rs3892097

This is a splice acceptor variant in the CYP2D6 gene.

Key Literature Trait Associations

Codeine Response

CYP2D6*4 is the most common null allele, carried by approximately 20% of Europeans. A splice site defect completely abolishes CYP2D6 enzyme activity, preventing activation of codeine to morphine and tramadol to its active metabolite. This variant also impairs tamoxifen conversion to its active metabolite endoxifen, and affects metabolism of ondansetron and many antidepressants. CPIC recommends alternative analgesics for poor metabolizers.

Gierach M et al. Insulin resistance and thyroid disorders. Endokrynologia Polska 65(1):70-76 (2014)
Allele A
OR
p
Major Consortium Study

GWAS Catalog Trait Associations (3)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

solanidine measurement

Allele T
OR 0.82
p 5.0e-51
N 1,487
Large GWAS
European

urinary metabolite measurement

Allele T
OR 1.70
p 6.0e-16
N 1,221
Large GWAS

metabolite measurement

Allele T
OR 1.67
p 1.0e-15
N 423
Small GWAS
European

ClinVar annotation

Drug Response☆☆☆
6 submitters41 publications

Debrisoquine, poor metabolism of; Deutetrabenazine response; Tamoxifen response; Tramadol response; not specified

View on ClinVar →

Research that mentions this SNP (7)

Correlation between single-nucleotide polymorphisms and statin-induced myopathy: a mixed-effects model meta-analysis
Meta-analysisN=21,692Qian Xiang et al.(2021)· European Journal of Clinical Pharmacology

A meta-analysis of 32 studies (21,692 individuals) examined SNPs associated with statin-induced myopathy (SIM). SLCO1B1 rs4149056 C allele significantly increased SIM risk in heterozygous (OR ~1.58), homozygous (OR ~4.47), dominant (OR ~1.89), and recessive (OR ~4.54) models. SLCO1B1 rs4363657 C allele was protective, and GATM rs9806699 A allele carriers had lower SIM risk with rosuvastatin treatment.

Traits studied:Elevated creatine kinaseMuscle injuryMuscle weaknessMyalgiaMyopathyRhabdomyolysisStatin-induced myopathy
Interindividual Variability in the Hepatic Expression of the Human Breast Cancer Resistance Protein (BCRP/ABCG2): Effect of Age, Sex, and Genotype
AssociationN=1,000Bhagwat Prasad et al.(2013)· Journal of Pharmaceutical Sciences

Case-control study of 1,000 Han Chinese individuals (450 epilepsy cases, 550 controls) examining associations between STX1B polymorphisms and epilepsy treatment response. The rs140820592 variant showed significant association with reduced epilepsy risk (OR=0.542, p=0.004) and drug-resistant epilepsy risk (OR=0.260, p=0.004), with eQTL analysis confirming rs140820592 regulates STX1B expression in brain tissues.

Traits studied:Drug-resistant epilepsyDrug-responsive epilepsyEpilepsyImatinib response in chronic myelogenous leukemiaPraziquantel responseTacrolimus metabolism
Genetic sequence variants and the development of secondary primary cancers in patients with head and neck cancers
AssociationN=531Abul Kalam Azad et al.(2012)· Cancer

This case-control association study evaluated 23 genetic sequence variants in 17 genes across DNA repair, cell cycle, and other pathways in 531 stage I-II radiation-treated head and neck cancer (HNC) patients to identify associations with secondary primary cancers (SPCs). Among the variants tested, the DNMT3B C149T variant (rs2424913) showed a strong significant association with SPC development, with adjusted hazard ratios of 2.23 (95% CI, 1.32-3.78; P = .003) for TT versus CC genotype and 1.49 (95% CI, 1.15-1.95; P = .003) per T allele. A haplotype cluster of 5 DNMT3B variants in strong linkage disequilibrium also showed significant associations (P < .003), suggesting aberrant DNA methylation is an important modulator of field cancerization in HNC.

Traits studied:Head and neck cancerSecondary primary cancer (SPC)
Association of RANBP1 haplotype with smooth pursuit eye movement abnormality
ReviewHyun Sub Cheong et al.(2011)· American Journal of Medical Genetics Part B: Neuropsychiatric Genetics

This comprehensive review examines the genomics of schizophrenia and pharmacogenomics of antipsychotic drugs, synthesizing evidence on over 200 genes associated with psychotic disorders. The authors discuss five categories of genes relevant to antipsychotic response: disease-associated genes, mechanism-of-action genes, drug metabolism genes (particularly CYP2D6, CYP2C19, CYP2C9, CYP3A4), drug transporter genes, and pleiotropic genes. The review details pharmacogenomic profiles of 20+ antipsychotic drugs and demonstrates significant ethnic and interindividual variation in drug metabolism phenotypes, with examples including CYP2D6 extensive metabolizers (55.71% of population), intermediate metabolizers (34.7%), poor metabolizers (2.28%), and ultra-rapid metabolizers (7.31%).

Traits studied:Alzheimer diseaseAntipsychotic drug responseAntipsychotic drug side effectsAnxiety disordersBipolar disorderCNS disordersDepressive disorderParkinson's diseasePsychotic disordersSchizoaffective disorderSchizophreniaTardive dyskinesiaVascular dementia
Influence of neurexin 1 (NRXN1) polymorphisms in clozapine response
ReviewRenan P. Souza et al.(2010)· Human Psychopharmacology: Clinical and Experimental

This systematic review of 98 studies examined biological predictors of clozapine response in treatment-resistant schizophrenia patients. Of 379 different gene variants investigated across 70 genetic studies, only three variants (DRD3 Ser9Gly rs6280, HTR2A His452Tyr, and GNB3 C825T) achieved independent replication. Non-genetic predictors included higher prefrontal cortical volumes and lower HVA:5-HIAA ratio in cerebrospinal fluid.

Traits studied:Clozapine responseSchizophreniaTreatment-resistant schizophrenia
Lack of association of GPX1 and MnSOD genes with symptom severity and response to clozapine treatment in schizophrenia subjects
ReviewRenan P. Souza et al.(2009)· Human Psychopharmacology: Clinical and Experimental

A systematic review of 98 studies investigating biological predictors of clozapine response in treatment-resistant schizophrenia. Of 70 genetic studies examining 379 variants, only three genetic variants have independently replicated findings: DRD3 Ser9Gly (rs6280), HTR2A His452Tyr, and GNB3 C825T (rs5442/rs5443). Non-genetic predictors include higher prefrontal cortical structural integrity and activity, and lower HVA:5-HIAA ratio in cerebrospinal fluid.

Traits studied:Clozapine responseSchizophreniaTreatment-resistant schizophrenia
CYP2D6 polymorphism, pesticide exposure, and Parkinson's disease
Meta-analysisN=6,230Alexis Elbaz et al.(2004)· Annals of Neurology

Meta-analysis of 22 comparisons from 21 studies (2,629 Parkinson's disease patients, 3,601 controls) showing the CYP2D6*4 polymorphism (G1934A, Glu-to-Gly substitution) is significantly associated with increased PD risk overall (OR = 1.28, 95% CI = 1.14-1.43, P = 0.001), particularly in Caucasian populations but not in Asian populations.

Traits studied:Early-onset Parkinson's diseaseFamilial Parkinson's diseaseLate-onset Parkinson's diseaseParkinson's diseaseSporadic Parkinson's disease

Gene information from NCBI Gene. Variant classifications from ClinVar.

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