ABCB3 p.Ala565Thr
| Predicted by SNAP2: | C: N (97%), D: N (53%), E: N (82%), F: N (61%), G: N (93%), H: N (66%), I: N (78%), K: N (93%), L: N (82%), M: N (87%), N: N (72%), P: D (53%), Q: N (72%), R: N (87%), S: N (93%), T: N (97%), V: N (93%), W: N (53%), Y: N (57%), |
| Predicted by PROVEAN: | C: N, D: D, E: N, F: D, G: N, H: D, I: D, K: D, L: D, M: D, N: D, P: D, Q: N, R: D, S: N, T: N, V: N, W: D, Y: D, |
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[hide] TAP1 and TAP2 polymorphisms associated with ankylo... Hum Immunol. 2009 Apr;70(4):257-61. Epub 2009 Feb 4. Feng M, Yin B, Shen T, Ma Q, Liu L, Zheng J, Zhao Y, Qian K, Liu D
TAP1 and TAP2 polymorphisms associated with ankylosing spondylitis in genetically homogenous Chinese Han population.
Hum Immunol. 2009 Apr;70(4):257-61. Epub 2009 Feb 4., [PMID:19480848]
Abstract [show]
Human leukocyte antigen (HLA)-B27 is strongly associated with the autoimmune disease ankylosing spondylitis (AS). Other autoimmune disease-associated genes, such as transporter associated with antigen processing (TAP) genes, could also influence AS susceptibility. In this study, we investigated the association of TAP1 and TAP2 polymorphisms in genetically homogenous Chinese AS patients. Six TAP1 single nucleotide polymorphisms (SNPs) and three TAP2 SNPs sites were analyzed in B27-positive AS cases, healthy B27-negative controls, and healthy B27-positive controls. In the allele and genotype analysis, the results indicated that TAP1 site 1910 allele G, genotype AG and TAP2 site 1693 genotype AA were associated with increased AS risk in a case-B27 negative control (p < 0.05). In the haplotype analysis, TAP1 SNP haplotype (GGGGGG, TAP1*020101) and TAP1-TAP2 SNP haplotypes (GGGGGG-GGG, TAP1*020101-TAP2*0101, and GGAAGG-GAG, TAP1*0101-TAP2*0102) increased AS risk in case-B27 negative control (p < 0.05). In contrast, TAP1-TAP2 SNP haplotype GGGGGG-GAG (TAP1*020101-TAP2*0102) was less common in cases than in B27-negative controls (p < 0.05). Moreover, TAP1-TAP2 SNP haplotype GGGAGG-GGG (TAP1*0301-TAP2*0101) was less common in cases than in B27-positive controls. The two haplotypes appeared to confer protection in AS (p < 0.05). These results suggest a potential mechanism of altered antigen-peptide selection and transport in AS pathogenesis.
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No. Sentence Comment
101 Both TAP1 site 1910 SNP AϾG and TAP2 site 1693 GϾA result in amino acid changes (Asp637Gly and Ala565Thr, respectively).
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ABCB3 p.Ala565Thr 19480848:101:107
status: NEW[hide] MHC loci affecting cervical cancer risk: distingui... Genes Immun. 2008 Oct;9(7):613-23. Epub 2008 Jul 24. Ivansson EL, Magnusson JJ, Magnusson PK, Erlich HA, Gyllensten UB
MHC loci affecting cervical cancer risk: distinguishing the effects of HLA-DQB1 and non-HLA genes TNF, LTA, TAP1 and TAP2.
Genes Immun. 2008 Oct;9(7):613-23. Epub 2008 Jul 24., [PMID:18650831]
Abstract [show]
Cervical cancer has been associated with specific human leukocyte antigen (HLA) haplotypes/alleles and with polymorphisms at the nearby non-HLA loci TNF, LTA, TAP1 and TAP2. Distinguishing effects of individual loci in the major histocompatibility complex (MHC) region are difficult due to the complex linkage disequilibrium (LD) pattern characterized by high LD, punctuated by recombination hot spots. We have evaluated the association of polymorphism at HLA class II DQB1 and the TNF, LTA, TAP1 and TAP2 genes with cervical cancer risk, using 1306 familial cases and 288 controls. DQB1 was strongly associated; alleles *0301, *0402 and (*)0602 increased cancer susceptibility, whereas *0501 and *0603 decreased susceptibility. Among the non-HLA loci, association was only detected for the TAP2 665 polymorphism, and interallelic disequilibrium analysis indicated that this could be due to LD with DQB1. As the TAP2 665 association was seen predominantly in non-carriers of DQB1 susceptibility alleles, we hypothesized that TAP2 665 may have an effect not attributable to LD with DQB1. However, a logistic regression analysis suggested that TAP2 665 was strongly influenced by LD with DQB1. Our results emphasize the importance of large sample sizes and underscore the necessity of examining both HLA and non-HLA loci in the MHC to assign association to the correct locus.
Comments [show]
The TAP2 A565T, which is homologous to position 507 in CFTR, does not significantly affect cervical cancer risk (see Table 2).
hegedus on 2013-03-20 18:59:52
hegedus on 2013-03-20 18:59:52
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.
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ABCB3 p.Ala565Thr 18650831:138:417
status: NEWX
ABCB3 p.Ala565Thr 18650831:138:437
status: NEW[hide] No difference in polymorphism frequency in a Turki... Acta Otolaryngol. 2006 Oct;126(10):1110-1. Yilmaz I, Atac FB, Erkan AN, Verdi H, Cagici CA, Aslan S, Sahin FI, Ozluoglu LN
No difference in polymorphism frequency in a Turkish population with allergic rhinitis.
Acta Otolaryngol. 2006 Oct;126(10):1110-1., [PMID:16923719]
Abstract [show]
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No. Sentence Comment
2 To clarify the contribution of TAP polymorphisms to allergic rhinitis, we determined the frequency of TAP1 (I333V) and TAP2 (A565T and R651C) polymorphisms in a Turkish population with allergic rhinitis.
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ABCB3 p.Ala565Thr 16923719:2:125
status: NEW8 Restriction fragment size analysis was performed for TAP1 (I333V) or TAP2 (A565T and R651C) by visualization of Sau3A1-, Scal-, or Smal- digested PCR products, respectively, after separation by polyacrylamide gel electrophoresis on a 10% ethidium bromide-stained gel.
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ABCB3 p.Ala565Thr 16923719:8:75
status: NEW21 Thus, the contribution of TAP1 (I333V) and TAP2 (A565T and R651C) polymorphisms to disease progression remains controversial.
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ABCB3 p.Ala565Thr 16923719:21:49
status: NEW3 To clarify the contribution of TAP polymorphisms to allergic rhinitis, we determined the frequency of TAP1 (I333V) and TAP2 (A565T and R651C) polymorphisms in a Turkish population with allergic rhinitis.
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ABCB3 p.Ala565Thr 16923719:3:125
status: NEW9 Restriction fragment size analysis was performed for TAP1 (I333V) or TAP2 (A565T and R651C) by visualization of Sau3A1-, Scal-, or Smal- digested PCR products, respectively, after separation by polyacrylamide gel electrophoresis on a 10% ethidium bromide-stained gel.
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ABCB3 p.Ala565Thr 16923719:9:75
status: NEW[hide] Distribution of TAP gene polymorphisms and extende... Genes Immun. 2002 Apr;3(2):78-85. Balladares S, Alaez C, Pujol J, Duran C, Navarro JL, Gorodezky C
Distribution of TAP gene polymorphisms and extended MHC haplotypes in Mexican Mestizos and in Seri Indians from northwest Mexico.
Genes Immun. 2002 Apr;3(2):78-85., [PMID:11960305]
Abstract [show]
The study of the genetic structure is very useful for investigating the biological significance of polymorphism and may provide clues to understand population origins. We present TAP1/TAP2 gene analysis in the Seri indians from Sonora, and in Mestizos from the highlands of Mexico. Thirty-two Seri and 89 Mestizos were studied. TAP genes were typed using the ARMS-PCR technique. The most frequent alleles in Seri were: TAP1*0101/02, (68.8%); TAP1*02011/02012, (31.2%); TAP2*0201, (38.7%) and TAP2*0101, (29.0%). TAP1*0301, TAP1*0401, TAP2*0102 TAP2*0103 and TAP2H were absent in them. For Mestizos, the prevalent alleles were: TAP1*0101/02 (75.8%); TAP1*02011/12 (20.3%); TAP2*0101 (45.4%) and TAP2*0201 (29.3%). These results are similar to those found in Kaingang and Caucasians from Brazil, four Mediterranean, other Caucasians, two Oriental and one African group. In Seri, the extended prevalent haplotypes are typically Amerindian, such as TAP1*0101/2-TAP2*0201-QBP3.21-DQB1*0302-QAP*3.1-DQA1*03011-DRB1*0407-B*3501-A*020 1 (HF = 16.6%). Thirty-two extended haplotypes were found in Seri, although TAP contributed scarcely to diversity. Mestizos show Amerindian and Caucasian combinations. No difference was detected in the distribution of amino acids in the individual variable sites, between both groups. These findings are the basis for further anthropological studies and to explore the contribution of TAP genes to disease expression in Mexicans.
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No. Sentence Comment
18 For TAP2, three dimorphic sites have been described: ILE379VAL, ALA565THR and ALA665THR; the different combinations result in eight distinct alleles, described in Table 1.3,4 Four of them have not been Correspondence: Dr C Gorodezky, Head of The Department of Immunogenetics, InDRE, SSA, Carpio 470-1st floor.
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ABCB3 p.Ala565Thr 11960305:18:64
status: NEW[hide] Analysis of MHC encoded antigen-processing genes T... Am J Respir Crit Care Med. 1999 Sep;160(3):1009-14. Foley PJ, Lympany PA, Puscinska E, Zielinski J, Welsh KI, du Bois RM
Analysis of MHC encoded antigen-processing genes TAP1 and TAP2 polymorphisms in sarcoidosis.
Am J Respir Crit Care Med. 1999 Sep;160(3):1009-14., [PMID:10471632]
Abstract [show]
Sarcoidosis is a chronic granulomatous disease of unknown etiology. Several studies have suggested involvement of human leukocyte antigen (HLA) genes in sarcoidosis susceptibility. HLA associations described have not been consistent, possibly because of additional susceptibility genes adjacent to or within the major histocompatibility complex (MHC) such as genes for the transporter associated with antigen processing (TAP). The aim of this study was to analyze TAP gene polymorphisms in patients with sarcoidosis using the amplificatory refraction mutation system (ARMS) PCR. To determine whether any association between TAP gene variation and sarcoidosis was ethnic-independent we examined two European populations: 117 unrelated UK Caucasoid patients with sarcoidosis and 290 healthy UK control subjects, and 87 unrelated Polish Slavonic patients with sarcoidosis and 158 healthy Polish control subjects. We detected significant differences in TAP2 between the UK control and patient groups, and in TAP2 between the Polish control and patient groups. Comparing the UK and Polish control groups, we observed a difference in TAP1. Examination of HLA-DPB1 in our UK population showed no associations with disease or between variants at the TAP gene loci and HLA-DPB1 variants. These results suggest associations at the TAP loci occur independently of HLA-DPB1 associations, that TAP associations seen may be involved in determining sarcoidosis susceptibility, and that such susceptibilities differ between UK and Polish populations. This first study of TAP genes in UK and Polish sarcoid populations has demonstrated the importance of using multiple defined ethnic populations in defining the role genetic factors play in sarcoidosis susceptibility and the importance of candidate gene studies.
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No. Sentence Comment
67 Statistical Analysis Statistical analysis was performed on the individual polymorphism results for the two populations studied using chi-square contingency ta- TABLE 2 COMPARISON OF TAP1 AND TAP2 POLYMORPHISM IN UK PATIENTS WITH SARCOIDOSIS AND CONTROL SUBJECTS STUDIED TAP Polymorphism Frequencies UK Control Subjects (%) (n ϭ 290) UK Patients with Sarcoidosis (%) (n ϭ 117) 2 * p Value Odds Ratio (95% CI)† TAP1 P333 Phenotypes Ile-333 97.9 97.4 NS NS - Val-333 33.4 35.0 NS NS - Genotypes Ile-333/Ile-333 66.6 65.0 Ile-333/Val-333 31.4 32.5 NS NS - Val-333/Val-333 2.1 2.5 TAP1 position 637 Phenotypes Asp-637 99.3 100 NS NS - Gly-637 31.4 27.4 NS NS - Genotypes Asp-637/Asp-637 68.6 72.6 Asp-637/Gly-637 30.7 27.4 NS NS - Gly-637/Gly-637 0.7 0 TAP2 position 379 Phenotypes Val-379 99.7 99.1 NS NS - Ile-379 25.2 25.6 NS NS - Genotypes Val-379/Val-379 74.8 74.4 Val-379/Ile-379 24.8 24.8 NS NS - Ile-379/Ile-379 0.3 0.9 TAP2 position 565 Phenotypes Ala-565 99.7 100 NS NS - Thr-565 19.0 8.5 6.74 0.009 0.4 (0.18-0.85) Genotypes Ala-565/Ala-565 81.0 91.5 2.5 (1.18-5.45) Ala-565/Thr-565 18.6 8.5 6.86 0.03 0.41 (0.19-0.87) Thr-565/Thr-565 0.3 0 TAP2 position 665 Phenotypes Thr-665 95.5 97.4 NS NS - Ala-665 51.4 35.0 8.93 0.003 0.51 (0.32-0.81) Genotypes Thr-665/Thr-665 48.6 65.0 1.96 (1.23-3.13) Thr-665/Ala-665 46.9 32.5 9.01 0.01 0.54 (0.34-0.87) Ala-665/Ala-665 4.5 2.6 0.56 (0.12-2.16) * The chi-square test with 1 df was performed for the comparison of overall phenotype frequencies.
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ABCB3 p.Ala565Thr 10471632:67:1100
status: NEW91 When we examined the HLA-DPB1 allele and phenotype frequencies in the UK control and patient groups, no difference was seen in the frequency of participants carrying HLA- TABLE 3 COMPARISON OF TAP1 AND TAP2 POLYMORPHISM IN THE POLISH PATIENTS WITH SARCOIDOSIS AND THE CONTROL SUBJECTS STUDIED TAP Polymorphism Frequencies Polish Control Subjects (%) (n ϭ 158) Polish Patients with Sarcoidosis (%) (n ϭ 87) 2 p Value TAP1 position 333 Phenotypes Ile-333 98.7 96.6 NS NS Val-333 31.0 29.5 NS NS Genotypes Ile-333/Ile-333 69.0 70.1 Ile-333/Val-333 29.7 26.4 NS NS Val-333/Val-333 1.3 3.4 TAP1 position 637 Phenotypes Asp-637 98.7 95.4 NS NS Gly-637 22.5 32.2 NS NS Genotypes Asp-637/Asp-637 77.5 67.8 Asp-637/Gly-637 21.2 27.6 NS NS Gly-637/Gly-637 1.3 5 TAP2 position 379 Phenotypes Val-379* 97.5 93.1 5.63 0.02 Ile-379 25.0 31.0 NS NS Genotypes Val-379/Val-379 75.0 69.0 Val-379/Ile-379 22.5 24.1 NS NS Ile-379/Ile-379 2.5 6.9 TAP2 position 565 Phenotypes Ala-565 100 100 NS NS Thr-565 23.1 20.5 NS NS Genotypes Ala-565/Ala-565 76.9 79.3 Ala-565/Thr-565 23.1 20.7 NS NS Thr-565/Thr-565 0.0 0 TAP2 position 665 Phenotypes Thr-665 96.2 97.7 NS NS Ala-665 46.9 38.6 NS NS Genotypes Thr-665/Thr-665 53.1 62.1 Thr-665/Ala-665 43.1 35.6 NS NS Ala-665/Ala-665 3.8 2.3 * Odds ratio ϭ 0.17; 95% CI ϭ 0.02-1.0.
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ABCB3 p.Ala565Thr 10471632:91:1057
status: NEW[hide] TAP1 and TAP2 polymorphism in HLA-B27-positive sub... Hum Immunol. 1995 Dec;44(4):236-42. Westman P, Partanen J, Leirisalo-Repo M, Koskimies S
TAP1 and TAP2 polymorphism in HLA-B27-positive subpopulations: no allelic differences in ankylosing spondylitis and reactive arthritis.
Hum Immunol. 1995 Dec;44(4):236-42., [PMID:8770637]
Abstract [show]
The polymorphic TAP1 and TAP2 genes encode subunits of the transporter that delivers peptides to the HLA class I molecules. Because the polymorphism of the TAP genes has been shown to affect peptide transport, it has been suggested that TAP genes are potential regulators of the immune response. We studied TAP1 and TAP2 polymorphism in two multifactorial HLA-B27-associated diseases, ankylosing spondylitis (N = 30) and reactive arthritis (N = 30), in order to establish whether TAP genes are involved in the different pathogenesis of these diseases. Healthy HLA-B27-positive individuals (N = 55) were chosen as the primary controls and 93 individuals represented the random Finnish population as secondary controls. We found differences between the random and HLA-B27-positive populations, thus suggesting that certain TAP alleles are prevalent in HLA-B27 haplotypes. No differences were found between the AS and ReA groups nor between either of them and the healthy HLA-B27-positive controls. Thus it seems unlikely that TAP polymorphism, ar the level studied, has a dominant role in the pathogenesis of these diseases. However, a family study is needed in order to determine whether the same TAP complexes are carried by the same haplotypes in these diseases.
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No. Sentence Comment
49 In addition, because individuals typed as TAP2 Val-3791 Be-379, Ala-565/Thr-565, Thr-665 could be either 2AD or 2CE heterozygotes, the exact frequencies of these alleles cannot be counted.
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ABCB3 p.Ala565Thr 8770637:49:64
status: NEW[hide] TAP polymorphism in patients with Behcet's disease... Ann Rheum Dis. 1995 May;54(5):386-8. Gonzalez-Escribano MF, Morales J, Garcia-Lozano JR, Castillo MJ, Sanchez-Roman J, Nunez-Roldan A, Sanchez B
TAP polymorphism in patients with Behcet's disease.
Ann Rheum Dis. 1995 May;54(5):386-8., [PMID:7794046]
Abstract [show]
OBJECTIVE: To determine if susceptibility to Behcet's disease (BD) is associated with polymorphism of HLA-DRB1, HLA-DQB1, DQB1, and TAP1 and TAP2 genes. METHODS: Fifty eight Spanish BD patients and 116 ethnically matched unrelated healthy subjects were typed at the HLA-DRB1 and HLA-DQB1 loci using polymerase chain reaction/sequence specific oligotyping (PCR/SSO). TAP1 and TAP2 alleles were assigned using amplification refractory mutation system-PCR. RESULTS: TAP1C was absent in BD patients, but was found in 12.1% of control subjects (pcorr < 0.05; relative risk = 0.06). Additionally, a linkage disequilibrium between HLA-DQB1*0501 and TAP2B was observed in BD patients (delta = 0.095, pcorr < 0.02), but not in the control group (delta = -0.0031, p > 0.05). CONCLUSIONS: The complete absence of TAP1C alleles in BD patients may indicate that TAP1 polymorphism is not without some significance in the development of BD. Furthermore, the existence of a linkage disequilibrium between HLA-DQB1*0501 and TAP2B in our patients suggests that the gene conferring susceptibility for BD is inherited as an extended haplotype in the population studied.
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No. Sentence Comment
22 Alleles were defined by haplotype association of these dimorphic variants: TAPlA = Ile-333/Asp-637, TAPlB = Val-333/Gly-637, and TAP1C = Val-333/Asp-637; TAP2A = Val-379/Ala-565F/hr-665, TAP2B = Val-379/Ala-565/Ala-665, and TAP2C = Ile- 379/Ala-565/Thr-665.
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ABCB3 p.Ala565Thr 7794046:22:241
status: NEW[hide] Alleles and haplotypes of the MHC-encoded ABC tran... Immunogenetics. 1993;37(5):373-80. Powis SH, Tonks S, Mockridge I, Kelly AP, Bodmer JG, Trowsdale J
Alleles and haplotypes of the MHC-encoded ABC transporters TAP1 and TAP2.
Immunogenetics. 1993;37(5):373-80., [PMID:8428770]
Abstract [show]
TAP1 and TAP2 are two major histocompatibility complex (MHC) genes, located between HLA-DP and -DQ, whose products form a transporter molecule involved in endogenous antigen processing. Polymorphic residues have been described in both genes and, in this study, we have identified another polymorphic site within the adenosine triphosphate (ATP)-binding domain of TAP2. We have used the amplification refractory mutation system (ARMS) polymerase chain reaction (PCR) to characterize TAP1 and TAP2 alleles and haplotypes in a reference panel of 115 homozygous typing cell lines. Of four possible TAP1 alleles, we observed three, and of eight possible TAP2 alleles, we observed five. Among 88 (homozygous typing cells) (HTCs) homozygous at HLA-DR, -DQ and -DP, 80 were also homozygous at TAP1 and TAP2. Of 27 HTCs homozygous at HLA-DR and -DQ, but heterozygous at -DP, 14 were homozygous at TAP1 or TAP2 and 13 heterozygous, consistent with recombination taking place either side of the TAP loci. Of the fifteen possible combinations of TAP1 and TAP2 alleles, we observed eleven, each at a frequency similar to that predicted by individual allele frequencies. In this ethnically heterogenous panel there is no indication that particular combinations of TAP1 and TAP2 have been maintained together.
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No. Sentence Comment
53 We now report a further polymorphism within the ATP-binding cassette of TAP2, A for G at nucleotide position 1693, resulting in the substition of Thr for Ala at amino acid position 565.
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ABCB3 p.Ala565Thr 8428770:53:146
status: NEW[hide] TAP1 and TAP2 polymorphism in coeliac disease. Immunogenetics. 1993;38(5):345-50. Powis SH, Rosenberg WM, Hall M, Mockridge I, Tonks S, Ivinson A, Ciclitira PJ, Jewell DP, Lanchbury JS, Bell JI, et al.
TAP1 and TAP2 polymorphism in coeliac disease.
Immunogenetics. 1993;38(5):345-50., [PMID:8344720]
Abstract [show]
Coeliac disease is strongly associated with HLA-DQ2, but it is possible that additional major histocompatibility complex genes also confer disease susceptibility. Encoded close to HLA-DQ are two genes, TAP1 and TAP2, whose products are believed to transport antigenic peptides from the cytoplasm into the endoplasmic reticulum. Comparison of 81 coeliac disease patients with caucasoid controls revealed an increased frequency of the alleles TAP1A and TAP2A in the patient population. However, no significant difference was found when patients were compared with HLA-DR and -DQ matched controls, indicating linkage disequilibrium between TAP1A, TAP2A, and HLA-DQ2. The TAP gene products do not have a major influence on susceptibility or resistance to coeliac disease in a Northern European Caucasoid population.
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No. Sentence Comment
37 TAP polymorphism Controls CD (n = 69) (n = 81) n % n % TAP2 position 379: Phenotype frequencies Val-379/Val-379 43 62.3 Val-379/Ile-379 25 36.2 Ile-379/Ile-379 1 1.4 Val-379 68 98.6 Ile-379 26 37.7 Gene frequencies Val-379 111 80.4 Ile-379 27 19.6 TAP2 position 565: Phenotype frequencies Ala-565/Ala-565 49 71 Ala-565/Thr-565 20 29 Thr-565/Thr-565 0 0 Ala-565 69 100 Thr-565 20 29 Gene frequencies Ala-565 118 85.5 Thr-565 20 14.5 TAP2 position 665: Phenotype frequencies Thr-665/Thr-665 39 56.5 Thr-665/Ala-665 27 39.1 Ala-665/Ala-665 3 4.3 Thr-665 66 95.7 Ala-665 30 43.5 Gene frequencies Thr-665 105 76.1 Ala-665 33 23.9 TAP1 position 333: Phenotype frequencies Ile-333/Ile-333 51 73.9 Ile-333/Val-333 16 23.2 Val-333/Val-333 2 2.9 Iie-333 67 97.1 Val-333 18 26.1 Gene frequencies Ile-333 118 85.5 Val-333 20 14.5 TAP1 position 637: Phenotype frequencies Asp-637/Asp-637 54 78.3 Asp-637/Gly-637 13 18.8 Gly-637/Gly-637 2 2.9 Asp-637 67 97.1 Gly-637 15 21.7 Gene frequencies Asp-637 121 87.7 Gly-637 17 12.3 74 91.4 * 7 8.6 * 0 0 81 100 7 8.6 * 155 95.7 * 7 4.3 * 75 92.6 * 6 7.4 * 0 0 81 100 6 7.4 * 156 96.3 * 6 3.7 * 69 85.2 * 10 12.3 * 2 2.5 79 97.5 12 14.8 * 148 91.4 * 14 8.6 * 68 84 12 14.8 1 1.2 80 98.8 13 16 148 91.4 14 8.6 71 87.7 9 11.1 1 1.2 80 98.8 10 12.3 151 93.2 11 6.8 Chi-square or Fisher's exact test: *p <0.001.
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ABCB3 p.Ala565Thr 8344720:37:311
status: NEW46 The remaining 13 individuals were typed as TAP2Val-379fIle-379, Ala-565/Thr-565, Thr-665/Thr-665 compound heterozygotes and could therefore be either TAP2A/TAP2Dor TAP2C/TAP2Eheterozygotes.
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ABCB3 p.Ala565Thr 8344720:46:64
status: NEW[hide] New transporter associated with antigen processing... Hum Immunol. 2003 Jul;64(7):733-40. Lajoie J, Zijenah LS, Faucher MC, Ward BJ, Roger M
New transporter associated with antigen processing (TAP-2) polymorphisms in the Shona people of Zimbabwe.
Hum Immunol. 2003 Jul;64(7):733-40., [PMID:12826376]
Abstract [show]
Most studies, to date, on transporter associated with antigen processing (TAP2) polymorphism have been conducted in Caucasians or Asians from industrialized countries. Because of the essential role of this molecule in antigen processing, the implication that polymorphism could be a major factor in human disease and the possible genetic variation at this locus among ethnically diverse populations, we undertook a study to analyze the full extent of TAP2 polymorphism in an indigenous Zimbabwean population (Shona ethnic group). Using single-stranded conformation polymorphism and DNA direct sequencing procedures, we detected the presence of 17 nucleotide sequence variations in the entire coding region of TAP2. Of these variants, 11 are nonconservative substitutions with respect to amino acid composition and are located in a region of the protein that could modulate its function. Six new polymorphic sites were identified in exon 1 (codons 15 Val-->Ala, 53 Leu-->Val), exon 3 (codon 220 Arg-->Arg), exon 4 (codons 257 Thr-->Ile, 313 Arg-->His), and exon10 (codon 609 Ala-->Val). Significant differences were seen in the distribution of the known 374Thr, 565Thr and 651Cys variants between African and non-African populations. These differences may reflect evolutionary pressures generated by environmental factors, such as prevalent pathogens in these geographically distinct regions. Further studies are needed to elucidate the net impact of TAP2 polymorphism on the protein's function and it's role in disease pathogenesis.
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No. Sentence Comment
101 It is interesting to note that 565Thr and 651Cys variants in Rwandans do not follow TABLE 4 Allelic frequencies of TAP 2 single nucleotide polymorphisms in different populations Population Number of alleles T257I R313H A374T V379I A565T A609V R651C T665A Zimbabwean 384 3.4% 4.7% 9.1% 19.3% 13.5% 3.9% 0% 20.3% Caucasiansa 152 - - 0% 18.4% 0.7% - 5.3% 15.1% Braziliansa 296 - - 2.0% 13.2% 10.1% - 4.0% 32.4% Rwandansa 570 - - 6.7% 11.8% 0% - 10.0% 30.2% Zambiansa 234 - - 6.8% 10.2% 18.3% - 0% 23.5% a From [41].
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ABCB3 p.Ala565Thr 12826376:101:231
status: NEW[hide] Genetic evidence of TAP1 gene variant as a suscept... Hum Immunol. 2013 Jun;74(6):803-7. doi: 10.1016/j.humimm.2013.01.001. Epub 2013 Feb 5. Shinde V, Marcinek P, Rani DS, Sunder SR, Arun S, Jain S, Nath I, Thangaraj K, Velavan TP, Valluri VL
Genetic evidence of TAP1 gene variant as a susceptibility factor in Indian leprosy patients.
Hum Immunol. 2013 Jun;74(6):803-7. doi: 10.1016/j.humimm.2013.01.001. Epub 2013 Feb 5., [PMID:23395648]
Abstract [show]
The heterodimeric transporter associated with antigen processing (TAP) gene loci is known to play a vital role in immune surveillance. We investigated a possible association of gene polymorphisms both in TAP1 and TAP2 in a cohort of clinically classified leprosy patients (n=222) and in ethnically matched controls (n=223). The TAP1 and TAP2 genes were genotyped for four single nucleotide polymorphisms TAP1 (rs1057141 Iso333Val and rs1135216 Asp637Gly) and TAP2 (rs2228396 Ala565Thr and rs241447 Ala665Thr) by direct sequencing and ARMS-PCR. The minor allele of TAP1 637G contributes to an increased risk to leprosy compared to controls (OR: 1.68, 95% CI 1.2-2.36, P=0.0057). An increased risk for the variant minor allele of the TAP1 637G to multibacillary (BL+LL) or paucibacillary (BT+TT) infections was also observed [multibacillary vs. controls (OR: 1.56, 95% CI 1.07-2.28, P=0.054); paucibacillary vs. controls (OR: 1.92, 95% CI 1.21-3.01, P=0.013)]. In the dominant model, the genotypes of the TAP1 rs1135216AG+GG additionally contributed to an increased risk. Overall our findings demonstrate that the TAP1 gene variant (rs1135216 Asp637Gly) influences the susceptibility to clinically classified leprosy patients in Indian population.
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2 The TAP1 and TAP2 genes were genotyped for four single nucleotide polymorphisms TAP1 (rs1057141 Iso333Val and rs1135216 Asp637Gly) and TAP2 (rs2228396 Ala565Thr and rs241447 Ala665Thr) by direct sequencing and ARMS-PCR.
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ABCB3 p.Ala565Thr 23395648:2:151
status: NEW36 Since the causative organism of both leprosy and tuberculosis represent the same genus Mycobacterium, we aim to investigate the association of TAP1 (rs1057141 Iso333Val and rs1135216 Asp637Gly) and TAP2 (rs2228396 Ala565Thr and rs241447 Ala665Thr) gene polymorphisms to the infection outcome in Indian leprosy cohort with clinically classified patient groups.
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ABCB3 p.Ala565Thr 23395648:36:214
status: NEW[hide] Characterization and allelic variation of the tran... Dev Comp Immunol. 2013 Dec;41(4):578-86. doi: 10.1016/j.dci.2013.07.011. Epub 2013 Jul 25. Gojanovich GS, Ross P, Holmer SG, Holmes JC, Hess PR
Characterization and allelic variation of the transporters associated with antigen processing (TAP) genes in the domestic dog (Canis lupus familiaris).
Dev Comp Immunol. 2013 Dec;41(4):578-86. doi: 10.1016/j.dci.2013.07.011. Epub 2013 Jul 25., [PMID:23892057]
Abstract [show]
The function of the transporters associated with antigen processing (TAP) complex is to shuttle antigenic peptides from the cytosol to the endoplasmic reticulum to load MHC class I molecules for CD8(+) T-cell immunosurveillance. Here we report the promoter and coding regions of the canine TAP1 and TAP2 genes, which encode the homologous subunits forming the TAP heterodimer. By sampling genetically divergent breeds, polymorphisms in both genes were identified, although there were few amino acid differences between alleles. Splice variants were also found. When aligned to TAP genes of other species, functional regions appeared conserved, and upon phylogenetic analysis, canine sequences segregated appropriately with their orthologs. Transfer of the canine TAP2 gene into a murine TAP2-defective cell line rescued surface MHC class I expression, confirming exporter function. This data should prove useful in investigating the association of specific TAP defects or alleles with immunity to intracellular pathogens and cancer in dogs.
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198 However, there was no overlap between canine (G127R, R373C, I425T and R695H) and human (V379I, A565T, R651C and Q665A) polymorphisms (http://hla.alleles.org/data/txt/tap2_prot.txt).
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ABCB3 p.Ala565Thr 23892057:198:95
status: NEW197 However, there was no overlap between canine (G127R, R373C, I425T and R695H) and human (V379I, A565T, R651C and Q665A) polymorphisms (http://hla.alleles.org/data/txt/tap2_prot.txt).
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ABCB3 p.Ala565Thr 23892057:197:95
status: NEW[hide] Significant association between TAP2 polymorphisms... Diagn Pathol. 2014 Jun 27;9:129. doi: 10.1186/1746-1596-9-129. Dai D, Chen Y, Ru P, Zhou X, Tao J, Ye H, Hong Q, Tang L, Pan G, Lin D, Gong Q, Lv Y, Xu L, Duan S
Significant association between TAP2 polymorphisms and rheumatoid arthritis: a meta-analysis.
Diagn Pathol. 2014 Jun 27;9:129. doi: 10.1186/1746-1596-9-129., [PMID:24972609]
Abstract [show]
BACKGROUND: Rheumatoid arthritis (RA) is a severe chronic immune mediated inflammatory disease that has been shown to be associated with human leukocyte antigen (HLA) loci. The transporter associated with antigen processing 2 (TAP2) has been identified to play an important role in the HLA-associated diseases and immune response. The goal of our meta-analysis was to summarize the contribution of TAP2 polymorphisms to the risk of RA. METHODS: Meta-analyses were performed between RA and 3 TAP2 coding polymorphisms that comprised TAP2-379Ile > Val (rs1800454), TAP2-565Ala > Thr (rs2228396) and TAP2-665Thr > Ala (rs241447). The meta-analyses were involved with 9 studies (24 individual studies) among 973 cases and 965 controls. RESULTS: Meta-analyses showed that TAP2-379Ile allele was significantly associated with an increased risk of RA (p = 0.0002, odds ratio (OR) = 1.44, 95% confidence interval (CI) = 1.18-1.74). This association was further shown only in the dominant model (p = 0.006, OR = 1.59, 95% CI = 1.14-2.22). Subgroup analyses by ethnicity revealed that the association of TAP2-379Ile was significant in Asians (p = 0.03, OR = 1.38, 95% CI = 1.04-1.83). In addition, another significant association of TAP2-565Thr allele with RA was observed in Europeans (p = 0.002, OR = 1.62, 95% CI = 1.20-2.20). CONCLUSIONS: Our meta-analyses suggested that TAP2-379Ile allele was significantly associated with a 59% increased risk in the dominant effect model. Subgroup analyses by ethnicity showed that TAP2-379-Ile increased the risk of RA by 38% in Asians and TAP2-565Thr increased the risk of RA by 38% in Europeans. VIRTUAL SLIDES: The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/2097080313124700.
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20 Among them, Ile379Val, Ala565Thr and Thr665Ala are * Correspondence: duanshiwei@nbu.edu.cn ߤ Equal contributors 1 Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China Full list of author information is available at the end of the article (c) 2014 Dai et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
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ABCB3 p.Ala565Thr 24972609:20:23
status: NEW