Table 1.
Human BHMT and BHMT2 genetic polymorphisms. Polymorphism locations, alterations in nucleotide and amino acid sequences, as well as minor allele frequencies for all four ethnic groups studied are listed. Polymorphisms within exons are shaded. SNPs in exons and 5′-FRs have been numbered on the basis of their locations in the cDNA, with the ‘A’ in the translation initiation codon assigned (+1). Negative numbers are located 5′, and positive numbers 3′ to this position. SNPs in introns have been numbered based on their distance to the nearest 5′ or 3′ exon-intron splice junctions, using positive and negative numbers, respectively. The final column indicates whether the polymorphism was already present in dbSNP.
| BHMT Polymorphisms | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| # | Gene Location | Nucleotide Location | Nucleotide Sequence Alteration | Amino Acid Sequence Alteration | Minor allele frequencies | dbSNP designation | |||
| AA | CA | HCA | MA | ||||||
| 1 | 5′FR | −809 | A to C | 0.000 | 0.000 | 0.008 | 0.000 | ||
| 2 | 5′FR | −773 | T to C | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 3 | 5′FR | −448 | C to T | 0.117 | 0.117 | 0.000 | 0.042 | rs16876512 | |
| 4 | 5′FR | −412 | C to A | 0.017 | 0.000 | 0.000 | 0.000 | ||
| 5 | 5′FR | −142 | G to T | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 6 | Intron 1 | −164 | T to C | 0.067 | 0.083 | 0.100 | 0.042 | rs16876527 | |
| 7 | Intron 1 | −93 | C to T | 0.042 | 0.000 | 0.000 | 0.000 | ||
| 8 | Exon 2 | 46 | C to T | Arg(16)Cys | 0.008 | 0.000 | 0.000 | 0.000 | |
| 9 | Intron 2 | 41 | G to A | 0.008 | 0.000 | 0.000 | 0.008 | ||
| 10 | Exon 3 | 222 | C to T | 0.033 | 0.000 | 0.000 | 0.000 | ||
| 11 | Intron 3 | 132 | G to A | 0.000 | 0.000 | 0.017 | 0.000 | ||
| 12 | Exon 4 | 438 | G to A | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 13 | Intron 4 | 52 | C to T | 0.092 | 0.375 | 0.492 | 0.408 | rs567754 | |
| 14 | Exon 5 | 589 | C to T | Pro(197)Ser | 0.033 | 0.000 | 0.000 | 0.000 | |
| 15 | Exon 5 | 595 | G to A | Gly(199)Ser | 0.000 | 0.017 | 0.000 | 0.000 | |
| 16 | Intron 5 | −132 | G to C | 0.000 | 0.000 | 0.000 | 0.008 | ||
| 17 | Intron 5 | −89 | A to G | 0.392 | 0.292 | 0.150 | 0.183 | rs694290 | |
| 18 | Exon 6 | 716 | G to A | Arg(239)Gln | 0.192 | 0.292 | 0.292 | 0.383 | rs3733890 |
| 19 | Exon 6 | 792 | C to T | 0.000 | 0.000 | 0.000 | 0.200 | rs4703772 | |
| 20 | Intron 6 | 68 | T to C | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 21 | Exon 7 | 852 | C to T | 0.017 | 0.000 | 0.133 | 0.042 | ||
| 22 | Exon 7 | 858 | A to G | 0.000 | 0.008 | 0.000 | 0.000 | ||
| 23 | Exon 7 | 966 | A to G | 0.008 | 0.025 | 0.000 | 0.008 | ||
| 24 | Intron 7 | −51 | A to G | 0.000 | 0.000 | 0.008 | 0.000 | ||
| 25 | 3′UTR | 1251 | C to G | 0.000 | 0.000 | 0.025 | 0.000 | ||
| BHMT2 Polymorphisms | |||||||||
| Gene Location | Nucleotide Location | Nucleotide Sequence Alteration | Amino Acid Sequence Alteration | Minor allele frequencies | dbSNP designation | ||||
| # | AA | CA | HCA | MA | |||||
| 1 | 5′FR | −799 | T to G | 0.033 | 0.000 | 0.000 | 0.000 | rs6877474 | |
| 2 | 5′FR | −762 | A to C | 0.442 | 0.192 | 0.175 | 0.208 | rs642934 | |
| 3 | 5′FR | −671 | T to C | 0.008 | 0.000 | 0.000 | 0.033 | ||
| 4 | 5′FR | −622 | T to C | 0.217 | 0.575 | 0.642 | 0.575 | rs4998017 | |
| 5 | 5′FR | −616 to −617 | deletion of GC | 0.150 | 0.575 | 0.642 | 0.575 | rs5868949 | |
| 6 | 5′FR | −519 | A to G | 0.175 | 0.158 | 0.050 | 0.175 | rs644191 | |
| 7 | 5′FR | −431 | A to G | 0.000 | 0.000 | 0.008 | 0.000 | ||
| 8 | 5′FR | −406 | T to A | 0.025 | 0.000 | 0.000 | 0.008 | ||
| 9 | 5′FR | −334 | C to G | 0.000 | 0.000 | 0.000 | 0.008 | ||
| 10 | 5′FR | −265 | A to G | 0.000 | 0.000 | 0.008 | 0.000 | ||
| 11 | 5′FR | −151 | G to C | 0.033 | 0.000 | 0.000 | 0.000 | ||
| 12 | Intron 1 | 72 | C to T | 0.033 | 0.000 | 0.000 | 0.000 | ||
| 13 | Intron 1 | 136 | A to G | 0.033 | 0.000 | 0.000 | 0.000 | ||
| 14 | Intron 1 | −262 | G to A | 0.042 | 0.000 | 0.000 | 0.000 | ||
| 15 | Intron 1 | −158 | T to C | 0.075 | 0.108 | 0.008 | 0.100 | ||
| 16 | Intron 1 | −142 | T to C | 0.000 | 0.000 | 0.008 | 0.000 | ||
| 17 | Exon 2 | 162 | C to T | 0.333 | 0.692 | 0.625 | 0.617 | rs682985 | |
| 18 | Intron 2 | 56 | A to G | 0.025 | 0.000 | 0.000 | 0.008 | ||
| 19 | Intron 2 | −52 | T to A | 0.025 | 0.000 | 0.000 | 0.000 | ||
| 20 | Exon 3 | 197 | C to T | Ala(66)Val | 0.033 | 0.000 | 0.000 | 0.008 | |
| 21 | Intron 3 | −95 | C to T | 0.000 | 0.008 | 0.000 | 0.000 | ||
| 22 | Intron 3 | −92 | A to G | 0.000 | 0.000 | 0.008 | 0.000 | ||
| 23 | Intron 4 | 59 | C to T | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 24 | Intron 4 | 99 | A to G | 0.008 | 0.000 | 0.000 | 0.000 | ||
| 25 | Exon 5 | 463 | G to T | Val(155)Phe | 0.000 | 0.008 | 0.000 | 0.000 | |
| 26 | Intron 5 | 1 | G to A | 0.017 | 0.000 | 0.000 | 0.000 | ||
| 27 | Intron 5 | 45 | C to T | 0.042 | 0.117 | 0.000 | 0.033 | ||
| 28 | Intron 5 | 46 | G to A | 0.000 | 0.000 | 0.000 | 0.067 | ||
| 29 | Intron 5 | −109 | A to G | 0.000 | 0.000 | 0.000 | 0.033 | ||
| 30 | Intron 5 | −69 | C to A | 0.000 | 0.000 | 0.000 | 0.008 | ||
| 31 | Intron 5 | −48 | Deletion of A | 0.025 | 0.008 | 0.000 | 0.000 | ||
| 32 | Intron 5 | −1 | G to A | 0.008 | 0.008 | 0.000 | 0.000 | ||
| 33 | Exon 6 | 648 | G to A | 0.033 | 0.000 | 0.000 | 0.000 | ||
| 34 | Exon 6 | 653 | C to T | Thr(218)Met | 0.008 | 0.000 | 0.000 | 0.000 | |
| 35 | Exon 6 | 699 | G to T | 0.000 | 0.017 | 0.000 | 0.008 | ||
| 36 | Exon 6 | 709 | G to A | Val(237)Met | 0.000 | 0.008 | 0.000 | 0.000 | |
| 37 | Intron 6 | 17 | A to G | 0.000 | 0.000 | 0.008 | 0.000 | ||
| 38 | Intron 7 | −90 | T to A | 0.025 | 0.000 | 0.000 | 0.008 | ||
| 39 | 3′UTR | 1126 | C to G | 0.008 | 0.000 | 0.000 | 0.000 | ||