TABLE 5.
Overview of novel variants and their putative functional consequencesa
| Gene | Genomic location | Reference | Alternative | Variant type (variant) | No. of alleles | Predicted consequence (estimated activity) |
|---|---|---|---|---|---|---|
| ABCC3 | Chr17:48750862 | C | T | Synonymous (P814) | 1/96 | Neutral |
| ABCC4 | Chr13:95748442 | G | GA | Intronic | 3/96 | Neutral |
| Chr13:95695981 | G | A | Synonymous (T1230) | 1/96 | Neutral | |
| CYP1A1 | Chr15:75014905 | C | G | Missense (M178I) | 1/96 | Deleterious (60% of reference enzyme) |
| Chr15:75014854 | G | C | Synonymous (T195) | 1/96 | Neutral | |
| CYP2A6 | Chr19:41354168 | TG | T | Frameshift (M204fs) | 2/96 | Deleterious (0% of reference enzyme) |
| CYP2B6 | Chr19:41497294 | CCG | C | Frameshift (R29fs) | 1/96 | Deleterious (0% of reference enzyme) |
| Chr19:41512975 | GGGAGAC | G | Intronic | 1/96 | Neutral | |
| CYP2D6 | Chr22:42523973 | G | C | Missense (P286A) | 2/96 | Deleterious (60% of reference enzyme) |
| CYP3A4 | Chr7:99364013 | A | G | Synonymous (T284) | 1/96 | Neutral |
| Chr7:99359750 | G | A | Synonymous (P389) | 1/96 | Neutral | |
| NR1I3 | Chr1:161205730 | A | AGG | Frameshift (F49fs) | 2/96 | Deleterious (0% of reference enzyme) |
| SLCO1B1 | Chr12:21375306 | GAAAAAAA | G | Intronic | 4/96 | Neutral |
| Chr12:21375306 | GAAAA | G | Intronic | 2/96 | Neutral | |
| Chr12:21375306 | GAAAAAA | G | Intronic | 1/96 | Neutral | |
| Chr12:21327652 | TA | T | Intronic | 1/96 | Neutral | |
| UGT1A9 | Chr2:234579874 | G | A | Promoter | 1/80b | Neutral |
| Chr2:234580024 | G | C | Promoter | 1/80b | Neutral | |
a
Residual function was estimated using the pharmacogene-specific ensemble classifier APF. Genomic locations are provided according to GRCh37.
b
The presence of the novel UGT1A9 variants was evaluated in only 40 individuals.