ABCC5 p.Thr1383Asn
| Predicted by SNAP2: | A: N (61%), C: N (66%), D: D (75%), E: D (75%), F: N (53%), G: D (71%), H: D (71%), I: N (93%), K: D (80%), L: N (57%), M: N (72%), N: D (66%), P: D (80%), Q: D (71%), R: D (80%), S: N (57%), V: N (93%), W: D (75%), Y: N (57%), |
| Predicted by PROVEAN: | A: D, C: D, D: D, E: D, F: D, G: D, H: D, I: D, K: D, L: D, M: D, N: D, P: D, Q: D, R: D, S: D, V: D, W: D, Y: D, |
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[hide] Strong linkage disequilibrium at the nucleotide an... Pharmacogenet Genomics. 2005 Feb;15(2):91-104. Gwee PC, Tang K, Sew PH, Lee EJ, Chong SS, Lee CG
Strong linkage disequilibrium at the nucleotide analogue transporter ABCC5 gene locus.
Pharmacogenet Genomics. 2005 Feb;15(2):91-104., [PMID:15861033]
Abstract [show]
The ABCC5 transporter is a ubiquitously expressed ATP-dependent efflux pump that exports nucleotide analogues, including thiopurine anticancer drugs and antiviral drugs. Polymorphisms within this gene may be associated with differences in response to these drugs between different individuals. Haplotype mapping may facilitate the identification of causal genetic variations in association studies. Here, we report the characterization of the haplotype and linkage disequilibrium (LD) profiles across the entire 100 kb of the ABCC5 gene in five ethnically unique populations. Of 24 single nucleotide polymorphisms (SNPs) examined, 16 were observed to occur at high frequency in all five populations and were used for further haplotype and LD analyses. The ABCC5 gene was found to be in strong LD in all populations with half-length LD (LD0.5) estimated to be between 106 and 293 kb long and useful LD extending beyond 100 kb. Low haplotype diversity was observed in the four non-African populations, where the total number of observed haplotypes constituted less than 22% of the predicted number of haplotypes in a simulated population that has undergone maximum recombination. Four and six tagging SNPs, which could account for approximately 90% of observed haplotypes, were identified in the non-African and African-American populations, respectively.
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55 92 Pharmacogenetics and Genomics 2005, Vol 15 No 2 Fig. 1 0 kb 10 kb 20 kb 30 kb 40 kb 50 kb 60 kb 0 kb 115 bp 5723 bp 1kb 2 kb 3 kb 4 kb 5 kb 6 kb 70 kb 80 kb 90 kb 100 kb * * * * * * * * * * * * * * * * Transcription start site 3' Flanking region5' Flanking region Genomic DNA Exons 1 2 34 5 678 910 11 12 1314 15 16 17 18192021222324 25 26 27 28 29 30 + 3'UTR cDNA ATG Translation start site 1 2 3 4 5 6 7 8 10 11 13 15 16 18 1920 212223 26 28 Exon Intron From sequencing From published reports From public databases Polymorphic in at least one ethnic population Used for haplotype and LD analyses e8 1145A > G (Gln382Gln) e12 1782A > C (Cys594Cys) e25 3606C > A (Tyr1202*) e29 4148C > A (Thr1383Asn) e25 3624C > A (Leu1208Leu) e9 1185C > T (Ala385Ala) e9 1200C > T (Ser400Ser) e30 5557A>G e30 5159C>T e30 4896G>A i-1-1990G>A i-1-1821T>C i-1-1679T>A i-1-1205C>T i-1-889T>C i-1-793C>A i-1-177C>T i-1-115A>C i1628G>C i11834C>T i27980C>T i5374C>T e81145A>G e91185C>T e91200C>T e121782C>T e253606C>A e253624C>T e294148C>A e304896G>A e305159C>T e305557A>G i306272A>G i307161G>A Distribution of single nucleotide polymorphisms (SNPs) across the ABCC5 gene.
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ABCC5 p.Thr1383Asn 15861033:55:693
status: NEW