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Table 1 Grouping of novel SNPs and functional effect prediction

From: Novel variants of major drug-metabolising enzyme genes in diverse African populations and their predicted functional effects

Gene

SNP grouping†

cDNA position

Amino acid change

Functional effect prediction (PSIC score)

CYP2C9

42519T > C (*31)

980

I327T

Possible functional damage (2.761)

 

50294A > G

1421

N474S

No functional damage (0.162)

 

47545A > T

   
 

50298A > T

   
 

50341G > T (*32)

1468

V490F

Possible functional damage (1.806)

 

10535A > G (*9)

752

H251R

Possible functional damage (2.239)

 

50196C > T

1323

A441A

 

CYP2C19

12122G > A

   
 

12690G > A

337

V113I

No functional damage (0.198)

 

57453G > C

   
 

90533C > T

   
 

57575T > C

   
 

87290C > T (*13)

1228

R410C

 
 

90209A > C (*12)

1473

X491C

26 extra amino acids

 

90302C > T

   
 

17869G > C (*22)

557

R186P

Possible functional damage (3.159)

 

80161G > A

991

I331V

 

CYP2D6

-175G > A

   
 

310G > T

   
 

843T > G

   
 

1608G > A (*70)

 

V119M

No functional damage (0.054)

 

1659G > A

 

V136M

Functional damage - reduced enzyme activity

 

1661G > C

   
 

3183G > A

 

V338M

Functional damage - reduced enzyme activity

 

3384A > C

   
 

4180G > C

 

S486T

No functional damage (0.267)

 

4722T > G

   
 

214G > C

   
 

223C > G

   
 

227T > C

   
 

843T > G

   
 

1621G > T

 

R123L

No functional damage (1.236)

 

1661G > C

   
 

2850C > T

 

R296C

No functional damage (0.254)

 

3384A > C

   
 

3584G > A

   
 

3790C > T

   
 

4180G > C

 

S486T

No functional damage (0.267)

 

843T > G

   
 

1661G > C

   
 

2850C > T

 

R296C

No functional damage (0.254)

 

3384A > C

   
 

4057G > A

 

G445E

Possible functional damage, contact with functional site (3.063)

 

4180G > C

 

S486T

No functional damage (0.267)

NAT2

10542A > C

472

I158L

No functional damage (0.615)

 

10659C > T

589

R197X

No protein expressed

 

10711C > T

641

T214I

Possible functional damage, involved in ligand binding (1.257)

 

10879T > C

809

I270T

No functional damage (0.526)

  1. Abbreviations: PSIC, position-specific independent counts; SNP, single nucleotide polymorphism.
  2. †Bold: novel non-synonymous SNPs; italic bold: novel intronic SNPs; italics: known non-synonymous SNPs; (*) = described alleles carrying that particular mutation; SNP positions are according to reference sequences (Tables S2-S5).
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Human Genomics

ISSN: 1479-7364