While PGx is often thought of as just an analysis of CYP450 enzymes, it's important to note that not all of the PGx changes observed with drug metabolism are due to CYP450 enzymes. There are other enzymes that, while not in the CYP450 class, can still have mutations or polymorphisms that lead to variable functions. The following is a list of enzymes for which known mutations have been associated with clinical effects. Note that not all the enzymes on the list are CYP450 enzymes.
| Enzymes | Substrates (Drugs) |
| Acetylaldehyde dehydrogenase | Alcohol |
| Acetylcholinesterase | Succinylcholine |
| Alcohol dehydrogenase | Alcohol |
| Dihydropyrimidine dehydrogenase | Fluorouracil |
| CYP2C9 | Warfarin, phenytoin, losartan |
| CYP2C19 | Diazepam, omeprazole (Prilosec) |
| CYP2D6 | Many antidepressants, opioids, antiarrhythmics |
| Glucose-6-phosphate dehydrogenase | Aspirin, quinidine |
| N-acetyltransferase | Procainamide, isoniazid |
| Thiopurine methyltransferase | 6-mercaptopurine |
| UDP-glucuronosyl transferase | Acetaminophen, tolbutamide, irinotecan |
