ABCB2 p.Val518Ile
| Predicted by SNAP2: | A: D (91%), C: D (63%), D: D (95%), E: D (85%), F: N (57%), G: D (80%), H: D (80%), I: N (78%), K: D (95%), L: N (87%), M: N (72%), N: D (85%), P: D (91%), Q: D (80%), R: D (85%), S: D (75%), T: D (95%), W: D (75%), Y: D (80%), |
| Predicted by PROVEAN: | A: D, C: D, D: D, E: D, F: D, G: D, H: D, I: N, K: D, L: N, M: N, N: D, P: D, Q: D, R: D, S: D, T: D, W: D, Y: D, |
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[hide] Variation in HLA class I antigen-processing genes ... J Infect Dis. 2008 Feb 1;197(3):371-81. Deshpande A, Wheeler CM, Hunt WC, Peyton CL, White PS, Valdez YE, Nolan JP
Variation in HLA class I antigen-processing genes and susceptibility to human papillomavirus type 16-associated cervical cancer.
J Infect Dis. 2008 Feb 1;197(3):371-81., [PMID:18248301]
Abstract [show]
BACKGROUND: Persistent infection with human papillomavirus type 16 (HPV16) is a primary etiological factor for the development of cervical cancer. Genes involved in antigen processing influence both the repertoire of antigens presented by HPV16-infected cells and the nature of HPV16-specific immune responses. Genetic variation in these genes may affect protein structure and function and, consequently, the ability of an individual to clear HPV infection. METHODS: Thirty-five single-nucleotide polymorphisms (SNPs) in 5 genes (LMP2, TAP1, LMP7, TAP2, and Tapasin) were investigated for association with susceptibility to HPV16-associated cervical cancer. Sequencing of these genes resulted in the discovery of 15 previously unreported SNPs. Microsphere-array flow cytometry-based genotyping was conducted on 787 samples from Hispanic and non-Hispanic white women (241 randomly selected control subjects, 205 HPV16-positive control subjects, and 341 HPV16-positive case subjects with cervical cancer). RESULTS: For 9 SNPs, 8 of which had not previously been reported in the context of cervical cancer, there were statistically significant differences between the genotype distribution in case subjects and that in control subjects. Haplotype analysis of 3 haplotype blocks revealed 3 haplotypes with significant differences in frequency in case-control comparisons. Both HPV16-specific and non-type-specific differences in genotype distribution were seen. CONCLUSIONS: Genes involved in antigen processing for HLA class I presentation may contribute to susceptibility to cervical cancer.
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No. Sentence Comment
163 SNP designation Allele Function Minor-allele risk/protection status TAP1-03 G/T Changes codon 458 from valine to leucine; included in peptide-binding region of transporter [35, 36]; effect on function unknown Protective TAP1-04 G/T Intron 6 Protective TAP1-06 G/A Changes codon 518 from valine to isoleucine; contributes to hydrophilic nucleotide-binding domain of transporter for processed antigens; functional effect demonstrated for kinase-binding domain of the A kinase-anchoring protein 2 [37] Risk TAP1-07 A/G Changes codon 637 from aspartate to glycine; contributes to nucleotide-binding domain of transporter for processed antigens; affects transporter preference for peptides [38] Risk TAP2-02 G/T Synonymous change in codon 386; contributes to nucleotide-binding domain of transporter for processed antigens; effect on function unknown Risk TAP2-04 A/G New SNP in intron 6, discovered and validated Protective TAP2-09 A/G Changes codon 577 from methionine to valine; sequence alignment predicts involvement in ATP binding by transporter; effect on function unknown Risk Tapasin-02 G/T New SNP; changes codon 59 from aspartate to tyrosine; part of N-terminal ER lumenal domain of tapasin protein; effect on function unknown.
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ABCB2 p.Val518Ile 18248301:163:278
status: NEW164 SNP designation Allele Function Minor-allele risk/protection status TAP1-03 G/T Changes codon 458 from valine to leucine; included in peptide-binding region of transporter [35, 36]; effect on function unknown Protective TAP1-04 G/T Intron 6 Protective TAP1-06 G/A Changes codon 518 from valine to isoleucine; contributes to hydrophilic nucleotide-binding domain of transporter for processed antigens; functional effect demonstrated for kinase-binding domain of the A kinase-anchoring protein 2 [37] Risk TAP1-07 A/G Changes codon 637 from aspartate to glycine; contributes to nucleotide-binding domain of transporter for processed antigens; affects transporter preference for peptides [38] Risk TAP2-02 G/T Synonymous change in codon 386; contributes to nucleotide-binding domain of transporter for processed antigens; effect on function unknown Risk TAP2-04 A/G New SNP in intron 6, discovered and validated Protective TAP2-09 A/G Changes codon 577 from methionine to valine; sequence alignment predicts involvement in ATP binding by transporter; effect on function unknown Risk Tapasin-02 G/T New SNP; changes codon 59 from aspartate to tyrosine; part of N-terminal ER lumenal domain of tapasin protein; effect on function unknown.
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ABCB2 p.Val518Ile 18248301:164:278
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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No. Sentence Comment
190 Conversely, none of the human TAP1 polymorphic sites (V80G, L131P, I333V, A370V, V458L, V518I, D637G and R648Q) were observed to vary in the deduced sequences from our dogs.
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ABCB2 p.Val518Ile 23892057:190:88
status: NEW189 Conversely, none of the human TAP1 polymorphic sites (V80G, L131P, I333V, A370V, V458L, V518I, D637G and R648Q) were observed to vary in the deduced sequences from our dogs.
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ABCB2 p.Val518Ile 23892057:189:88
status: NEW