 5Јflanking region, intron region, or 3Јflanking region, nucleotide positions are counted from the first intronic nucleotide at the exon/intron junction (for SNPs in the exon region, nucleotide positions are counted from the first exonic nucleotide at the exon/intron junction) b SNPs previously reported by Hoffmeyer et al. (2000) c SNPs previously reported by Cascorbi et al. (2001) d SNPs previously reported by Tanabe et al. (2001) Table 1B. Summary of SNPs detected in the TAP1 gene No. Location Positiona SNP NCBI SNP ID 1 5Ј Flanking -673 G/C rs1351382 2 5Ј Flanking -646 T/G rs1351383 3 5Ј Flanking -563 A/C 4 5Ј Flanking -236 G/T 5 Intron 3 408 C/T 6 Exon 4 153 A/G(Ile393Val)b,c rs1057141 7 Intron 4 289 G/T 8 Intron 4 291 C/G rs2071539 9 Intron 5 1139 C/T 10 Intron 7 375 C/T rs735883 11 Exon 11 284 G/T(3ЈUTR)b rs1057373 12 3Ј Flanking 71 G/A rs2071540 13 3Ј Flanking 129 T/C rs2071541 14 3Ј Flanking 459 G/A rs2071463 TAP1, transporter associated with antigen processing 1 b SNPs previously reported by Colonna et al. (1992) c SNP previously reported by Jackson and Capra (1993) Table 1C. Summary of genetic variations detected in the TAP2 gene No. Location Positiona Genetic variation NCBI SNP ID 1 5Ј Flanking -63 C/Tb 2 5Ј Flanking -55 G/Ab 3 Exon 1 61 T/C(5ЈUTR)b 4 Intron 1 39 G/Ab 5 Intron 1 311 A/Gb 6 Intron 2 48 G/Cb 7 Intron 3 7 G/Ab 8 Intron 3 8 G/A 9 Intron 3 265 A/Gb 10 Intron 3 1474 T/Cb rs241429 11 Intron 4 104 C/T 12 Intron 5 111 G/Ab rs241430 13 Intron 5 124 G/Ab 14 Exon 6 190 G/A(Val379Ile)b,c rs1800454 15 Exon 7 15 G/T(Gly386Gly)b 16 Intron 7 1379 G/A rs1015166 17 Intron 7 1399 G/A rs117821 18 Intron 9 168 C/T rs241436 19 Intron 10 23 C/T rs241437 20 Intron 10 87 G/A rs241438 21 Intron 10 170 A/C rs241439 22 Intron 10 219 A/G 23 Intron 10 346 G/A rs241440 24 Exon 11 17 G/A(Gly604Gly) rs241441 25 Intron 11 9 C/T rs241442 26 Intron 11 62 C/A rs241443 27 Intron 11 68 C/T rs241444 28 Intron 11 105 G/A rs241445 29 Intron 11 210 C/T rs241446 30 Intron 11 317-319 GTG/del 31 Exon 12 19 T/C(Cys651Arg) 32 Exon 12 61 A/G(Thr665Ala)c,d rs241447 33 Exon 12 127 T/C(stop687Gln)c,d rs241448 34 Exon 12 159 G/T(3ЈUTR)c,d rs241449 35 Exon 12 291 G/A(3ЈUTR) rs1871666 36 Exon 12 332 A/G(3ЈUTR) rs241451 37 Exon 12 356-357 GG/TGGTGGGGTGGA(3ЈUTR) TAP2, transporter associated with antigen processing 2 b SNPs previously reported by Jeffreys et al. (2000) c SNPs previously reported by Colonna et al. (1992) d SNPs previously reported by Powis et al. (1992) Materials and methods Exon-intron boundaries of the ABCB1, TAP1, TAP2, ABCB4, ABCB7, ABCB8, ABCB9, ABCB10, and ABCB11 genes were defined by comparing genomic sequences with mRNA sequences. Login to comment

PMID: 21796142 [PubMed] Kim JH et al: "Genetic association analysis of TAP1 and TAP2 polymorphisms with aspirin exacerbated respiratory disease and its FEV1 decline."

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12 Value significant at Po0.05 is shown in bold. Table 2 Polymorphisms of TAP1 and TAP2 investigated in this study Gene SNP ID Polymorphism Position Amino-acid change Genotype (n) MAF HWE* TAP1 rs2071481 A/G Intron AA (109) AG (60) GG (10) 0.223 0.648 rs2284190 T/C Intron TT (132) TC (50) CC (3) 0.151 0.479 rs4148880 A/G Exon Ile393Val AA (124) AG (55) GG (8) 0.190 0.549 rs2395269 T/G Intron TT (125) TG (52) GG (8) 0.184 0.391 rs12529313 A/G Intron AA (124) AG (55) GG (8) 0.190 0.549 rs2071482 G/T Intron GG (125) GT (53) TT (7) 0.181 0.643 rs735883 C/T Intron CC (78) CT (85) TT (22) 0.349 0.875 rs1800453 A/G Exon Asp697Gly AA (130) AG (48) GG (7) 0.168 0.341 rs4711312 A/G Intron AA (130) AG (48) GG (7) 0.168 0.341 rs1057373 G/T 3'UTR GG (132) GT (46) TT (7) 0.162 0.248 rs2071540 G/A 3'near GG (61) GA (94) AA (30) 0.416 0.535 rs2071541 T/C 3'near TT (127) TC (50) CC (8) 0.178 0.289 TAP2 rs3763366 C/G 5'near CC (51) CG (94) GG (44) 0.481 0.957 rs4148870 G/A Intron GG (55) GA (89) AA (43) 0.468 0.546 rs2071544 G/A Intron GG (50) GA (95) AA (44) 0.484 0.931 rs2071465 G/C Intron GG (89) GC (78) CC (19) 0.312 0.755 rs2239701 A/G Intron AA (44) GA (101) GG (42) 0.495 0.272 rs241424 C/T Intron CC (49) CT (94) TT (44) 0.487 0.934 rs3819721 G/A Intron GG (101) GA (72) AA (14) 0.267 0.814 rs241426 T/A Intron TT (74) TA (91) AA (22) 0.361 0.453 rs3819714 G/A Intron GG (63) GA (98) AA (26) 0.401 0.214 rs241429 C/T Intron CC (74) CT (86) TT (27) 0.374 0.804 rs4148871 C/T Intron CC (122) CT (62) TT (3) 0.182 0.118 rs241430 G/A Intron GG (68) GA (95) AA (25) 0.386 0.362 rs241432 A/C Intron AA (66) AC (95) CC (28) 0.399 0.512 rs4148873 G/A Exon Val379Ile GG (141) GA (43) AA (3) 0.131 0.893 rs2228397 G/T Exon Synonymous (Gly386Gly) GG (90) GT (78) TT (19) 0.310 0.730 rs241433 T/G Intron TT (63) TG (96) GG (28) 0.406 0.381 rs1015166 C/T Intron CC (99) CT (75) TT (13) 0.270 0.813 rs4576294 G/A Exon Synonymous (Asn436Asn) GG (177) GA (10) AA (0) 0.027 0.707 rs241436 C/T Intron CC (57) CT (82) TT (48) 0.476 0.098 rs241437 C/T Intron CC (52) CT (92) TT (43) 0.476 0.851 rs241438 G/A Intron GG (49) GA (91) AA (48) 0.497 0.662 rs241439 C/A Intron CC (52) CA (91) AA (44) 0.479 0.733 rs4148876 C/T Exon/intron Arg651Cys CC (132) CT (52) TT (3) 0.155 0.403 rs241454 T/C 3'UTR/intron TT (71) TC (92) CC (24) 0.374 0.492 rs10484565 G/A 3'UTR/intron GG (146) GA (38) AA (3) 0.118 0.772 rs2857101 A/G 3'UTR/intron AA (71) AG (94) GG (24) 0.376 0.407 rs13501 G/A 3'UTR/intron GG (56) GA (96) AA (35) 0.444 0.586 rs1894411 A/G 3'near/intron AA (141) AG (42) GG (5) 0.138 0.390 rs2856993 C/G 3'near/intron CC (89) CG (83) GG (15) 0.302 0.473 rs2857103 G/T 3'near/intron GG (56) GT (96) TT (35) 0.444 0.586 rs2621321 T/C 3'near TT (81) TC (88) CC (18) 0.332 0.399 Abbreviations: HWE, Hardy-Weinberg equilibrium; MAF, minor allele frequency; SNP, single-nucleotide polymorphism; UTR, untranslated region. Login to comment
54 Four non-synonymous SNPs in coding regions (Ile393Val and Asp697Gly in TAP1; Val379Ile and Arg651Cys in TAP2) were included. Login to comment

PMID: 18650831 [PubMed] Ivansson EL et al: "MHC loci affecting cervical cancer risk: distinguishing the effects of HLA-DQB1 and non-HLA genes TNF, LTA, TAP1 and TAP2."

No. Sentence Comment

138 Genomic location on chr6 Minor allele frequency in controls Genotyping method LTA IntronA A/G rs909253 31648292 0.376 Inflastripa TNF À857 C/T rs1799724 31650461 0.067 TaqMan TNF À572 A/C rs4248161 31650746 0.014 TaqMan TNF À308 G/A rs1800629 31651010 0.167 Inflastripa TNF À238 G/A rs361525 31651080 0.047 Inflastripa TAP2 T665A T/C rs241447 32904729 0.244 TaqMan TAP2 R651C G/A rs4148876 32904771 0.070 TaqMan TAP2 A565T C/T rs2228396 32905787 0.112 TaqMan TAP2 V379I C/T rs1800454 32908390 0.164 TaqMan TAP1 D697G T/C rs1135216 32922953 0.167 TaqMan TAP1 I393V T/C rs1057141 32926752 0.190 TaqMan Abbreviations: HLA, human leukocyte antigen; LTA, lymphotoxin-alpha; TAP, transporter associated with antigen processing; TNF, tumor necrosis factor. Login to comment

PMID: 25008864 [PubMed] Aissani B et al: "SNP screening of central MHC-identified HLA-DMB as a candidate susceptibility gene for HIV-related Kaposi's sarcoma."

No. Sentence Comment

5 A striking multiplicative effect on the estimated risk was associated with further carriage of two non-synonymous variants, rs1800453 A4G (Asp697Gly) and rs4148880 A4G (Ile393Val), in the linked TAP1 gene (OR &#bc; 10.5; 95% CI &#bc; 2.54-43.6; P &#bc; 0.0012). Login to comment
38 Within 95 kb from HLA-DMB toward HLA-DR, significant but moderate associations with risk were observed with two non-synonymous SNPs in TAP1, rs1800453 A4G (Asp697Gly) (OR &#bc; 1.54; 95% &#bc; 1.09-2.18; P &#bc; 0.014) and rs4148880 A4G (Ile393Val) (OR &#bc; 1.45; 95% CI &#bc; 1.05-1.99; P &#bc; 0.024), and with rs2071541 A4G, a SNP located in the overlapping microRNA TAPSAR1 (OR &#bc; 1.60; 95% CI &#bc; 1.11-2.32; P &#bc; 0.012). Login to comment
61 A significant increase of risk (adjusted OR &#bc; 10.5) was associated with further carriage of non-synonymous rs1800453 (A4G) and rs4148880 (A4G) alleles encoding Asp697Gly and Ile393Val mutations in TAP1, respectively. Login to comment
64 Association of gene variants in central MHC with HIV-related Kaposi`s sarcoma in HIV-positive men enrolled in the Multicenter AIDS Cohort Study Obs Polymorphism Position Gene/closest gene Function MAF, count (%) ORa (95% CI) P-value Cases Controls 66 rs356971 (A4C) 30087776 ZNRD1-AS1 ncRNA 88 (0.14) 118 (0.19) 0.73 (0.53-0.99) 0.0422 72 rs1116221 (G4A) 30179309 TRIM31 Glu421Lys 141 (0.23) 177 (0.28) 0.74 (0.56-0.96) 0.0328 88 rs9357097 (G4A) 30393100 HCG18 Intron 185 (0.30) 157 (0.25) 1.32 (1.02-1.72) 0.0394 100 rs2429657 (A4G) 30579499 HLA-E Intergenic 119 (0.19) 152 (0.24) 0.68 (0.51-0.90) 0.0081 105 rs1076829 (A4G) 30735195 DHX16 Intron 194 (0.31) 230 (0.37) 0.76 (0.60-0.96) 0.0229 169 rs2071594 (G4C) 31620699 NFKBIL1 3`UTR 188 (0.30) 220 (0.35) 0.74 (0.58-0.96) 0.0220 170 rs2071592 (T4A) 31623319 NFKBIL1 Intron 174 (0.28) 212 (0.34) 0.70 (0.54-0.90) 0.0063 172 rs6929796 (G4A) 31630648 NFKBIL1 Intron 89 (0.14) 119 (0.19) 0.74 (0.55-0.99) 0.0444 174 rs2239707 (A4G) 31633298 NFKBIL1 Intron 217 (0.35) 189 (0.30) 1.26 (0.98-1.60) 0.0683 185 rs1800683 (G4A) 31648050 LTA 5`UTR 188 (0.30) 220 (0.35) 0.75 (0.58-0.96) 0.0223 187 rs909253 (A4G) 31648292 LTA 5` Region 188 (0.30) 220 (0.35) 0.75 (0.58-0.96) 0.0223 189 rs1041981 (C4A) 31648763 LTA Thr60Asn 188 (0.30) 220 (0.35) 0.75 (0.58-0.96) 0.0223 200 rs3093665 (A4C) 31653370 TNF 3`UTR 19 (0.03) 7 (0.01) 2.00 (0.89-4.53) 0.0965 214 rs2844477 (A4G) 31686751 AIF-1, NCR3 Intergenic 220 (0.35) 263 (0.42) 0.75 (0.59-0.96) 0.0207 221 rs7029 (A4G) 31737932 GPANK1 3`UTR 167 (0.27) 137 (0.22) 1.55 (1.17-2.05) 0.0022 224 rs1065356 (G4A) 31794987 LY6G6C cds-syn 137 (0.22) 109 (0.17) 1.60 (1.18-2.16) 0.0024 225 rs3749953 (A4G) 31821103 MSH5-SAPCD1 Intronic 92 (0.13) 76 (0.11) 1.45 (1.01-2.10) 0.0459 227 rs707926 (G4A) 31856799 VARS cds-syn 107 (0.17) 84 (0.13) 1.42 (1.03-1.97) 0.0323 264 rs3749962 (G4A) 32144335 TNXB cds-syn 41 (0.07) 60 (0.10) 0.57 (0.38-0.87) 0.0084 349 rs2071541 (A4G) 32920836 TAP1, TAPSAR1 nearGene-3 100 (0.16) 75 (0.12) 1.60 (1.11-2.32) 0.0124 350 rs1800453 (A4G) 32922953 TAP1 Asp697Gly 116 (0.19) 91 (0.14) 1.54 (1.09-2.18) 0.0136 352 rs4148880 (A4G) 32926752 TAP1 Ile393Val 143 (0,21) 117 (0.17) 1.45 (1.05-1.99) 0.0236 353 rs4713600 (C4A) 32930836 TAP1 nearGene-5 331 (0.48) 293 (0.42) 1.31 (1.04-1.66) 0.0236 355 rs9276820 (G4A) 32937254 PSMB9 Downstream 305 (0.49) 279 (0.44) 1.33 (1.06-1.67) 0.0140 356 rs1383266 (G4A) 32942710 PSMB9, HLA-DMB Intergenic 135 (0.22) 169 (0.27) 0.75 (0.58-0.97) 0.0309 359 rs2187688 (G4A) 32979979 PSMB9, HLA-DMB Intergenic 274 (0.44) 307 (0.49) 0.75 (0.59-0.96) 0.0199 367 rs151719 (A4G) 33011878 HLA-DMB Intron 161 (0.26) 121 (0.19) 1.39 (1.03-1.86) 0.0291 370 rs194675 (T4A) 33013724 HLA-DMB Intron 272 (0.44) 309 (0.49) 0.77 (0.61-0.99) 0.0383 372 rs6902982 (A4G) 33015859 HLA-DMB Intron 32 (0.05) 10 (0.02) 4.09 (1.90-8.80) 0.0003 377 rs209475 (G4A) 33033563 HLA-DMA Upstream 215 (0.35) 254 (0.41) 0.78 (0.60-1.04) 0.0533 379 rs683208 (A4G) 33045879 BRD2 nearGene-5 219 (0.35) 257 (0.41) 0.78 (0.60-1.00) 0.0539 388 rs12174395(A4G) 33122296 HLA-DPA1 Upstream 191 (0.31) 230 (0.37) 0.75 (0.59-0.97) 0.0270 389 rs375912 (A4G) 33124706 HLA-DPA1 Upstream 198 (0.32) 236 (0.38) 0.76 (0.60-0.98) 0.0319 408 rs461338 (A4G) 33326158 VPS52 3`UTR 88 (0.14) 115 (0.18) 0.66 (0.47-0.92) 0.0152 411 rs466384 (A4G) 33362643 WDR46 Val287Ala 84 (0.13) 110 (0.17) 0.64 (0.45-0.91) 0.0132 415 rs1061801 (G4A) 33390316 ZBTB22 UTR-3 123 (0.18) 150 (0.22) 0.72 (0.53-0.97) 0.0288 Abbreviations: CI, confidence interval; MAF, minor allele frequency; MHC, major histocompatibility complex; OR, odds ratio; UTR, untranslated region. Login to comment