Table 2.
Frequencies of the primary SAM-dependent methyltransferases polymorphisms1 in the 1000 Genomes Project2, ExAC3, and the BUSHMAN Population4.
| MTases | dbSNP rs# [Minor Allele Frequency (MAF)] | Amino Acid change | Base change | Allele frequency (numbers of individuals)5 | Genotype frequency (numbers of individuals)6 | Data source |
|---|---|---|---|---|---|---|
| COMT | rs4680 (0.37) | Val158Met Val108 Met |
472G > A | G: 0.631 (3159) A: 0.369 (1849) |
G|G: 0.413 (1034) A|G: 0.436 (1091) A|A: 0.151 (379) |
1000 Genomes Project |
| COMT | rs4633 (0.37) | His62His Synonymous Variant Leu136Leu |
186C > T | C: 0.628 (3147) T: 0.372 (1861) C: 0.703 (3521) |
C|C: 0.411 (1028) C|T: 0.436 (1091) T|T: 0.154 (385) C|C: 0.509(1275) |
1000 Genomes Project |
| COMT | rs4818 (0.30) | Synonymous Variant | 408C > G/T | G: 0.297 (1487) | C|G: 0.388(971) G|G: 0.103 (258) |
1000 Genomes Project |
| COMT | rs6267 (0.01) | Ala72Thr/Ser | 214G > A / T | G: 0.987 (4941) T: 0.013 (67) |
G|G: 0.973 (2437) G|T: 0.027 (67) |
1000 Genomes Project |
| COMT | rs2020917 (0.21) | intron variant (Promotor region) | −628C > T | C: 0.787 (3941) T: 0.213 (1067) |
C|C: 0.625 (1566) C|T: 0.323 (809) T|T: 0.052 (129) |
1000 Genomes Project |
| COMT | rs737865 (0.23) | intron variant (Promotor region) | 92 + 701A > G | A: 0.773 (3873) G: 0.227 (1135) |
A|A: 0.602 (1507) A|G: 0.343 (859) G|G: 0.055 (138) |
1000 Genomes Project |
| AS3MT | rs201702937 (0.01) | His51Arg | 152A > G | A: 0.9998 (5007) G: 0.000199 (1) |
A|A: 0.9996 (2503) A|G: 0.00039 (1) |
1000 Genomes Project |
| AS3MT | rs80317306 (<0.01) | Cys61Trp | 183T > G | T: 0.995 (120200) G: 0.005 (646) |
T|T 0.991 (60100) T|G 0.009 (646) |
Exome Aggregation Consortium (ExAC) |
| AS3MT | rs112056792 (< 0.01) | Ile136Thr | 407T > C | NA 1 |
NA 1 (Male) |
BUSHMAN POP |
| AS3MT | rs35232887 (0.01) | Arg173Trp | 517C > T | C: 0.999 (5003) T: 0.001 (5) |
C|C: 0.998 (2499) C|T: 0.002 (5) |
1000 Genomes Project |
| AS3MT | rs370022454 (< 0.01) | Trp203Cys | 609G > T | G: 0.999734 (3763) T: 0.000265675 (1) |
G|G: 0.999 (1881) G|T: 0.001 (1) |
African-American of NHLBI Exome Sequencing Project7 |
| AS3MT | rs139656545 (<0.01) | Arg251His | 752G > A | G: 0.998 (4997) A: 0.002 (11) T: 0.923 (4622) |
G|G: 0.996 (2493) A|G: 0.004 (11) T|T: 0.854 (2138) |
1000 Genomes Project |
| AS3MT | rs11191439 (0.08) | Met287Thr | 860 T > C/A | C: 0.077 (386) | C|T: 0.138 (346) C|C: 0.008 (20) |
1000 Genomes Project |
| AS3MT | rs34556438 (<0.01) | Thr306Ile | 917C > T | C: 0.99951 (8164) T: 0.000489716 (4) T: 0.765 (3829) |
C|C: 0.999 (4080) C|T: 0.001 (4) T|T: 0.589 (1475) |
European-American of NHLBI Exome Sequencing Project7 |
| AS3MT | rs3740392 (0.24) | Intron Variant | 610 + 63T > C | C: 0.235 (1179) A: 0.230 (1153) |
C|T: 0.351 (879) C|C: 0.060 (150) A|A: 0.082 (205) |
1000 Genomes Project |
| INMT | rs6970396 (0.23) | 3 Prime UTR Variant | 8797A > G | G: 0.770 (3855) | A|G: 0.297 (743) G|G: 0.621 (1556) |
1000 Genomes Project |
| INMT | rs77743549 (0.01) | His46Pro | 137A > C | A: 0.995 (4984) C: 0.005 (24) C: 0.744 (3728) |
A|A: 0.990 (2480) A|C: 0.010 (24) C|C: 0.558 (1397) |
1000 Genomes Project |
| NNMT | rs694539 (0.26) | Intron variant | −216–151C > T | T: 0.256 (1280) A: 0.443 (2218) |
C|T: 0.373 (934) T|T: 0.069 (173) A|A: 0.204 (510) |
1000 Genomes Project |
| NNMT | rs1941404 (0.44) | Intron variant | −224 + 122A > G | G: 0.557 (2790) G: 0.510 (2555) |
A|G: 0.478 (1198) G|G: 0.318 (796) G|G: 0.276 (691) |
1000 Genomes Project |
| NNMT | rs10891644 (0.49) | Intron variant | −129–11693G > T | T: 0.490 (2453) G: 0.587 (2940) |
G|T: 0.468 (1173) T|T: 0.256 (640) G|G: 0.368 (921) |
1000 Genomes Project |
| PNMT | rs876493 (0.41) | 5 prime UTR variant | 93 + 222G > A | A: 0.413 (2068) C: 0.940 (4710) |
A|A: 0.194 (485) A|G: 0.438 (1098) C|C: 0.886 (2219) |
1000 Genomes Project |
| HNMT | rs11558538 (0.06) rs1800460 |
Thr105Ile | 314C > T | T: 0.060 (298) C: 0.987 (4944) |
C|T: 0.109 (272) T|T: 0.005 (13) C|C: 0.975 (2441) |
1000 Genomes Project |
| TPMT | TPMT*3B (0.01) rs1142345 |
Ala154Thr | 460C > T | T: 0.013 (64) T: 0.961 (4812) |
C|T: 0.025 (62) T|T: 0.0004 (1) T|T: 0.925 (2316) |
1000 Genomes Project |
| TPMT | TPMT*3C (0.04) | Tyr240Cys Pro463Pro |
719T > C | C: 0.039 (196) T: 0.466 (2334) |
C|C: 0.003 (8) C|T: 0.072 (180) T|T: 0.228 (570) |
1000 Genomes Project |
| Dnmt1 | rs2228611 (0.47) | Synonymous Variant | 1389T > A/C | C: 0.534 (2674) T: 0.802 (4015) |
C|T: 0.477 (1194) C|C: 0.296 (740) T|T: 0.653 (1636) |
1000 Genomes Project |
| Dnmt1 | rs2228612 (0.20) | Ile327Phe | 979T > A/C /G | C: 0.198 (993) G: 0.722 (3615) |
C|T: 0.297 (743) C|C: 0.050 (125) G|G: 0.534 (1338) |
1000 Genomes Project |
| DNMT1 | rs2162560 (0.28) | Intron Variant | G > A | A: 0.278 (1393) T: 0.955 (4782) |
A|G: 0.375 (939) A|A: 0.091 (227) T|T: 0.918 (2299) |
1000 Genomes Project |
| DNMT1 | rs16999593 (0.05) | His97Arg | 290 T > C | C: 0.045 (226) | C|T: 0.073 (184) C|C: 0.008 (21) |
1000 Genomes Project |
| Dnmt3A | rs1550117 (0.11) | Upstream Transcript Variant | A > G/T | A: 0.114 (572) G: 0.886 (4436) C: 0.312 (1562) |
A|A: 0.018 (46) A|G: 0.192 (480) G|G: 0.790 (1978) C|C: 0.134 (336) |
1000 Genomes Project |
| Dnmt3B | rs2424913 (0.31) | Intron Variant | C > A/T/G | T: 0.688 (3446) G: 0.276 (1383) |
C|T: 0.355 (890) T|T: 0.510 (1278) G|G: 0.125 (312) |
1000 Genomes Project |
| Dnmt3B | rs1569686 (0.28) | Intron Variant | G > T/A/C | T: 0.724 (3625) | G|T: 0.303 (759) T|T: 0.572 (1433) |
1000 Genomes Project |
1
Original data were mined from the Ensembl genome browser database (http://useast.ensembl.org/index.html) accessed April 5, 2021. For the 1000 Genomes Project, all donors were over 18 and declared themselves to be healthy at the time of collection. The health conditions for other data source populations are unknown.
2
1000 Genomes Project population: African, American, East Asian, European, South Asian.
3
Exome Aggregation Consortium (ExAC) population: African/African American, Latino, East Asian, Finnish, Non-Finnish European, South Asian and others.
4
BUSHMAN Population: Northern Kalahari of Africa.
5
Presented in order as Ancestral; Variants.
6
Presented in order as Homozygous dominant; Heterozygous; Homozygous recessive.
7
African-American (AA), European-American (EA) of NHLBI Exome Sequencing Project are AA or EA population from National Heart Lung and Blood Institute (NHLBI) Exome Sequencing Project using deep whole exome resequencing of >7000 individuals to study genetic contributions to the risk of several heart, lung and blood phenotypes.