Interpretive Handbook

Test 60346 :
Cytochrome P450 1A2 Genotype, Saliva

Clinical Information Discusses physiology, pathophysiology, and general clinical aspects, as they relate to a laboratory test

Primary metabolism of many drugs is performed by cytochrome P450 (CYP), a group of oxidative/dealkylating enzymes localized in the microsomes of many tissues including the intestines and liver. One of these CYP enzymes, CYP1A2, is wholly or partially responsible for the hydroxylation or dealkylation of many commonly prescribed drugs (see below). The current clinical application of this test is focused on the impact of allelic variation on antidepressant and antipsychotic metabolism.  


CYP1A2-mediated drug metabolism is highly variable. CYP1A2*1A is the wild type or normal allele. Some individuals have altered CYP1A2 gene sequences that result in synthesis defective enzyme. These individuals metabolize CYP1A2 substrates poorly. Changes in the promoter impacting gene induction of the CYP1A2 gene has been observed, which results in either an increase or decrease of overall metabolic activity. Dosing of drugs that are metabolized through CYP1A2 may require adjustment based on the individual patient's genotype. Patients who are poor metabolizers may require lower than usual doses to achieve optimal response. Patients who are ultrarapid metabolizers may benefit from increased doses. Patients with either ultrarapid or poor metabolism also may benefit by conversion to other comparable drugs that are not primarily metabolized by CYP1A2.  


A number of specific polymorphisms have been found in the CYP1A2 gene that results in enzymatic deficiencies. The frequency of these polymorphisms varies within the major ethnic groups.  


All of the identified polymorphisms associated with CYP1A2 are autosomal recessive. Consequently, only individuals who are homozygous or compound heterozygous for these polymorphisms are poor metabolizers. Individuals who are heterozygous, with 1 normal gene and 1 defective polymorphic gene, will have metabolism intermediate between the extensive (normal) and poor metabolizers.


The following information outlines the relationship between the polymorphisms detected in this assay and the effect on the activity of the enzyme produced by that allele:




Effect on

Enzyme Metabolism*


Lower inducibility in Asians but increased inducibility in Northern Europeans

-2467T->del T

Increased inducibility


Decreased activity and decreased inducibility


Increased inducibility


Greatly reduced activity


Greatly reduced activity


Decreased activity


Decreased activity


Greatly reduced activity


Decreased activity


Decreased activity


No activity


Greatly reduced activity


Decreased activity

*Effect of a specific polymorphism on the activity of the CYP1A2 enzyme can only be estimated since the literature does not provide precise data.


A complicating factor in correlating CYP1A2 genotype with phenotype is that some drugs or their metabolites are inhibitors of CYP1A2 catalytic activity. These drugs may reduce CYP1A2 catalytic activity. Consequently, an individual may require a dosing decrease greater than predicted based upon genotype alone. Another complicating factor is that the CYP1A2 gene is inducible by several drugs and environmental agents (eg, cigarette smoke) and the degree of inducibility is under genetic control. It is important to interpret the results of testing in the context of other coadministered drugs and environmental factors.

Useful For Suggests clinical disorders or settings where the test may be helpful

Identifying patients who are poor, intermediate, extensive, or ultrarapid metabolizers of drugs metabolized by CYP1A2


Adjusting dosages for drugs that are metabolized by CYP1A2


Genotyping patients who prefer not to have venipuncture done

Interpretation Provides information to assist in interpretation of the test results

An interpretive report will be provided that includes assay information, genotype, and an interpretation indicating whether results are consistent with a poor, intermediate, extensive, or ultra-rapid metabolizer phenotype. The report will list drugs known to affect metabolism by CYP1A2. Direct polymorphism analysis for -3860G->A, -2467T->del T, -729C->T, -163C->A, 125C->G, 558C->A, 2116G->A, 2385G->A, 2473G->A, 2499A->T, 3497G->A, 3533G->A, 5090C->T, or 5166G->A is performed following PCR amplification. Direct DNA testing will not detect all the known mutations that result in decreased or inactive CYP1A2 alleles. This assay does not test for some known polymorphisms because those polymorphisms have not been associated with alterations in enzymatic activity. Rare or undescribed variants may not have been found during validation but will be sequence verified upon detection. See http:/// for a full description of CYP1A2 alleles. Absence of a detectable gene mutation or polymorphism does not rule out the possibility that a patient has a metabolizer status other than predicted above. The frequency of polymorphisms causing poor metabolism has not been fully characterized in various ethnic groups. Patients with an ultrarapid, extensive, or intermediate genotype may have CYP1A2 enzyme activity inhibited or induced by a variety of substances, medications, or their metabolites. The following is a listing of substances known to affect CYP1A2 activity as the date of this report.


Drugs and substances known to increase (induce) CYP1A2 activity include:

-Broccoli, brussel sprouts, char-grilled meat, insulin, methylcholanthrene, modafinil, nafcillin, beta-naphthoflavone, omeprazole, tobacco

Coadministration will increase the rate of metabolism of CYP1A2-metabolized drugs and may change the effectiveness of the drug.


Drugs and substances known to decrease CYP1A2 activity include:

-Amiodarone, cimetidine, ciprofloxacin, fluoroquinolones, fluvoxamine, furafylline, interferon, methoxsalen, mibefradil

Coadministration will decrease the rate of metabolism of CYP1A2-metabolized drugs, increasing the possibility of toxicity.


Drugs and substances that undergo metabolism by CYP1A2 include:

-Acetaminophen, amitriptyline, caffeine, clomipramine, clozapine, cyclobenzaprine, estradiol, fluvoxamine, haloperidol, imipramine, mexiletine, naproxen, olanzapine, ondansetron, phenacetin, propranolol, riluzole, ropivacaine, tacrine, theophylline, tizanidine, verapamil, (R)warfarin, zileuton, zolmitriptan

Coadministration may decrease the rate of elimination of other drugs metabolized by CYP1A2.


Drug-drug interactions and drug-metabolite inhibition or induction must be considered when dealing with heterozygous individuals. Drug-metabolite inhibition occurs with the drugs noted above resulting in inhibition of residual functional CYP1A2 catalytic activity. Drug-metabolite induction occurs with the drugs noted above resulting in variable increase in CYP1A2 enzyme function. This inducibility is under genetic control and this is further varies per ethnicity. Each report will include a list of commonly prescribed drugs that are known to alter CYP1A2 activity. This list includes only those drugs for which established, peer-reviewed literature substantiates the effect. The list provided may not be all-inclusive.


CYP1A2 activity also is dependent upon hepatic and renal function status, as well as age. Patients also may develop toxicity if hepatic or renal function is decreased. Drug metabolism also is known to decrease with age. It is important to interpret the results of testing and dose adjustments in the context of hepatic and renal function and age.

Cautions Discusses conditions that may cause diagnostic confusion, including improper specimen collection and handling, inappropriate test selection, and interfering substances

Note that in patients who have received heterologous blood transfusions before a saliva sample was acquired, the saliva sample may contain donor DNA. Return to recipient genotype usually occurs after 6 weeks. Similarly, saliva samples obtained from patients after allogeneic blood or marrow transplantation can contain donor DNA. In both cases, this may result in genotyping results that reflect the genotype of the recipient, the donor, or a blend of the donor and recipient. Results obtained under these circumstances may not accurately reflect the recipient’s genotype.

Reference Values Describes reference intervals and additional information for interpretation of test results. May include intervals based on age and sex when appropriate. Intervals are Mayo-derived, unless otherwise designated. If an interpretive report is provided, the reference value field will state this.

An interpretive report will be provided.

Clinical References Provides recommendations for further in-depth reading of a clinical nature

1. Shirley KL, Hon YY, Penzak SR, et al: Correlation of cytochrome P450 (CYP) 1A2 activity using caffeine phenotyping and olanzapine disposition in healthy volunteers. Neuropsychopharmacology, 2003;28(5):961-966

2. Shimoda K, Someya T, Morita S, et al: Lack of impact of CYP1A2 genetic polymorphism (C/A polymorphism at position 734 in intron 1 and G/A polymorphism at position -2964 in the 5'-flanking region of CYP1A2) on the plasma concentration of haloperidol in smoking male Japanese with schizophrenia. Prog Neuropsychopharmacol Biol Psychiatry 2002;26(2):261-265

3. Obase Y, Shimoda T, Kawano T, at al: Polymorphisms in the CYP1A2 gene and theophylline metabolism in patients with asthma. Clin Pharmacol Ther 2003;73(5):468-474

4. Cornelis MC, El-Sohemy A, Kabagambe EK, et al: CYP1A2 genotype, and risk of myocardial infarction. JAMA 2006 Aug 16; 296(7):764-765