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CYP2D6

CYP2D6 is a phase I drug-metabolizing enzyme belonging to the cytochrome P450 superfamily, encoded by the highly polymorphic CYP2D6 gene located on chromosome 22q13.2, and is primarily expressed in the liver, brain, and intestines.^[1] It catalyzes the oxidation of approximately 20–25% of commonly prescribed medications through monooxygenation reactions, including key substrates such as opioids (e.g., codeine and tramadol), antidepressants (e.g., paroxetine and nortriptyline), beta-blockers (e.g., metoprolol), antiarrhythmics, and the anticancer prodrug tamoxifen.^[1]^[2] This enzyme plays a pivotal role in pharmacogenomics due to its genetic variability, which influences drug efficacy, toxicity, and personalized dosing strategies across diverse therapeutic areas like pain management, psychiatry, cardiology, and oncology.^[3] The CYP2D6 gene exhibits extensive polymorphism, with over 280 star (*) alleles identified and cataloged by the PharmVar Consortium as of 2025,^[4] including variants that result in no enzyme function (e.g., *3, *4, *5), decreased function (e.g., *10, *17), normal function (e.g., *1, *2), or increased function through gene duplications (e.g., *1xN).^[3] These genetic variations lead to distinct metabolic phenotypes: poor metabolizers (PMs, activity score 0, affecting 5–10% of Caucasians), intermediate metabolizers (IMs, score 0.25–1), normal/extensive metabolizers (NMs/EMs, score 1.25–2.25, 43–67% globally), and ultrarapid metabolizers (UMs, score >2.25, 1–2% in Caucasians but up to 11% in certain Middle Eastern populations).^[1]^[3] Copy number variations, such as duplications or deletions, occur in 12–23% of individuals and further modulate enzyme activity, with population-specific allele frequencies—e.g., *4 and *5 predominant in Europeans, *10 in East Asians (up to 59%), and *17 in Africans—contributing to inter-ethnic differences in drug response.^[1]^[3] Clinically, CYP2D6 polymorphisms have profound implications for therapeutic outcomes, as evidenced by Clinical Pharmacogenetics Implementation Consortium (CPIC) guidelines for over 48 drugs, with actionable recommendations for 26, including avoiding codeine in UMs due to risk of morphine overdose and reducing tamoxifen doses or alternatives for PMs to prevent diminished efficacy in breast cancer treatment.^[1] For instance, PMs exhibit reduced conversion of codeine to its active metabolite morphine, rendering the drug ineffective for analgesia, while UMs experience therapeutic failure or toxicity from rapid metabolism of antidepressants like tricyclic agents.^[3]^[2] Genetic testing for CYP2D6 variants is increasingly integrated into clinical practice, supported by FDA drug labels, to optimize dosing and minimize adverse drug reactions, potentially affecting up to 5.4% of prescriptions.^[1] Historically, CYP2D6's importance was established in the 1970s–1980s through observations of bimodal responses to probe drugs like debrisoquine and sparteine, marking it as a cornerstone of pharmacogenetics research.^[2]

Gene

Location and Organization

The CYP2D6 gene is located on the long arm of human chromosome 22 at the cytogenetic band 22q13.2.^[5] This positioning places it within a cluster of related cytochrome P450 genes on chromosome 22.^[6] The gene spans approximately 4.4 kb of genomic DNA and is organized into 9 exons, with the coding sequence distributed across these exons to encode the CYP2D6 enzyme.^[7] Upstream of the coding region lies the promoter, which contains regulatory elements that control basal gene expression, including binding sites for transcription factors such as hepatocyte nuclear factor 4α (HNF4α) and CCAAT/enhancer-binding protein α (C/EBPα).^[8] These elements contribute to tissue-specific and inducible expression patterns, with positive and negative regulatory motifs identified within approximately 500 bp of the transcription start site.^[9] Within the CYP2D subfamily, CYP2D6 demonstrates evolutionary conservation across primates, sharing structural similarities with paralogs like CYP2D7 (a pseudogene) and CYP2D8P, which arose from gene duplications in the lineage leading to humans and great apes.^[10] This conservation reflects the subfamily's role in xenobiotic metabolism, with the CYP2D cluster on chromosome 22 showing tandem arrangements that have persisted through mammalian evolution.^[11]

Allelic Variants

The CYP2D6 gene is highly polymorphic, with allelic variants designated using the star () nomenclature system developed by the Pharmacogene Variation (PharmVar) Consortium and endorsed by the Clinical Pharmacogenetics Implementation Consortium (CPIC). Under this system, the reference allele, CYP2D61, represents the wild-type sequence with no known variants that alter the protein. Alleles are assigned sequential numbers upon discovery (e.g., *2, *3), and suballeles are distinguished by letters (e.g., *4A, *4B) to denote specific combinations of single nucleotide variants (SNVs) or other changes. This nomenclature standardizes reporting across genetic testing platforms and databases.^[4]^[12] Several common alleles arise from point mutations, insertions, or deletions that disrupt the coding sequence. For instance, CYP2D6*3 features a frameshift mutation caused by a single adenine deletion at position 2549 (2549delA; PV00221), which shifts the reading frame and introduces a premature stop codon. The 4 allele is defined by a guanine-to-adenine transition at the splice acceptor site of intron 3 (c.506-1G>A; rs3892097), leading to a splicing defect that causes a frameshift and truncated protein. CYP2D66 includes a thymine deletion at position 1707 (1707delT; PV00714), resulting in another frameshift and truncated protein. These splice and frameshift variants are among the most frequently studied due to their structural impacts on the gene product.^[4] Structural variants also contribute to allelic diversity, notably CYP2D6*5, which represents a complete gene deletion (x0 copy number; PV00259) encompassing the entire locus. In contrast, gene duplications create multi-copy alleles such as *1×N or *2×N, where N denotes the number of identical copies (e.g., *1×2 for two copies), often arising from unequal crossing-over during meiosis. These copy number variations (CNVs) are detected via quantitative PCR, long-range PCR, or next-generation sequencing and are critical for accurate genotyping.^[4]^[13] Decreased-function alleles like *10 and 17 involve missense mutations altering amino acids in the protein. CYP2D610 carries a cytosine-to-guanine transversion at c.100C>T (rs1065852; PV00179), substituting proline for serine at position 34 (P34S). Similarly, *17 includes a cytosine-to-thymine transition at c.1023C>T (rs28371725; PV00120), changing threonine to isoleucine at residue 107 (T107I). These substitutions affect protein folding or stability.^[4] Resources such as PharmVar provide a comprehensive database of over 160 defined alleles, including detailed variant mappings, rsIDs, and structural annotations, updated periodically based on submissions from expert panels. PharmGKB complements this by curating allele-specific data, haplotype definitions, and links to clinical annotations, facilitating allele tracking and integration with pharmacogenetic guidelines.^[4]^[14]

Protein

Structure

CYP2D6 is a 497-amino acid membrane-bound hemoprotein belonging to the cytochrome P450 2 family, anchored to the endoplasmic reticulum via an N-terminal transmembrane helix.^[15] Its overall architecture features the canonical P450 fold, comprising twelve α-helices (labeled A through L) and five β-sheets, which form a triangular tructure that cradles the heme prosthetic group essential for its monooxygenase activity.^[16] The heme-binding region is located in helix I and includes the conserved motif FxxGxRxCxG (residues 438–446: FGAPFCPAG), where the cysteine at position 443 serves as the proximal ligand coordinating the heme iron.^[16] This motif anchors the heme group within a hydrophobic pocket, positioning it for electron transfer and oxygen activation. Six substrate recognition sites (SRS1–6), identified through comparative sequence analysis, contribute to substrate specificity by lining the access channels and active site cavity; these include SRS1 (residues 106–120), SRS2 (residues 207–219), SRS3 (residues 227–237), SRS4 (residues 276–286), SRS5 (residues 354–364), and SRS6 (residues 443–450). Key residues within these sites, such as Asp301 and Glu216 in SRS4 and SRS5, interact with substrates bearing basic nitrogen atoms.^[17] Crystal structures of CYP2D6, first determined at 3.0 Å resolution in 2006 (PDB ID: 2F9Q), reveal a relatively closed active site cavity of approximately 540 Å³ above the heme, bordered by helices F, G, I, and the β4 sheet, with limited solvent exposure that influences ligand access.^[16] Subsequent structures, such as those with inhibitors like prinomastat (PDB ID: 3QM4) at 2.85 Å resolution, confirm this compact fold and highlight conformational flexibility in the B–C loop (SRS1) for substrate accommodation. Homology models based on these structures have further refined predictions of variant impacts on folding.^[18] Post-translational modifications include phosphorylation at Ser135, potentially modulating enzyme stability or localization, though its precise functional role in CYP2D6 remains undetermined.^[19]

Catalytic Mechanism

CYP2D6 functions as a monooxygenase enzyme, catalyzing the NADPH- and O₂-dependent oxidation of organic substrates by inserting one atom of molecular oxygen into the substrate while reducing the other to water.^[20] This activity is characteristic of the cytochrome P450 superfamily, to which CYP2D6 belongs, enabling the hydroxylation of diverse compounds.^[20] The catalytic cycle of CYP2D6 follows the canonical cytochrome P450 mechanism, initiating with substrate binding to the active site near the heme prosthetic group, which displaces a water ligand from the ferric iron (Fe³⁺).^[20] The first electron from NADPH, delivered via cytochrome P450 reductase, reduces the heme iron to ferrous (Fe²⁺), allowing O₂ to bind and form a ferrous-dioxy complex.^[20] A second electron transfer and sequential protonations convert this intermediate to a hydroperoxy species, which rearranges to the reactive oxo-ferryl species known as Compound I (Fe⁴⁺=O).^[20] Compound I then abstracts a hydrogen atom from the substrate, generating a substrate radical that rapidly rebounds with the iron-bound oxygen to form hydroxylated products, such as alcohols, or epoxides in certain cases; the cycle concludes with product release and regeneration of the resting ferric state.^[20] The overall reaction can be represented as:

\text{RH} + \text{O}_2 + \text{NADPH} + \text{H}^+ \rightarrow \text{ROH} + \text{H}_2\text{O} + \text{NADP}^+

where RH denotes the substrate and ROH the hydroxylated product.^[20] CYP2D6 exhibits marked stereoselectivity in its oxidations, attributable to the chiral environment of its active site, which discriminates between prochiral centers in substrates.^[20] For instance, in the 4-hydroxylation of debrisoquine, CYP2D6 preferentially produces the S-(+)-4-hydroxydebrisoquine enantiomer, with the R-(-) enantiomer undetectable in urine from extensive metabolizers.^[21] This enantioselectivity underscores the enzyme's role in precise metabolic transformations.^[21]

Genetic Variability

Phenotypes

The metabolic phenotypes of CYP2D6 are classified based on the enzyme's in vivo activity, which determines the rate of metabolism for its substrates. These phenotypes arise from variations in enzyme function and are categorized into four main types: poor metabolizer (PM), intermediate metabolizer (IM), normal metabolizer (extensive metabolizer, EM, also termed normal metabolizer, NM), and ultrarapid metabolizer (UM). This classification system was established following the discovery of genetic polymorphism in drug metabolism, initially identified through the polymorphic hydroxylation of debrisoquine in a study of healthy volunteers in 1977. Phenotypes are assigned using an activity score (AS) derived from the summed functional contributions of an individual's CYP2D6 alleles, where fully functional alleles (*1, *2) are scored as 1.0, no-function alleles as 0, decreased-function alleles as 0.25 or 0.5, and increased-function alleles or duplications as >1.0. Specifically, PM corresponds to an AS of 0 (no CYP2D6 activity), IM to an AS of 0.25–1 (substantially reduced activity), EM/NM to an AS of 1.25–2.25 (normal activity), and UM to an AS >2.25 (increased activity). These scores provide a quantitative framework to predict metabolic capacity and guide pharmacotherapy.^[22]^[23] Diagnostic criteria for these phenotypes traditionally rely on phenotyping assays using probe drugs that are selectively metabolized by CYP2D6. For example, debrisoquine, the drug central to the initial polymorphism discovery, is administered orally, and the urinary metabolic ratio (MR) of debrisoquine to its metabolite 4-hydroxydebrisoquine is measured; an MR >12.6 typically indicates PM status, while lower values delineate EM. Similarly, dextromethorphan serves as a safe, non-invasive probe, where the MR of dextromethorphan to dextrorphan in urine or plasma distinguishes phenotypes, with bimodal distributions separating PM (MR >0.3) from EM. Codeine is another probe, particularly useful for assessing UM and PM in clinical contexts like opioid response, as its conversion to active morphine is CYP2D6-dependent; low morphine levels flag PM, while elevated levels indicate UM. These assays remain gold standards for direct functional assessment, complementing genotypic predictions.^[24]^[22]

Genotypes

CYP2D6 genotypes are typically reported as diplotypes, which represent the combination of two star (*) alleles inherited from each parent, and these diplotypes are translated into predicted metabolic phenotypes using standardized systems. For instance, a homozygous no-function diplotype such as *4/*4 predicts a poor metabolizer (PM) phenotype, while a normal-function homozygous diplotype like *1/*1 or duplications such as *1/*1xN predict an ultrarapid metabolizer (UM) phenotype. Other examples include *1/*10 or *10/*10 predicting an intermediate metabolizer (IM) phenotype, and *1/*1 predicting a normal metabolizer (NM) phenotype. These translations align with the four main phenotype categories of PM, IM, NM, and UM, as detailed in the phenotypes section.^[25] The activity score (AS) system provides a quantitative framework for this translation by assigning numerical values to individual alleles based on their predicted functional impact: fully functional alleles like *1 and *2 receive a score of 1.0, decreased-function alleles like *10 receive 0.5 (or 0.25 in updated consensus for certain contexts), and no-function alleles like *3, *4, *5, and *6 receive 0. The total AS is the sum of the two allele scores, adjusted for copy number variations (e.g., multiplied by the number of copies for duplications). Phenotypes are then assigned as follows: PM (AS = 0), IM (0.25 ≤ AS ≤ 1), NM (1.25 ≤ AS ≤ 2.25), and UM (AS > 2.25). This system, developed through consensus by the Clinical Pharmacogenetics Implementation Consortium (CPIC) and Dutch Pharmacogenetics Working Group (DPWG), ensures consistent phenotype predictions across laboratories.^[25] Genotyping methods for CYP2D6 focus on detecting single nucleotide variants (SNVs) in alleles and copy number variations (CNVs) due to the gene's structural complexity and homology with the pseudogene CYP2D7. PCR-based allele-specific detection, such as TaqMan assays or multiplex primer extension (e.g., Luminex xTAG), targets common SNVs to identify alleles like *2, *3, *4, *6, *10, *17, *35, and *41, often combined with long-range PCR for haplotype phasing in multi-copy scenarios. For CNVs, including gene deletions (*5) and duplications/multiplications (xN), next-generation sequencing (NGS) approaches like targeted amplicon sequencing (e.g., Ion AmpliSeq panels) or whole-genome sequencing with specialized callers (e.g., Cyrius) provide high-resolution detection by analyzing read depth and structural variants. These methods enable comprehensive diplotype resolution, though hybrid alleles may require additional Sanger sequencing for confirmation.^[26] The concordance between CYP2D6 genotypes and measured phenotypes, assessed via probe drug metabolism (e.g., dextromethorphan), is generally high at 90-95%, though it can vary with rare variants, structural complexity, or environmental factors. Standardization efforts have improved predictive accuracy by reducing inter-laboratory discrepancies in diplotype-to-phenotype assignments.^[25]^[27]

Ethnic Differences

The CYP2D6 gene exhibits significant inter-ethnic variation in allele frequencies, which directly influences the distribution of metabolic phenotypes across global populations. The no-function allele *4 is most prevalent in individuals of European ancestry, with a frequency of approximately 18.5%, compared to 3-5% in those of African ancestry and 0.5-9.1% in Asian populations.^[3] In contrast, the decreased-function allele *10 predominates in East and Southeast Asian groups, reaching frequencies of 9-44%, while it is rare (<2%) in Europeans and occurs at 4-6% in Africans.^[3] Similarly, the reduced-function allele *17 is common in African populations at 17-19%, but nearly absent (<0.5%) in both European and Asian ancestries.^[3] These patterns are derived from large-scale genomic databases, including the 1000 Genomes Project and gnomAD analyses up to 2023, which highlight *1 as the most frequent functional allele overall, ranging from 29% in African ancestry to 47% in Hispanic/Latino groups.^[3] These allele frequency disparities translate into distinct phenotype prevalences. Poor metabolizer (PM) phenotypes, characterized by two no-function alleles, occur at 5-10% in European populations, driven largely by the high *4 frequency, but drop to less than 1% in East Asians due to the scarcity of *4 and reliance on *10 for reduced activity.^[28]^[29] Intermediate metabolizer (IM) rates are elevated in Asians (up to 44%) owing to frequent *10/*10 diplotypes, while ultrarapid metabolizer (UM) phenotypes, often from gene duplications, are notably higher in certain African subgroups, such as Ethiopians at around 29%, compared to 1-3% in Europeans.^[28]^[30] Overall, non-normal metabolizer phenotypes affect approximately 36% of the global population, with the highest PM rates in Europeans (up to 12.1% in British cohorts) and the lowest in Asians (0.4-1.2%).^[28] Population history plays a key role in these distributions, with founder effects and migration patterns contributing to allele clines. For instance, CYP2D6 duplications show a southeast-to-northwest gradient in Europe, from <1% in Scandinavia to 6% in Greece, likely reflecting ancient migratory flows.^[31] Similarly, elevated UM frequencies in Ethiopian and other East African groups may stem from founder events amplifying functional duplications, while admixture in admixed populations like African Americans introduces hybrid frequencies of alleles such as *17 and *29.^[30]^[3] These historical dynamics, analyzed through genomic projects like 1000 Genomes, underscore how genetic drift and gene flow have shaped CYP2D6 variability beyond neutral expectations.^[3]

Substrates and Ligands

Endogenous Substrates

CYP2D6 plays a significant role in the metabolism of endogenous neurotransmitters, particularly in the brain, where it contributes to the synthesis of key monoamines. One prominent pathway involves the conversion of tyramine to dopamine through aromatic hydroxylation, primarily acting on p-tyramine and m-tyramine substrates. This reaction, catalyzed efficiently by CYP2D6 with Km values of approximately 20 μM for p-tyramine, provides an alternative route for dopamine production independent of tyrosine hydroxylase, which may be particularly relevant under conditions of enzymatic deficiency or high tyramine availability.^[32] Similarly, CYP2D6 facilitates the O-demethylation of 5-methoxytryptamine to serotonin, regenerating this neurotransmitter from a melatonin-derived precursor; this process exhibits polymorphic variation, with poor metabolizers showing reduced activity.^[33] Beyond catecholamines and indolamines, CYP2D6 participates in the biosynthesis of endogenous opioids, including the conversion of codeine to morphine, highlighting its involvement in pain modulation and stress response pathways. Evidence suggests that ultrarapid metabolizers may exhibit elevated endogenous morphine levels, potentially influencing analgesic sensitivity.^[34] Additionally, CYP2D6 metabolizes certain neurosteroids, such as progesterone derivatives, in brain tissue, though its overall contribution to steroid hormone metabolism remains minor compared to isoforms like CYP3A4 and CYP17A1, which dominate systemic steroid catabolism.^[35] The physiological implications of CYP2D6 variability in endogenous substrate processing are evident in neurological contexts, particularly Parkinson's disease. Poor metabolizers, characterized by reduced enzyme activity, display lower CYP2D6 expression in the substantia nigra and are at increased risk for disease development, potentially due to impaired dopamine synthesis and accumulation of neurotoxic intermediates. This association underscores CYP2D6's neuroprotective role, with enzyme levels rising with age in healthy individuals but declining in affected patients.

Xenobiotic Substrates

CYP2D6 plays a critical role in the metabolism of numerous xenobiotic compounds, primarily through phase I oxidative reactions such as O-demethylation, N-dealkylation, and hydroxylation, which facilitate their detoxification and elimination.^[1] These substrates include a wide range of therapeutic drugs and environmental chemicals, accounting for approximately 20-25% of commonly prescribed medications.^[36] The enzyme's activity on these compounds can lead to significant interindividual variability in drug response and toxin clearance due to genetic polymorphisms.^[37] Among pharmaceutical substrates, CYP2D6 extensively metabolizes antidepressants, particularly tricyclic antidepressants like amitriptyline, imipramine, nortriptyline, and desipramine, via N-demethylation and aromatic hydroxylation to form active or inactive metabolites.^[1] Selective serotonin reuptake inhibitors such as paroxetine and fluoxetine are also substrates, undergoing O-demethylation and N-demethylation, respectively, which can result in auto-inhibition during therapy.^[36] For antipsychotics, CYP2D6 catalyzes the hydroxylation of risperidone to 9-hydroxyrisperidone and the metabolism of haloperidol and aripiprazole, influencing their efficacy and side effect profiles.^[1] Beta-blockers like metoprolol and propranolol are primarily hydroxylated by CYP2D6, with metoprolol undergoing alpha-hydroxylation to its active metabolite, contributing to its cardiovascular effects.^[36] In the opioid class, codeine is converted via O-demethylation to the active analgesic morphine, while tramadol and oxycodone undergo similar O-demethylation to form potent metabolites like O-desmethyltramadol and oxymorphone, respectively; poor metabolizers may experience reduced analgesia from these prodrugs.^[1] Probe substrates for CYP2D6 phenotyping include debrisoquine, which is metabolized by 4-hydroxylation, and sparteine, which undergoes N-oxidation and dehydrogenation; these have been historically used to classify individuals as poor, intermediate, extensive, or ultrarapid metabolizers based on urinary metabolic ratios.^[1] Dextromethorphan serves as a modern probe, transformed via O-demethylation to dextrorphan.^[36] CYP2D6 also metabolizes certain environmental toxins, including nicotine derivatives and pesticides. It contributes minorly to the metabolism of nicotine itself but plays a role in inactivating neurotoxic nicotine-derived compounds and inducing enzyme expression in response to nicotine exposure.^[38] For pesticides, CYP2D6 participates in the phase I oxidation of organophosphates such as diazinon, parathion, and chlorpyrifos, converting them into more polar, excretable forms, with reduced activity increasing susceptibility to toxicity.^[37]

Inhibitors

CYP2D6 activity is predominantly modulated by inhibitors rather than inducers, with inhibition being a more common pharmacological interaction due to the enzyme's role in metabolizing numerous therapeutic agents. Inhibitors can be classified as competitive, non-competitive, or mechanism-based, where the latter involves the formation of reactive intermediates that covalently bind to the enzyme, leading to irreversible inactivation. Strong inhibitors exhibit high binding affinity, typically with inhibition constants (Ki) in the range of 0.1–1 μM, significantly reducing CYP2D6-mediated metabolism even at therapeutic doses.^[39]^[40] Prominent strong inhibitors include quinidine, fluoxetine, and paroxetine. Quinidine, a class Ia antiarrhythmic, potently inhibits CYP2D6 with a Ki of approximately 30 nM, making it a classic probe for assessing enzyme activity. Fluoxetine, an antidepressant, and its metabolite norfluoxetine display Ki values ranging from 0.17 to 3.0 μM, with the S-enantiomer showing particularly high affinity (Ki ≈ 68 nM). Paroxetine, another selective serotonin reuptake inhibitor, acts as a strong competitive inhibitor and also demonstrates mechanism-based inhibition, with an apparent Ki of about 4.85 μM and inactivation rate (k_inact) of 0.17 min⁻¹. These compounds can shift CYP2D6 phenotypes toward poor metabolizer status in vivo.^[41]^[42]^[40] Moderate inhibitors, such as duloxetine and terbinafine, exhibit lower potency with Ki values around 0.25–1 μM but still pose risks for drug interactions at higher doses. Duloxetine, used for depression and neuropathic pain, has a Ki of approximately 0.26 μM against CYP2D6*1. Terbinafine, an antifungal agent, is classified as a moderate inhibitor and can elevate plasma levels of CYP2D6 substrates like aripiprazole. Weak inhibitors are less clinically significant but contribute to cumulative effects in polypharmacy.^[43]^[44]^[45] Mechanism-based inhibition of CYP2D6 is exemplified by 3,4-methylenedioxymethamphetamine (MDMA), which undergoes oxidation to form reactive metabolites that inactivate the enzyme. MDMA acts as a high-affinity substrate and potent time-dependent inhibitor, with kinetic parameters indicating rapid inactivation following metabolism. This self-inhibition can profoundly alter MDMA pharmacokinetics, particularly in extensive metabolizers.^[46]^[47] Inducers of CYP2D6 are rare, as the enzyme lacks robust response elements for common nuclear receptors like PXR or CAR. Rifampicin, a potent inducer of other CYPs, shows only minor effects on CYP2D6, with some studies reporting up to 7-fold increase in mRNA but limited impact on protein or activity levels. Thus, inhibition remains the primary concern for CYP2D6 modulation.^[48]^[49]

Clinical Significance

Drug Metabolism Variability

The metabolism of drugs by CYP2D6 exhibits significant interindividual variability due to genetic phenotypes, ranging from poor metabolizers (PMs) with negligible enzyme activity to ultrarapid metabolizers (UMs) with enhanced activity, which directly impacts drug efficacy, pharmacokinetics, and safety.^[50]^[51] In PMs, the lack of functional CYP2D6 enzyme prevents the bioactivation of prodrugs like codeine to its active metabolite morphine, resulting in inadequate analgesia and therapeutic failure.^[50] Similarly, for tamoxifen used in breast cancer treatment, PMs show reduced formation of the potent active metabolite endoxifen, leading to lower plasma concentrations and diminished clinical efficacy, including increased risk of disease recurrence.^[51] Pharmacokinetic alterations are pronounced across phenotypes; for instance, PMs exhibit approximately a 10-fold increase in area under the curve (AUC) for nortriptyline, a tricyclic antidepressant primarily metabolized by CYP2D6, elevating exposure and potential adverse effects.^[52] Conversely, UMs face heightened toxicity risks from excessive metabolite production, such as elevated morphine levels from codeine, which can cause opioid overdose symptoms like respiratory depression.^[50] Drug-drug interactions further amplify this variability, as co-administration of strong CYP2D6 inhibitors (e.g., paroxetine or fluoxetine) with substrates can phenoconvert extensive metabolizers (EMs) to a PM-like state by inhibiting enzyme activity, thereby increasing substrate concentrations and mimicking genetic PM outcomes.^[53]^[44] Recent studies post-2020 highlight the role of polypharmacy in exacerbating CYP2D6 variability; for example, concomitant use of inhibitors in patients on opioids or antidepressants frequently induces phenoconversion, with up to 70% of such cases shifting EMs toward PM phenotypes and increasing adverse event risks, as evidenced by analyses of clinical cohorts and guideline updates.^[44]^[54]

Therapeutic Implications

Variability in CYP2D6 activity significantly impacts treatment outcomes for drugs metabolized by this enzyme, leading to risks of subtherapeutic efficacy or toxicity depending on the phenotype. Poor metabolizers (PMs) experience reduced drug clearance, resulting in higher plasma concentrations and increased adverse events, while ultrarapid metabolizers (UMs) face enhanced activation of prodrugs, potentially causing overdose. These differences underscore the need for pharmacogenetically guided dosing to optimize safety and efficacy in personalized medicine.^[55] In PMs, beta-blockers like metoprolol exhibit prolonged exposure, with four- to sixfold higher concentrations and a twofold to threefold longer half-life, elevating the risk of cardiac adverse events such as excessive bradycardia and severe hypotension.^[56] For instance, PMs have a fivefold increased likelihood of metoprolol-related toxicity compared to extensive metabolizers.^[57] Conversely, UMs treated with codeine, a prodrug converted to morphine by CYP2D6, produce excessive morphine levels, leading to life-threatening respiratory depression and fatal overdose, even at standard doses. This risk is particularly acute in pediatric populations post-tonsillectomy, where UMs have shown rapid conversion to toxic morphine concentrations.^[58]^[55]^[50] Ethnic variations in CYP2D6 phenotypes influence therapeutic strategies, notably for antidepressants. Europeans exhibit a higher PM frequency of 7–10%, which can necessitate dose adjustments for tricyclic antidepressants (TCAs) to avoid accumulation and side effects like anticholinergic toxicity. This prevalence contributes to variable responses, prompting tailored dosing in this population to balance efficacy and safety.^[59] Regulatory and professional guidelines address these risks to mitigate adverse outcomes. The FDA has contraindicated codeine for pain or cough relief in children under 12 years due to ultra-rapid metabolism risks in CYP2D6 UMs, which have been linked to at least five deaths in reported cases involving rapid morphine production.^[60]^[61] In oncology, CYP2D6 variability affects the activation of tamoxifen to its potent metabolite endoxifen in breast cancer therapy. PMs achieve 2- to 4-fold lower endoxifen levels, correlating with up to a twofold increased risk of disease recurrence in some cohorts, highlighting the enzyme's role in endocrine treatment efficacy. Although evidence remains mixed and routine genotyping is not universally endorsed, these findings support ongoing research into genotype-directed tamoxifen alternatives like aromatase inhibitors for PMs.^[62]

Testing and Guidelines

Genotyping for CYP2D6 involves analyzing DNA to identify specific alleles that predict an individual's inherent enzyme activity, providing a stable, lifelong assessment unaffected by temporary factors such as concurrent medications or environmental influences.^[1] In contrast, phenotyping measures current enzyme function, typically through administration of probe substrates like dextromethorphan or tramadol followed by metabolite quantification in urine or plasma, offering insight into real-time activity that may be altered by inhibitors, leading to discrepancies known as phenoconversion.^[44] Genotyping is preferred for routine clinical use due to its reproducibility and non-invasive nature, while phenotyping is advantageous in scenarios where external factors might override genetic predictions, such as in patients on strong CYP2D6 inhibitors.^[63] Several commercial tests are available for CYP2D6 genotyping, with the xTAG CYP2D6 Kit v3 from Luminex Molecular Diagnostics being FDA-cleared as an in vitro diagnostic assay that detects 16 common alleles (*2-*10, *17, *20, *29, *35-*39, *41, *68) from blood samples to guide therapeutic decisions for CYP2D6-metabolized drugs.^[64] This multiplex assay uses Luminex's bead-based technology for simultaneous variant identification, aiding in classifying patients as poor, intermediate, normal, or ultrarapid metabolizers.^[65] The Clinical Pharmacogenetics Implementation Consortium (CPIC) provides evidence-based guidelines for CYP2D6, assigning activity scores to diplotypes (e.g., 0 for poor metabolizers with two no-function alleles, 0.25-1 for intermediate, 1.25-2 for normal, >2 for ultrarapid) to inform dosing; a 2023 update for tricyclic antidepressants downgraded the activity score for the CYP2D6*10 allele from 0.5 to 0.25.^[61] For example, CPIC recommends avoiding codeine in poor and intermediate metabolizers due to risk of ineffective analgesia or toxicity from alternative pathways, while ultrarapid metabolizers require dose reductions or alternative opioids to prevent overdose.^[22] Similarly, for tricyclic antidepressants, standard dosing applies to normal metabolizers, but 25% dose increases are advised for ultrarapid metabolizers, with monitoring for intermediates.^[61] The Dutch Pharmacogenetics Working Group (DPWG) offers comparable recommendations, classifying metabolizer status using activity scores and advising dose adjustments or alternatives for drugs like antipsychotics and antidepressants.^[66] For instance, DPWG suggests dose reductions for risperidone in poor metabolizers to mitigate side effects and increases for ultrarapid metabolizers to achieve efficacy, aligning closely with CPIC but tailored to European populations.^[67] Despite these advances, CYP2D6 testing faces limitations, including incomplete allele coverage in commercial panels, which may miss rare or population-specific variants like CYP2D6*29 in African ancestry groups, potentially leading to misclassification in up to 20% of cases.^[68] Cost-effectiveness remains debated, with 2022 analyses indicating pharmacogenetic testing for CYP2D6 (alongside CYP2C19) is cost-effective for major depressive disorder at willingness-to-pay thresholds above $75,000 per quality-adjusted life year, though broader implementation requires further evidence from real-world studies.^[69] Updated 2024 reviews emphasize the need for expanded allele detection via long-read sequencing to improve accuracy without proportionally increasing costs.^[70]

References

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Transcriptional Regulation of CYP2D6 Expression - PMC - NIH
These transcription factors include hepatocyte nuclear factor (HNF) 4α and CCAAT/enhancer-binding protein (C/EBP) α. HNF4α is a member of the nuclear receptor ...
[8]
Characterization of the human cytochrome P4502D6 promoter. A ...
Oct 11, 1996 · The functional mapping of the human cytochrome P4502D6 (CYP2D6) promoter in HepG2 cells revealed the presence of both positive and negative regulatory elements.Missing: region | Show results with:region
[9]
Molecular Evolution of the CYP2D Subfamily in Primates - NIH
Our findings reveal that the CYP2D7 gene has been duplicated from CYP2D6 in a stem lineage of humans and great apes, and the origin of CYP2D6 and CYP2D8P genes ...
[10]
Complex gene expansion of the CYP2D gene subfamily - PMC - NIH
Additionally, the CYP2D subfamily, especially the CYP2D6 gene, is responsible for plant toxin detoxification. Thus, the study here intended to explore whether ...
[11]
PharmVar
### Summary of CYP2D6 Alleles and Resources
[12]
CYP2D6 CPIC guidelines
For gene-specific information tables (i.e. CYP2D6 allele definition, allele functionality, frequency and diplotype-phenotype tables) see guideline pages or ...
[13]
[PDF] Structural Variation CYP2D6 - PharmVar
These alleles may have increased, normal, decreased or no function. All allelic variants with SNPs and/or indels are defined in the PharmVar database.
[14]
https://www.pharmgkb.org/gene/PA128
[15]
CYP2D6 - Cytochrome P450 2D6 - Homo sapiens (Human) - UniProt
A cytochrome P450 monooxygenase involved in the metabolism of fatty acids, steroids and retinoids.
[16]
Crystal structure of human cytochrome P450 2D6 - PubMed
Mar 17, 2006 · The 2D6 structure has a well defined active site cavity above the heme group, containing many important residues that have been implicated in ...
[17]
Residues glutamate 216 and aspartate 301 are key determinants of ...
CYP2D6 substrates typically contain a basic nitrogen atom, and the active-site residue Asp-301 has been implicated in substrate recognition through ...
[18]
https://www.rcsb.org/structure/2F9Q
[19]
Impact of physiological, pathological and environmental factors on ...
Post-translational modifications such as phosphorylation of CYP2D6 Ser135 have been observed, but the functional impact is unknown.
[20]
Mechanisms of Cytochrome P450-Catalyzed Oxidations - PMC - NIH
Most oxidations of chemicals are catalyzed by cytochrome P450 (P450, CYP) enzymes, which generally utilize mixed-function oxidase stoichiometry.
[21]
Enantioselectivity of debrisoquine 4-hydroxylation in Brazilian ...
Debrisoquine hydroxylation at position 4 by CYP2D6 creates a chiral centre in the molecule, with the possible formation of the S-(+)-4-hydroxydebrisoquine ...Missing: stereoselectivity | Show results with:stereoselectivity
[22]
CPIC® Guideline for Opioids and CYP2D6, OPRM1, and COMT
Tables and figures included in the supplementa or referenced in the guideline: · CYP2D6 allele definition table · CYP2D6 allele functionality table · CYP2D6 ...
[23]
Clinical Pharmacogenetics Implementation Consortium (CPIC ...
Dec 21, 2016 · The CYP2D6 activity score relates to the phenotype classification system as follows (CYP2D6 Allele Definition Table 1): patients with an ...
[24]
Evaluation of probe drugs and pharmacokinetic metrics for CYP2D6 ...
Conclusion: Application of the validation criteria suggests that dextromethorphan and debrisoquine are the best CYP2D6 phenotyping drugs, with debrisoquine ...Missing: diagnostic codeine
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Standardizing CYP2D6 Genotype to Phenotype Translation
Oct 24, 2019 · Translating CYP2D6 genotype to metabolizer phenotype is not standardized across clinical laboratories offering pharmacogenetic (PGx) testing ...
[26]
Methodology for clinical genotyping of CYP2D6 and CYP2C19
Nov 22, 2021 · The aim of this paper was to cross-validate multiple technologies for genotyping CYP2D6 and CYP2C19 against each other, and to contribute to feasibility for ...
[27]
CYP2D6 - an overview | ScienceDirect Topics
... phenotype with 90 to 95% accuracy. Among the multiple alleles listed in Table 1.1, both CYP2D6∗1 and CYP2D6∗2 exhibit normal enzyme activity, whereas the ...7 The Cyp2d6 · 7.2 The Cyp2d6 Alleles · Understanding Molecular...<|control11|><|separator|>
[28]
Meta-analysis of probability estimates of worldwide variation of ...
Feb 24, 2021 · The mean total probability estimates of having a non-NM predicted phenotype worldwide were 36.4% and 61.9% for CYP2D6 and CYP2C19, respectively.Methods · Results · Cyp2d6
[29]
The variation landscape of CYP2D6 in a multi-ethnic Asian population
Jul 20, 2024 · This aligns with previous reports indicating that the *5/*5 diplotype occurs at a very low frequency, ranging from 0% to 1.9% in Southeast Asian ...
[30]
CYP2D6 Genotype Predicts Plasma Concentrations of Tamoxifen ...
Sep 12, 2019 · About 29% of Ethiopians carry functionally active CYP2D6 gene duplications and multiplications associated with increased enzyme activity [15].
[31]
Frequencies of clinically important CYP2C19 and CYP2D6 alleles ...
Jul 29, 2019 · We found that frequencies of CYP2D6 gene duplications showed a clear South-East to North-West gradient ranging from <1% in Sweden and Denmark to 6% in Greece ...
[32]
Dopamine Formation from Tyramine by CYP2D6 - ScienceDirect.com
This is the first report showing that CYP2D is capable of converting tyramine to dopamine. The Km values of CYP2D6, expressed in yeast, forp-tyramine andm- ...
[33]
Regeneration of serotonin from 5-methoxytryptamine by ... - PubMed
The production of 5-HT from 5-MT catalyzed by CYP2D6 was inhibited by selective serotonin reuptake inhibitors, and their inhibition potency (K(i), micromol/l) ...Missing: et al
[34]
Impact of CYP2D6 Genetic Polymorphisms on Postoperative ...
Recent studies have shown that CYP2D6 plays an important role not only in the metabolism of exogenous opioids but also in the endogenous morphine synthesis ...The Impact Of Cyp2d6 Genetic... · Genotyping Cyp2d6 By... · ResultsMissing: substrates | Show results with:substrates
[35]
[PDF] Role of brain cytochrome P450 (CYP2D) in the metabolism of ...
Abstract: This article focuses on recent research on the cytochrome P450 2D (CYP2D) catalyzed synthesis of the monoaminergic neurotransmit- ters dopamine ...
[36]
Biochemistry, Cytochrome P450 - StatPearls - NCBI Bookshelf - NIH
Inducers: carbamazepine, phenytoin, rifampin,. Substrates: omeprazole, phenobarbital. CYP2D6: Inhibitors: bupropion, duloxetine, fluoxetine, paroxetine, ...Missing: 2020-2025 | Show results with:2020-2025
[37]
Further evidence for the association of CYP2D6*4 gene ...
Jul 1, 2017 · Our data provide further evidence that a poor metabolizer status may increase the risk to develop PD especially in populations that are exposed ...
[38]
CYP2D6 Phenotype and the Metabolism of Nicotine and Cotinine
That CYP2D6 activity is an important determinant of nicotine metabolism and that people who have abnormal CYP2D6 genes are poor metabolizers of nicotine has ...
[39]
Table of Substrates, Inhibitors and Inducers - Drug Interactions - FDA
Jun 5, 2023 · This table provides examples of clinical sensitive or moderately sensitive index substrates and is not intended to be an exhaustive list.
[40]
Antidepressant–Drug Interactions are Potentially but Rarely ... - Nature
Jul 18, 2006 · The results across studies have been generally consistent in finding potent (ie Ki=∼⩽1.0 μM) CYP2D6 inhibition for fluoxetine (Ki=0.17–3.0 μM; ...
[41]
Pharmacokinetics and Pharmacodynamics - MDPI
This is analogous to the efficacy of quinidine (Ki = 30 nM), which is presently acknowledged as the most potent antagonist of CYP2D6 [45]. Most studies or case ...Pharmacokinetics And... · 2.1. 1. Fluoxetine · 2.2. 3. Metabolism<|control11|><|separator|>
[42]
Assessing the Mechanism of Fluoxetine-Mediated CYP2D6 Inhibition
Jan 23, 2021 · S-Fluoxetine and S-norfluoxetine are both substrates and exhibit a high binding affinity to CYP2D6 (Ki = 68 nM and 35 nM, respectively; Ki is ...
[43]
[PDF] In vitro comparative analysis of metabolic capabilities and inhibitory ...
Oct 10, 2024 · CYP2D6 variant alleles showed increased Ki values compared to CYP2D6*1 for all five inhibitors except for the bupropion/CYP2D6*2 pair. Quinidine ...
[44]
CYP2D6 pharmacogenetics and phenoconversion in personalized ...
The drug metabolizing enzyme, cytochrome P450 2D6 (CYP2D6) is estimated to contribute to the metabolism of approximately 20–25% of drugs.2. Cyp2d6 Pharmacogenetics · 2.1. Cyp2d6 Pharmacogenetics... · 3. Cyp2d6 Phenoconversion
[45]
Possible inhibitory effects of terbinafine on aripiprazole metabolism
Terbinafine is a moderate CYP2D6 inhibitor that may increase aripiprazole concentrations; however, no published reports have assessed this potential DDI. TDM is ...
[46]
Kinetic mechanism of time-dependent inhibition of CYP2D6 by 3,4 ...
Aug 13, 2018 · We investigate the mechanism of time-dependent inhibition (TDI) of human cytochrome P450 2D6 (CYP2D6) by 3,4-methylenedioxymethamphetamine ...
[47]
MDMA, methamphetamine, and CYP2D6 pharmacogenetics: what is ...
Methamphetamine behaves as both a weak substrate and competitive inhibitor of CYP2D6, while MDMA acts as a high affinity substrate and potent mechanism-based ...
[48]
[PDF] CYP2D6 Is Inducible by Endogenous and Exogenous Corticosteroids
The reverse was true of CYP2D6 induction by rifampin. Rifampin induced CYP2D6 mRNA to a greater extent (;7-fold) than either. CYP2D6 protein or activity.
[49]
Influence of rifampicin on the expression and function of human ...
No influence of rifampicin on the expression of CYP2D6 was observed in the present study. This finding is consistent with a previous in vivo work, in which ...
[50]
Codeine Therapy and CYP2D6 Genotype - NCBI - NIH
Sep 20, 2012 · The CYP2D6 enzyme converts codeine into its active metabolite, morphine, which provides its analgesic effect. Consequently, pain relief may be ...Introduction · Drug: Codeine · Gene: CYP2D6 · The CYP2D6 Gene...
[51]
Tamoxifen Therapy and CYP2D6 Genotype - NCBI - NIH
Oct 7, 2014 · Individuals who are intermediate or poor metabolizers may have reduced plasma concentrations of endoxifen and benefit less from tamoxifen ...Introduction · Drug: Tamoxifen · Gene: CYP2D6 · Therapeutic...
[52]
From evidence based medicine to mechanism ... - PubMed Central
The plasma levels of nortriptyline may vary almost tenfold depending on the number of functional CYP2D6 allelles. Still we accept to use the same dose in ...
[53]
Metoprolol and CYP2D6: A Retrospective Cohort Study Evaluating ...
Feb 26, 2023 · Strong inhibitors of CYP2D6 decrease the enzyme activity to near zero, causing individuals who display normal or intermediate genotypes to mimic ...
[54]
Clinical effects of CYP2D6 phenoconversion in patients with psychosis
Sep 23, 2024 · Conclusion: Polypharmacy and phenoconversion were prevalent and accounted for a significant increase in PMs. CYP2D6 may play a limited role in side effects, ...
[55]
Applications of CYP450 Testing in the Clinical Setting - PMC
CYP2D6 PM phenotype has been associated with an increased risk of toxicity of metoprolol, timolol, carvedilol and propafenone.
[56]
The role of pharmacogenomics in contemporary cardiovascular ...
Feb 26, 2021 · Several studies have investigated the clinical effects of CYP2D6 in patients taking metoprolol, mostly for heart failure (HF) or hypertension ( ...
[57]
The CYP2D6 polymorphism in relation to the metabolism of ...
The CYP2D6 polymorphism is an important determinant of TCA metabolism [2], and 7–10% of Europeans are CYP2D6 poor metabolizers (PMs) [3]. We have recently shown ...
[58]
FDA restricts use of prescription codeine pain and cough medicines ...
Apr 20, 2017 · FDA's strongest warning, called a Contraindication, alerting that codeine and tramadol should not be used to treat pain in children younger ...
[59]
CPIC® Guideline for Tricyclic Antidepressants and CYP2D6 and ...
CYP2D6 allele definition table · CYP2D6 allele functionality table · CYP2D6 frequency table · CYP2D6 diplotype-phenotype table · CYP2C19 allele definition table.
[60]
CYP2D6 Genotyping and Tamoxifen: An Unfinished Story in the ...
At 2 years, the patients on a moderate to potent CYP2D6 inhibitor had a significantly higher risk of breast cancer recurrence (13.9% v 7.5%; P <.001) than women ...
[61]
CYP2D6 Genotyping as an alternative to phenotyping for ...
Our results suggest that CYP2D6 genotyping is a valid alternative to traditional phenotyping in a clinical trial setting, and in some cases may be better.
[62]
[PDF] CYP2D6 Kit v3 - accessdata.fda.gov
The xTAG®. CYP2D6 Kit v3 is a qualitative genotyping assay which can be used as an aid to clinicians in determining therapeutic strategy for therapeutics that ...
[63]
Nucleic Acid Based Tests - FDA
Jun 23, 2025 · A full list of FDA cleared or approved companion diagnostic devices ... xTAG CYP2D6 Kit v3, Luminex Molecular Diagnostics, Inc. K130189 ...
[64]
Pharmacogenetics Guidelines: Overview and Comparison of the ...
The DPWG recommends increasing the dose of tricyclic antidepressants in CYP2D6 UM patients, and has specific calculated dose recommendations per gene-drug ...Missing: tiers | Show results with:tiers
[65]
Dutch Pharmacogenetics Working Group (DPWG) guideline for the ...
Mar 31, 2023 · For CYP2D6 UMs, a dose increase or an alternative drug is recommended for haloperidol and an alternative drug or titration of the dose for ...Missing: tiers | Show results with:tiers
[66]
Long-read sequencing of CYP2D6 may improve psychotropic ... - NIH
Sep 11, 2024 · The other FDA-approved test, xTAG CYP2D6 Kit v3, is capable of detecting only 16 star alleles, with none being unique from AmpliChip (Lyon et ...
[67]
Cost–Utility Analysis of Pharmacogenetic Testing Based on ... - NIH
Aug 5, 2022 · Our findings suggest that screenings for both CYP2C19 and CYP2D6 enzymes for patients with MDD are cost-effective for a WTP threshold of 75,000 ...Missing: incomplete coverage 2024
[68]
Efficacy and safety of pharmacogenomic-guided antidepressant ...
Jul 10, 2024 · Systematic evaluation of commercial pharmacogenetic testing in psychiatry: a focus on CYP2D6 and CYP2C19 allele coverage and results reporting.