Table 3

NAT2 haplotypea frequencies in samples of the worldwide genotyping surveyb.

NAT2 Haplotypee

*4
 *5A
 *5B
 *5C
 *5D
 *5E
 *5M
 *6A
 *6B
 *6C
 *7A
 *7B
 *11A
 *12A
 *12B
 *12C
 *13
 *13B
 *14A
 *14B
 *6Jf
 Global (2Ng)
SNP positionc (ancestral stated)
     191 (G)
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 A
 A
 .
     282 (C)
 .
 .
 .
 .
 .
 .
 T
 T
 .
 T
 .
 T
 .
 .
 T
 .
 T
 T
 .
 T
 T
     341 (T)
 .
 C
 C
 C
 C
 C
 C
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
     481 (C)
 .
 T
 T
 .
 .
 .
 .
 .
 .
 .
 .
 .
 T
 .
 .
 T
 .
 T
 .
 .
 .
     590 (G)
 .
 .
 .
 .
 .
 A
 .
 A
 A
 A
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 A
     803 (A)
 .
 .
 G
 G
 .
 .
 .
 .
 .
 G
 .
 .
 .
 G
 G
 G
 .
 .
 .
 .
 .
     857 (G)
 .
 .
 .
 .
 .
 .
 .
 .
 .
 .
 A
 A
 .
 .
 .
 .
 .
 .
 .
 .
 A
Population codeh
     1
 27
 1
 47
 17
 0
 0
 0
 34
 4
 0
 0
 0
 0
 34
 7
 1
 13
 0
 6
 11
 0
 202
     2
 10
 1
 37
 3
 0
 0
 1
 16
 0
 0
 0
 2
 0
 9
 2
 0
 6
 0
 3
 10
 0
 100
     3
 8
 0
 4
 0
 0
 0
 0
 11
 0
 0
 0
 0
 0
 39
 1
 0
 13
 0
 0
 4
 0
 80
     4
 4
 0
 13
 5
 0
 0
 0
 8
 0
 0
 0
 0
 0
 19
 3
 0
 6
 0
 0
 2
 0
 60
     6
 18
 2
 65
 3
 0
 0
 0
 32
 0
 0
 0
 13
 0
 30
 0
 0
 10
 0
 17
 3
 1
 194
     7
 13
 0
 22
 8
 0
 0
 0
 32
 5
 0
 2
 1
 0
 7
 1
 0
 4
 0
 2
 3
 0
 100
     8
 3
 0
 19
 0
 0
 0
 0
 17
 0
 0
 0
 1
 0
 7
 0
 0
 0
 0
 1
 0
 0
 48
     9
 13
 0
 45
 0
 0
 0
 0
 22
 0
 0
 0
 3
 0
 4
 0
 0
 1
 0
 0
 0
 0
 88
     10
 133
 1
 242
 0
 0
 0
 0
 127
 2
 0
 0
 3
 0
 6
 0
 0
 0
 0
 2
 0
 0
 516
     11
 20
 1
 52
 1
 0
 0
 0
 24
 0
 0
 0
 0
 0
 0
 0
 0
 0
 0
 0
 0
 0
 98
     12
 22
 6
 54
 2
 0
 0
 0
 30
 0
 0
 0
 1
 0
 0
 0
 0
 5
 0
 0
 0
 0
 120
     14
 44
 8
 104
 6
 0
 0
 0
 54
 1
 0
 0
 5
 0
 1
 0
 0
 1
 0
 0
 0
 0
 224
     15
 187
 20
 318
 17
 0
 0
 0
 206
 0
 0
 0
 15
 0
 3
 0
 0
 7
 0
 0
 1
 0
 774
     17
 11
 6
 50
 3
 0
 0
 0
 28
 0
 0
 0
 2
 0
 0
 0
 0
 0
 0
 0
 0
 0
 100
     18
 23
 3
 42
 0
 0
 0
 0
 15
 0
 0
 0
 13
 0
 0
 0
 0
 0
 0
 0
 0
 0
 96
     19
 383
 70
 647
 68
 0
 0
 0
 470
 0
 0
 0
 22
 0
 0
 0
 0
 26
 0
 0
 2
 0
 1688
     21
 109
 26
 164
 30
 0
 0
 0
 149
 0
 0
 0
 17
 0
 1
 0
 0
 0
 0
 0
 0
 0
 496
     23
 9
 0
 41
 0
 0
 0
 0
 29
 0
 0
 0
 1
 0
 0
 0
 0
 0
 0
 0
 0
 0
 80
     25
 134
 12
 213
 17
 0
 0
 0
 184
 0
 0
 0
 17
 0
 3
 0
 0
 0
 0
 0
 0
 0
 580
     26
 140
 8
 216
 29
 0
 0
 0
 185
 0
 0
 0
 27
 0
 1
 0
 0
 0
 0
 0
 0
 0
 606
     27
 13
 1
 29
 4
 0
 0
 0
 43
 0
 1
 0
 6
 0
 3
 0
 0
 0
 0
 0
 0
 0
 100
     28
 31
 0
 23
 3
 0
 0
 0
 30
 0
 0
 0
 12
 0
 1
 0
 0
 0
 0
 0
 0
 0
 100
     30
 132
 0
 4
 0
 1
 0
 0
 46
 0
 0
 0
 38
 0
 0
 0
 0
 3
 0
 0
 0
 0
 224
     32
 46
 0
 6
 0
 0
 0
 0
 22
 0
 0
 0
 13
 0
 0
 0
 0
 1
 0
 0
 0
 0
 88
     33
 208
 0
 1
 0
 0
 1
 0
 55
 0
 0
 0
 22
 0
 0
 0
 0
 1
 0
 0
 0
 0
 288
     36
 353
 1
 5
 0
 1
 0
 0
 126
 3
 0
 6
 70
 0
 4
 0
 1
 6
 0
 0
 0
 0
 576
     38
 26
 0
 10
 0
 0
 0
 0
 34
 0
 0
 0
 17
 0
 0
 0
 0
 1
 0
 0
 0
 0
 88
     41
 114
 7
 86
 5
 0
 0
 0
 46
 1
 1
 0
 0
 0
 8
 0
 2
 3
 0
 1
 0
 0
 274
Global
 2234
 174
 2559
 221
 2
 1
 1
 2075
 16
 2
 8
 321
 0
 180
 14
 4
 107
 0
 32
 36
 1
 7988

a NAT2 haplotypes were named in accordance with the consensus gene nomenclature of human NAT2 alleles [65]

b Only the 28 samples with no missing data (i.e., with genotype data available for the seven common SNPs in NAT2) were considered here

c Polymorphic sites were numbered considering +1 as the A of the translation start codon in the cDNA sequence (GenBank CR407631)

d The ancestral state of each SNP was deduced from both the chimpanzee and rhesus monkey sequences, and is represented here as a dot

e Nucleotide substitutions shown in bold have a functional consequence on enzyme activity. Bold-faced haplotypes are 'slow alleles' associated with as decreased acetylation capacity; the others display an enzymatic activity comparable to the reference 'rapid' allele NAT2*4

f NAT2*6J is a newly described allele found in the Mandenka sample in the present study (see Table 1). It was predicted to be a 'slow allele' since it contains two inactivating mutations

g Total number of chromosomes

h Samples are numbered according to their population code [see Additional file 1]: (1) 101 Tswana, (2) 50 Ateke Bantus, (3) 40 Bakola Pygmies, (4) 30 Baka Pygmies, (6) 97 Mandenka, (7) 50 Dogons, (8) 24 Somali, (9) 44 Moroccans, (10) 258 Spanish, (11) 49 Sardinians, (12) 60 French, (14) 112 UK Caucasians, (15) 387 US Caucasians, (17) 50 Swedes, (18) 48 Saami, (19) 844 Germans, (21) 248 Polish, (23) 40 Ashkenazi Jews, (25) 290 Russians, (26) 303 Turks, (27) 50 Gujarati, (28) 50 Turkmen, (30) 112 Han Chinese, (32) 44 Chinese, (33) 144 Japanese, (36) 288 Koreans, (38) 44 Thai, (41) 137 Nicaraguans.

Sabbagh et al. BMC Genetics 2008 9:21   doi:10.1186/1471-2156-9-21