CYP2C9
cytochrome P450 family 2 subfamily C member 9, the group of Cytochrome P450 family 2
Basic information
Region (hg38): 10:94938658-94990091
Previous symbols: [ "CYP2C10" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Drug metabolism, CYP2C9-related | AD | Pharmacogenomic | Selection and dosing of medications may be affected by the presence of variants | General | 10073515; 10901705; 19228618; 19300499; 19715737; 19794412; 20089352; 20402581; 21562147; 23089672 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (33 variants)
- not_provided (10 variants)
- Piroxicam_response (4 variants)
- Lesinurad_response (4 variants)
- Flurbiprofen_response (4 variants)
- Warfarin_response (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CYP2C9 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000771.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | |||||
| missense | 34 | 41 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 1 | 0 | 34 | 7 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CYP2C9 | protein_coding | protein_coding | ENST00000260682 | 9 | 50733 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.27e-10 | 0.100 | 125665 | 0 | 78 | 125743 | 0.000310 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -2.94 | 381 | 250 | 1.52 | 0.0000130 | 3242 |
| Missense in Polyphen | 125 | 82.504 | 1.5151 | 1094 | ||
| Synonymous | -4.07 | 141 | 91.4 | 1.54 | 0.00000459 | 929 |
| Loss of Function | 0.295 | 16 | 17.3 | 0.924 | 7.43e-7 | 248 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000507 | 0.000507 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00131 | 0.00131 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.000106 | 0.000105 |
| Middle Eastern | 0.00131 | 0.00131 |
| South Asian | 0.000856 | 0.000850 |
| Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Cytochromes P450 are a group of heme-thiolate monooxygenases. In liver microsomes, this enzyme is involved in an NADPH-dependent electron transport pathway. It oxidizes a variety of structurally unrelated compounds, including steroids, fatty acids, and xenobiotics (PubMed:25994031). This enzyme contributes to the wide pharmacokinetics variability of the metabolism of drugs such as S-warfarin, diclofenac, phenytoin, tolbutamide and losartan (PubMed:25994031). {ECO:0000269|PubMed:25994031}.;
- Pathway
- Celecoxib Pathway, Pharmacokinetics;Rosiglitazone Pharmacokinetic Pathway;Retinol metabolism - Homo sapiens (human);Serotonergic synapse - Homo sapiens (human);Metabolism of xenobiotics by cytochrome P450 - Homo sapiens (human);Drug metabolism - cytochrome P450 - Homo sapiens (human);Arachidonic acid metabolism - Homo sapiens (human);Linoleic acid metabolism - Homo sapiens (human);Chemical carcinogenesis - Homo sapiens (human);Imatinib Pathway, Pharmacokinetics/Pharmacodynamics;Losartan Pathway, Pharmacokinetics;Statin Pathway - Generalized, Pharmacokinetics;Atorvastatin/Lovastatin/Simvastatin Pathway, Pharmacokinetics;Fluvastatin Pathway, Pharmacokinetics;Warfarin Pathway, Pharmacokinetics;Phenytoin Pathway, Pharmacokinetics;Tamoxifen Pathway, Pharmacokinetics;Gefitinib Pathway, Pharmacokinetics;Anti-diabetic Drug Nateglinide Pathway, Pharmacokinetics;Clopidogrel Pathway, Pharmacokinetics;Fluoxetine Pathway, Pharmacokinetics;Zidovudine Pathway, Pharmacokinetics/Pharmacodynamics;Caffeine Pathway, Pharmacokinetics;Nevirapine Pathway, Pharmacokinetics;Sorafenib Pharmacokinetics;Valproic Acid Pathway, Pharmacokinetics;Doxepin Pathway, Pharmacokinetics;Ibuprofen Pathway, Pharmacokinetics;Cyclophosphamide Pathway, Pharmacokinetics;Ifosfamide Pathway, Pharmacokinetics;Ibuprofen Action Pathway;Phenytoin (Antiarrhythmic) Action Pathway;Rosiglitazone Metabolism Pathway;Fluoxetine Action Pathway;Ibuprofen Metabolism Pathway;Clopidogrel Metabolism Pathway;Celecoxib Action Pathway;Clopidogrel Action Pathway;Valproic Acid Metabolism Pathway;Cyclophosphamide Action Pathway;Ifosfamide Action Pathway;Sorafenib Metabolism Pathway;Doxepin Metabolism Pathway;Fluoxetine Metabolism Pathway;Celecoxib Metabolism Pathway;Nevirapine Metabolism Pathway;Caffeine Metabolism;Cyclophosphamide Metabolism Pathway;Ifosfamide Metabolism Pathway;Constitutive Androstane Receptor Pathway;Pregnane X Receptor pathway;Vitamin D Receptor Pathway;Nuclear Receptors Meta-Pathway;Nuclear Receptors in Lipid Metabolism and Toxicity;Cannabinoid receptor signaling;Valproic acid pathway;Liver steatosis AOP;Metabolism of Tetrahydrocannabinol (THC);Oxidation by Cytochrome P450;Arachidonate Epoxygenase - Epoxide Hydrolase;Tamoxifen metabolism;Metapathway biotransformation Phase I and II;Phase I - Functionalization of compounds;Metabolism of lipids;Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE);Arachidonic acid metabolism;Xenobiotics;Tyrosine metabolism;Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET);Androgen and estrogen biosynthesis and metabolism;Cytochrome P450 - arranged by substrate type;Leukotriene metabolism;Biological oxidations;Metabolism;Biosynthesis of maresin-like SPMs;Biosynthesis of maresins;Biosynthesis of DHA-derived SPMs;Biosynthesis of specialized proresolving mediators (SPMs);Fatty acid metabolism;Linoleate metabolism;C21-steroid hormone biosynthesis and metabolism;Xenobiotics metabolism;Tryptophan degradation;CYP2E1 reactions;Arachidonic acid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.383
Intolerance Scores
- loftool
- 0.903
- rvis_EVS
- 0.31
- rvis_percentile_EVS
- 72.71
Haploinsufficiency Scores
- pHI
- 0.0918
- hipred
- N
- hipred_score
- 0.112
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.937
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cyp2c66
- Phenotype
Gene ontology
- Biological process
- organic acid metabolic process;xenobiotic metabolic process;steroid metabolic process;monoterpenoid metabolic process;drug metabolic process;epoxygenase P450 pathway;urea metabolic process;monocarboxylic acid metabolic process;drug catabolic process;exogenous drug catabolic process;long-chain fatty acid biosynthetic process;cellular amide metabolic process;oxidation-reduction process;oxidative demethylation;omega-hydroxylase P450 pathway
- Cellular component
- cytoplasm;endoplasmic reticulum membrane;organelle membrane;intracellular membrane-bounded organelle
- Molecular function
- monooxygenase activity;iron ion binding;drug binding;arachidonic acid epoxygenase activity;steroid hydroxylase activity;oxidoreductase activity;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen;heme binding;caffeine oxidase activity