Table 3.
Occurrence of FMO2 SNP combinations among Hispanic-American individuals and inferred haplotype pairs for observed genotypes
| Observed genotype (expressed as the AA encoded by the underlying SNP)
|
Genotype
|
|||||||
|---|---|---|---|---|---|---|---|---|
| Exon 3 p.71Ddup | Exon 4 p.V113fs | Exon 5 p.S195L | Exon 8 p.N413K | Exon 9 p.Q472X | Exon 9p.C530fs | Occurrence | (%) | Haplotype pair (probability)a |
| FMO2*1 individuals (N = 29)b | ||||||||
| Q/Q | 1 | (3.4) | VSNQC VSNQC (1.000) | |||||
| Q/X | 20 | (69.0) | VSNQC VSNXC (1.000) | |||||
| S/L | Q/X | 3 | (10.3) | VSNQC VLNXC (0.990) | ||||
| S/L | Q/X | C/fs | 2 | (6.9) | VSNQC VLNXfs (0.990) | |||
| V/X | S/L | N/K | Q/X | 3 | (10.3) | VSNQC XLKXC (0.996)c | ||
| 0 | 10.3 | 27.6 | 10.3 | 96.6 | 6.9 | SNPs: % individuals | ||
| 0 | 5.2 | 13.8 | 5.2 | 48.3 | 3.4 | SNPs: % alleles | ||
| 0 | 10.7 | 28.6 | 10.7 | 100 | 7.1 | SNPs: % FMO2*2 allelesd | ||
| FMO2*2/*2 individuals (N = 124) | ||||||||
| X/X | NDe | 38 | (30.6) | VSNX VSNX (1.000) | ||||
| S/L | X/X | ND | 42 | (33.9) | VSNX VLNX (1.000) | |||
| L/L | X/X | ND | 13 | (10.5) | VLNX VLNX (1.000) | |||
| N/K | X/X | ND | 3 | (2.4) | VSNX VSKX (1.000) | |||
| V/X | S/L | N/K | X/X | ND | 19 | (15.3) | VSNX XLKX (0.999) | |
| V/X | L/L | N/K | X/X | ND | 9 | (7.3) | VLNX XLKX (1.000) | |
| 0 | 22.6 | 66.9 | 25.0 | 100 | ND | SNPs: % individuals | ||
| 0 | 11.3 | 42.3 | 12.5 | 100 | ND | SNPs: % alleles | ||
a
Haplotype pairs and the mean probability associated with the phase call were estimated using PHASE [24,25].
b
Undesignated alleles match the reference sequence (non-variant).
c
Cloning and repeat genotyping to confirm the indicated haplotype was performed for one of these individuals.
d
SNP occurrence observed (as percentage of FMO2*2 alleles) if all SNPs are limited to FMO2*2. This is also the expected allelic occurrence among the 124 FMO2*2/*2 individuals tested.
e
The presence or absence of this SNP was not determined.