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

Open Data