Variant alleles detected in the CYP2A13 gene
| Base Change (Location) | Samples Analyzed (n) | Samples with Shifted Band | Predicted Amino Acid Change |
|---|---|---|---|
| C → T (exon 2, 523) | 103 | 1 (het) | No (Silent) |
| G → C (exon 3, 1662) | 103 | 1 (het) | Gly144Arg |
| C → T (exon 5, 3375) | 104 | 11 (10 het; 1 hom) | Arg257Cys |
| C → A (intron 5, 3441) | 104 | 1 (het) | No |
| C → G (intron 7, 6404) | 94 | 13 (het)3-a | No |
| C → T (intron 7, 6424) | 88 | 36 (30 het; 6 hom)3-b 3-c | No |
| C → T (intron 7, 6432) | 88 | 20 (15 het; 5 hom)3-b 3-d | No |
About 100 individuals were analyzed for each exon by PCR-SSCP (or by direct sequencing of PCR products, as indicated). No band shift was detected in exons 1, 4, 6, 7, 8, and 9. The identities of all shifted bands were confirmed by sequencing. DNA from blood spots was used for PCR as described under Experimental Procedures. PCR product of the expected size was obtained with all blood spots. No other nucleotide was detected at the variant position. The CYP2A13sequence from the completed human genome data base (accession no.AC008962) was used as a reference for documenting the location of the SNPs, with the A of the ATG start codon (nucleotide 66807 in AC008962) designated as +1. The number of samples analyzed were slightly different for each position because there was insufficient isolated DNA from certain subjects.
het, heterozygote; hom, homozygote.
↵3-a The frequency of the G allele was 16% for white (n = 25), 8.7% for black (n = 23), 2.1% for Hispanic (n = 24), and 0% for Asian (n = 22) people. The frequency in white people was significantly higher than in Hispanic people (P = 0.031; Fisher's exact test) and Asian people (P = 0.006; Fisher's exact test).
↵3-b The three SNPs in intron 7 were identified by PCR using the same primer set (Table 1). The genotypes at the 6424 and the 6432 positions were determined by direct sequencing of the PCR products.
↵3-c The frequency of the T allele was 10.9% for white (n = 23; 5 het), 43.2% for black (n = 22; 4 hom and 11 het), 28.3% for Hispanic (n = 23; 1 hom and 11 het), and 12.5% for Asian (n = 20; 1 hom and 3 het) people. The frequency in black people was significantly higher than in white (χ2 = 12.0, P <0.001) and Asian (χ2 = 9.66,P = 0.002) people.
↵3-d The frequency of the T allele was 0% for white (n = 23), 40.9% for black (n = 22; 4 hom and 10 het), 8.7% for Hispanic (n = 23; 1 hom and 2 het), and 7.5% for Asian (n = 20; 3 het) people. The frequency in black people was significantly higher than in each of the other groups (χ2> 12.4, P < 0.001).