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HelpTest ID: 1A2Q Cytochrome P450 1A2 Genotype, Varies
Ordering Guidance
Testing is available as the single gene assay (this test) or as a part of a focused pharmacogenomics panel, which includes testing for the following genes: CYPs 1A2, 2C9, 2C19, 2D6, 3A4, 3A5, 4F2, SLCO1B1, and VKORC1. If multiple pharmacogenomic genotype testing is desired, order PGXQP / Focused Pharmacogenomics Panel, Varies .
CYP1A2 is also available as part of a panel designed for psychotropic pharmacogenomics. If this testing is desired, order PSYQP / Psychotropic Pharmacogenomics Gene Panel, Varies.
Specimen Required
Patient Preparation: A previous hematopoietic stem cell transplant from an allogenic donor or a liver transplant will interfere with testing. For information about testing patients who have received a hematopoietic stem cell or liver transplant call 800-533-1710.
Submit only 1 of the following specimens:
Specimen Type: Whole blood
Container/Tube: Lavender top (EDTA)
Specimen Volume: 3 mL
Collection Instructions:
1. Invert several times to mix blood.
2. Send whole blood specimen in original tube. Do not aliquot.
Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated 4 days/Frozen 4 days
Additional Information:
1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.
2. To ensure minimum volume and concentration of DNA are met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.
Specimen Type: Cord blood
Container/Tube: Lavender top (EDTA)
Specimen Volume: 3 mL
Collection Instructions:
1. Invert several times to mix blood.
2. Send cord blood specimen in original tube. Do not aliquot.
Specimen Stability Information: Ambient (preferred) 4 days/Refrigerated 4 days/Frozen 4 days
Additional Information:
1. Specimens are preferred to be received within 4 days of collection. Extraction will be attempted for specimens received after 4 days, and DNA yield will be evaluated to determine if testing may proceed.
2. To ensure minimum volume and concentration of DNA are met, the requested volume must be submitted. Testing may be canceled if DNA requirements are inadequate.
3. While a properly collected cord blood sample may not be at risk for maternal cell contamination, unanticipated complications may occur during collection. Therefore, maternal cell contamination studies are recommended to ensure the test results reflect that of the patient tested and are available at an additional charge. Order MATCC / Maternal Cell Contamination, Molecular Analysis, Varies on the maternal specimen.
Specimen Type: Saliva
Patient Preparation: Patient should not eat, drink, smoke, or chew gum 30 minutes prior to collection.
Supplies: Saliva Swab Collection Kit (T786)
Specimen Volume: 2 Swabs
Collection Instructions: Collect and send specimen per kit instructions.
Specimen Stability Information: Ambient (preferred) 30 days/Refrigerated 30 days
Additional information: Saliva specimens are acceptable but not recommended. Due to lower quantity/quality of DNA yielded from saliva, some aspects of the test may not perform as well as DNA extracted from a whole blood sample. When applicable, specific gene regions that were unable to be interrogated will be noted in the report. Alternatively, additional specimen may be required to complete testing.
Specimen Type: Extracted DNA
Container/Tube:
Preferred: Screw Cap Micro Tube, 2 mL with skirted conical base
Acceptable: Matrix tube, 1 mL
Collection Instructions:
1. The preferred volume is at least 100 mcL at a concentration of 75 ng/mcL.
2. Include concentration and volume on tube.
Specimen Stability Information: Frozen (preferred) 1 year/Ambient/Refrigerated
Additional Information: DNA must be extracted in a CLIA-certified laboratory or equivalent and must be extracted from a specimen type listed as acceptable for this test (including applicable anticoagulants). Our laboratory has experience with Chemagic, Puregene, Autopure, MagnaPure, and EZ1 extraction platforms and cannot guarantee that all extraction methods are compatible with this test. If testing fails, one repeat will be attempted, and if unsuccessful, the test will be reported as failed and a charge will be applied. If applicable, specific gene regions that were unable to be interrogated due to DNA quality will be noted in the report.
Forms
1. New York Clients-Informed consent is required. Document on the request form or electronic order that a copy is on file. The following documents are available in Special Instructions:
-Informed Consent for Genetic Testing (T576)
-Informed Consent for Genetic Testing-Spanish (T826)
2. If not ordering electronically, complete, print, and send 1 of the following forms with the specimen:
-Neurology Specialty Testing Client Test Request (T732)
-Therapeutics Test Request (T831)
Useful For
Identifying individuals who are poor, intermediate, normal (extensive) or rapid metabolizers of drugs metabolized by cytochrome P450 1A2 to assist drug therapy decision making
Method Name
Real-Time Polymerase Chain Reaction (PCR) with Allelic Discrimination Analysis
Reporting Name
CYP1A2 Genotype, VSpecimen Type
VariesSpecimen Minimum Volume
See Specimen Required
Specimen Stability Information
| Specimen Type | Temperature | Time |
|---|---|---|
| Varies | Varies | |
Clinical Information
The cytochrome P450 (CYP) family is involved in the primary metabolism of many drugs. The CYPs are 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.
Cytochrome P450 1A2-mediated drug metabolism is highly variable. A number of variants have been identified in the CYP1A2 gene that results in increased, diminished, or abolished catalytic activity and substrate metabolism. The frequency of these variants varies by ancestry.
Dosing of drugs that are metabolized through CYP1A2 may require adjustment based on the CYP1A2 genotype. Individuals who are poor metabolizers may require lower than usual doses to achieve optimal response, whereas individuals who are ultrarapid metabolizers may benefit from increased doses. The CYP1A2 phenotype is predicted based upon the number of functional, partially functional, nonfunctional, and inducible alleles present in a sample.
The following table outlines the relationship between the variations (star alleles) detected in this assay and the effect on the activity of the enzyme produced by that allele.
Table. Variations and Effect on Enzyme Metabolism
|
CYP1A2 allele |
Nucleotide change (legacy nomenclature) |
cDNA nucleotide change (NM_000761.4) |
Effect on enzyme metabolism(a) |
|
*1 |
None (wild type) |
None (wild type) |
Normal (extensive) activity |
|
*1F (renamed *30 on 12/16/2024) |
-163C>A |
c.-9-154C>A |
Increased inducibility |
|
*1K |
-729C>T |
c.-10+113C>T |
Decreased activity and decreased inducibility |
|
*6 |
5090C>T |
c.1291C>T |
No activity |
|
*7 |
3533G>A |
c.1253+1G>A |
No activity |
a. Effect of a specific allele on the activity of the CYP1A2 enzyme can only be estimated since the literature does not provide precise data.(1-5)
A complicating factor in correlating CYP1A2 genotype to CYP1A2 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 dose decrease greater than predicted based upon genotype alone. Another complicating factor is that CYP1A2 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.
Reference Values
An interpretive report will be provided.
Interpretation
An interpretive report will be provided.
The genotype, with associated star alleles, is assigned based on historical nomenclature as curated by the Karolinska Institutet Human Cytochrome P450 Nomenclature Database. CYP1A2 was transitioned to the Pharmacogene Variation (PharmVar) Consortium on December 16, 2024, and variants upstream of position -920 bp (based on the ATG) are no longer included in star allele definitions.(6) The *1K allele designation was not transferred to PharmVar and is based on the Karolinska Institutet's historical allele nomenclature.
Cytochrome P450 (CYP) 1A2 activity is also dependent upon hepatic function status, as well as age. Renal function may be important for drugs that are excreted in urine. Patients may develop drug toxicity if hepatic or renal function is decreased. Drug metabolism 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.
For additional information regarding pharmacogenomic genes and their associated drugs, see Pharmacogenomic Associations Tables. This resource also includes information regarding enzyme inhibitors and inducers, as well as potential alternate drug choices.
Clinical Reference
1. Ito M, Katono Y, Oda A, Hirasawa N, Hiratsuka M. Functional characterization of 20 allelic variants of CYP1A2. Drug Metab Pharmacokinet. 2015;30(3):247-252. doi:10.1016/j.dmpk.2015.03.001
2. Zhou H, Josephy PD, Kim D, Guengerich FP. Functional characterization of four allelic variants of human cytochrome P450 1A2. Arch Biochem Biophys. 2004;422(1):23-30. doi:10.1016/j.abb.2003.11.019
3. Murayama N, Soyama A, Saito Y, et al. Six novel nonsynonymous CYP1A2 gene polymorphisms: catalytic activities of the naturally occurring variant enzymes. J Pharmacol Exp Ther. 2004;308(3):1219
4. Murayama N, Soyama A, Saito Y, et al. J Pharmacol Exp Ther. 2004;308(1):300-306. doi:10.1124/jpet.103.055798
5. Saito Y, Hanioka N, Maekawa K, et al. Functional analysis of three CYP1A2 variants found in a Japanese population. Drug Metab Dispos. 2005;33(12):1905-1910. doi:10.1124/dmd.105.005819
6. PharmVar. Pharmacogene Variation Consortium. Updated December 16, 2024. Accessed May 15, 2025. Available at www.pharmvar.org/
Day(s) Performed
Varies
Report Available
3 to 8 daysTest Classification
This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. It has not been cleared or approved by the US Food and Drug Administration.CPT Code Information
0031U
LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| 1A2Q | CYP1A2 Genotype, V | 80687-7 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| 610075 | CYP1A2 Genotype | 72884-0 |
| 610076 | CYP1A2 Phenotype | 94254-0 |
| 610077 | Interpretation | 69047-9 |
| 610078 | Additional Information | 48767-8 |
| 610079 | Method | 85069-3 |
| 610080 | Disclaimer | 62364-5 |
| 610081 | Reviewed by | 18771-6 |
Reflex Tests
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| MATCC | Maternal Cell Contamination, B | Yes | No |
Testing Algorithm
For cord blood specimens that have an accompanying maternal blood specimen, maternal cell contamination studies will be performed at an additional charge.
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