Table 1.
Human NT5C3 polymorphisms. Locations in the gene, nucleotide sequence alterations, amino acid sequence alterations, and minor allele frequencies of polymorphisms in the four populations studied are listed. If a polymorphism had already been deposited in a public database (dbSNP or HapMap), an rs number is indicated. All other polymorphisms listed are unique to this study. Polymorphisms within exons have been boxed. IVS is intervening sequence. The numbering scheme for nucleotide positions is based on assignment of the (+1) position to the “A” in the translation initiation codon, with nucleotides 5’ to that position assigned negative, and those 3’ within the cDNA assigned positive numbers. Nucleotide positions in introns are numbered from the nearest splice site, with distances from 3’ splice junction assigned positive and distances from 5’ splice junctions assigned negative numbers. AA, African-American; CA, Caucasian-American; HCA, Han Chinese-American; MA, Mexican-American; FR, flanking region; UTR, untranslated region.
| NT5C3 Polymorphism | ||||||||
|---|---|---|---|---|---|---|---|---|
| Frequency of Variant Allele |
||||||||
| Gene Location | Nucleotide | Nucleotide Change | Amino Acid Change | AA | CA | HCA | MA | HapMap and/or dbSNP |
| 5’-FR | -1273 | A→C | 0.100 | 0.000 | 0.000 | 0.008 | ||
| 5’-FR | -1270 | T→C | 0.000 | 0.008 | 0.000 | 0.000 | ||
| 5’-FR | -1145 | T→G | 0.200 | 0.358 | 0.258 | 0.442 | rs34307182 | |
| 5’-FR | -1143 | G→A | 0.283 | 0.292 | 0.317 | 0.133 | rs6976843 | |
| 5’-FR | -1018 | T→C | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 5’-FR | -944 | T→C | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 5’-FR | -884 | G insertion | 0.033 | 0.008 | 0.000 | 0.000 | ||
| 5’-FR | -693 | C→G | 0.000 | 0.000 | 0.142 | 0.017 | ||
| 5’-FR | -656 | C→T | 0.000 | 0.017 | 0.000 | 0.008 | ||
| 5’-FR | -654 | G→A | 0.017 | 0.042 | 0.092 | 0.083 | ||
| 5’-FR | -653 | T→C | 0.000 | 0.000 | 0.008 | 0.000 | ||
| 5’-FR | -552 | G→C | 0.333 | 0.342 | 0.417 | 0.250 | rs10262141 | |
| 5’-FR | -496 | C→T | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 5’-FR | -373 | C→T | 0.000 | 0.008 | 0.000 | 0.000 | ||
| 5’-FR | -354 | T→C | 0.225 | 0.342 | 0.275 | 0.225 | rs13228827 | |
| 5’-FR | -340 | T→G | 0.042 | 0.017 | 0.008 | 0.000 | ||
| 5’-FR | -302 | A→G | 0.333 | 0.342 | 0.417 | 0.250 | rs13228639 | |
| 5’-FR | -267 | 15 nucleotide tandem repeat | 0.000 | 0.008 | 0.000 | 0.000 | ||
| 5’-FR | -258 | 20 nucleotide tandem repeat | 0.025 | 0.000 | 0.000 | 0.000 | ||
| 5’-UTR | -194 | T→C | 0.000 | 0.000 | 0.000 | 0.008 | ||
| 5’-UTR | -134 | deletion of GGTGGG | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 5’-UTR | -67 | T→C | 0.000 | 0.033 | 0.000 | 0.008 | ||
| IVS 1 | -5780 | C→G | 0.025 | 0.000 | 0.133 | 0.017 | ||
| IVS 1 | -5767 | A→T | 0.000 | 0.000 | 0.025 | 0.000 | ||
| IVS 1 | -5757 | A→T | 0.017 | 0.000 | 0.000 | 0.000 | ||
| IVS 1 | -5756 | T→A | 0.000 | 0.000 | 0.008 | 0.000 | ||
| IVS 1 | -5714 | A→G | 0.008 | 0.000 | 0.133 | 0.017 | ||
| IVS 1 | -5705 | C→A | 0.000 | 0.008 | 0.000 | 0.000 | ||
| IVS 1 | -5654 | A→G | 0.008 | 0.000 | 0.000 | 0.000 | ||
| IVS 1 | -5635 | G→A | 0.000 | 0.000 | 0.017 | 0.000 | ||
| IVS 1 | -5633 | A→G | 0.008 | 0.000 | 0.000 | 0.000 | ||
| IVS 1 | -5418 | G→A | 0.225 | 0.342 | 0.283 | 0.225 | rs10230500 | |
| IVS 1 | -5125 | T→G | 0.000 | 0.000 | 0.008 | 0.000 | ||
| IVS 1 | -5059 | G→A | 0.050 | 0.000 | 0.000 | 0.000 | ||
| IVS 1 | -4900 | G→A | 0.000 | 0.000 | 0.058 | 0.000 | ||
| IVS 1 | -4645 | G→T | 0.008 | 0.000 | 0.000 | 0.000 | ||
| IVS 1 | -19 | A→C | 0.000 | 0.009 | 0.000 | 0.000 | ||
| Exon 2 | 9 | T→C | 0.033 | 0.017 | 0.008 | 0.000 | rs17170223 | |
| IVS 2 | 139 | A→G | 0.008 | 0.000 | 0.000 | 0.000 | ||
| IVS 2 | -307 | T→A | 0.000 | 0.000 | 0.008 | 0.000 | ||
| IVS 2 | -237 | G→A | 0.017 | 0.000 | 0.000 | 0.000 | ||
| IVS 2 | -4 | T→G | 0.033 | 0.008 | 0.000 | 0.000 | ||
| IVS 3 | 103 | C→T | 0.008 | 0.000 | 0.000 | 0.000 | ||
| IVS 4 | 35 | C→T | 0.050 | 0.000 | 0.000 | 0.000 | ||
| IVS 4 | -114 | G→A | 0.025 | 0.017 | 0.008 | 0.000 | rs11974256 | |
| IVS 5 | 77 | C→G | 0.000 | 0.000 | 0.008 | 0.000 | ||
| IVS 5 | 266 | G→A | 0.250 | 0.342 | 0.417 | 0.242 | rs3750119 | |
| IVS 5 | 430 | G→A | 0.250 | 0.342 | 0.417 | 0.242 | rs3750118 | |
| IVS 5 | 533 | T→G | 0.008 | 0.000 | 0.000 | 0.000 | ||
| IVS 5 | 548 | A→T | 0.000 | 0.000 | 0.000 | 0.008 | ||
| IVS 5 | 647 | G→T | 0.000 | 0.000 | 0.000 | 0.008 | ||
| Exon 6 | 276 | C→T | 0.250 | 0.342 | 0.417 | 0.242 | rs3750117 | |
| Exon 6 | 306 | T→C | 0.100 | 0.000 | 0.000 | 0.000 | ||
| IVS 6 | 9 | A→G | 0.000 | 0.042 | 0.000 | 0.008 | ||
| IVS 6 | -71 | C→T | 0.117 | 0.325 | 0.275 | 0.225 | rs2392209 | |
| Exon 9 | 759 | G→A | 0.000 | 0.008 | 0.000 | 0.000 | ||
| IVS 9 | 52 | T→A | 0.000 | 0.000 | 0.000 | 0.008 | ||
| IVS 9 | 61 | A→G | 0.025 | 0.017 | 0.008 | 0.000 | ||
| IVS 9 | -267 | A→G | 0.225 | 0.342 | 0.283 | 0.225 | rs2893457 | |
| IVS 9 | -38 | C→T | 0.000 | 0.000 | 0.008 | 0.000 | ||
| Exon 10 | 847 | G→C | Asp (283) His | 0.000 | 0.000 | 0.000 | 0.008 | |