ABCB3 p.Leu3Val
| Predicted by SNAP2: | A: N (78%), C: N (93%), D: N (61%), E: N (66%), F: N (97%), G: N (78%), H: N (82%), I: N (97%), K: N (72%), M: N (97%), N: N (78%), P: N (72%), Q: N (82%), R: N (78%), S: N (82%), T: N (93%), V: N (97%), W: N (87%), Y: N (93%), |
| Predicted by PROVEAN: | A: N, C: N, D: D, E: D, F: N, G: D, H: N, I: N, K: N, M: N, N: D, P: N, Q: N, R: D, S: N, T: N, V: N, W: D, Y: N, |
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[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
4 Six new polymorphic sites were identified in exon 1 (codons 15 Val3Ala, 53 Leu3Val), exon 3 (codon 220 Arg3Arg), exon 4 (codons 257 Thr3Ile, 313 Arg3His), and exon10 (codon 609 Ala3Val).
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ABCB3 p.Leu3Val 12826376:4:75
status: NEW75 TABLE 3 TAP2 nucleotide sequence variations observed in Zimbabweans Location Nucleotide substitution Genomic position Amino acid change Reference Codon 15 GTG-GCG 40 471 Val 3 Ala New Codon 53 CTA-GTA 40 584 Leu 3 Val New Codon 220 CGA-AGA 42 947 None (Arg) New Codon 257 ACC-ATC 43 332 Thr 3 Ile New Codon 313 CGC-CAC 43 500 Arg 3 His New Codon 374 GCC-ACC 46 011 Ala 3 Thr [14] Codon 379 GTA-ATA 46 026 Val 3 Ile [5] Intron 5 TCTT (deletion) 46 184 [14] Intron 5 T-A 46 194 [14] Intron 5 T-C 46 195 [14] Codon 386 GGG-GGT 46 214 None (Gly) [13] Codon 458 ACG-ACA 47 956 None (Thr) [14] Codon 466 GGG-GGA 47 980 None (Gly) [14] Codon 467 GTT-ATT 47 981 Val 3 Ile [14] Codon 565 GCT-ACT 48 629 Ala 3 Thr [18] Codon 604 GGA-GGG 49 141 None (Gly) [16] Codon 609 GCG-GTG 49 155 Ala 3 Val New Intron 10 C-T 49 270 [24] Codon 665 ACA-GCA 49 687 Thr 3 Ala [9, 10] Codon 687 TAG-CAG 49 753 Stop 3 Gln [9, 10] Codon 697 GTG-GTT 49 785 None (Val) [9, 10] Variant nucleotides are in bold.
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ABCB3 p.Leu3Val 12826376:75:208
status: NEW