Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

ClinVar Genomic variation as it relates to human health

Advanced search

CYP2C9*2

Help
Interpretation:
Likely benign; drug response; other​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
7
First in ClinVar:
Apr 9, 2018
Most recent Submission:
Nov 6, 2020
Last evaluated:
Feb 11, 2019
Accession:
VCV000008409.11
Variation ID:
8409
Description:
single nucleotide variant
Help

CYP2C9*2

Allele ID
23448
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.33
Genomic location
10: 94942290 (GRCh38) GRCh38 UCSC
10: 96702047 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NM_000771.4:c.430C>T MANE Select NP_000762.2:p.Arg144Cys missense
NC_000010.11:g.94942290C>T
NC_000010.10:g.96702047C>T
... more HGVS
Protein change
R144C
Other names
NM_000771.3(CYP2C9):c.430C>T (p.Arg144Cys)
430C>T
Canonical SPDI
NC_000010.11:94942289:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.04792 (T)

Allele frequency
1000 Genomes Project 0.04792
The Genome Aggregation Database (gnomAD) 0.08975
The Genome Aggregation Database (gnomAD), exomes 0.09202
The Genome Aggregation Database (gnomAD) 0.08247
Trans-Omics for Precision Medicine (TOPMed) 0.08441
Trans-Omics for Precision Medicine (TOPMed) 0.08592
Exome Aggregation Consortium (ExAC) 0.09144
Links
PharmGKB Clinical Annotation: 637879781
ClinGen: CA119592
Genetic Testing Registry (GTR): GTR000552448
Genetic Testing Registry (GTR): GTR000556805
Genetic Testing Registry (GTR): GTR000562560
UniProtKB: P11712#VAR_008343
OMIM: 601130.0002
dbSNP: rs1799853
VarSome
Help

Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Mar 9, 2018 RCV000309101.5
other 1 criteria provided, single submitter Jul 9, 2015 RCV000723560.4
drug response 1 criteria provided, single submitter Feb 11, 2019 RCV000788099.3
drug response 1 criteria provided, single submitter Feb 11, 2019 RCV000788093.3
drug response 1 criteria provided, single submitter Feb 11, 2019 RCV000787929.3
drug response 1 no assertion criteria provided Aug 9, 2018 RCV000008920.3
drug response 1 no assertion criteria provided Sep 24, 2020 RCV001263463.2
Help
Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CYP2C9 - - GRCh38
GRCh37
15 42

Submitted interpretations and evidence

Help
Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
other
(Jul 09, 2015)
criteria provided, single submitter
Method: clinical testing
not provided
Affected status: unknown
Allele origin: germline
Eurofins NTD LLC (GA)
Accession: SCV000331315.4
First in ClinVar: Dec 06, 2016
Last updated: Dec 15, 2018
Other databases
http://www.egl-eurofins.com/emvc… http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP2C9
Number of individuals with the variant: 173
Zygosity: 11 Homozygote, 158 Single Heterozygote
Sex: mixed
Likely benign
(Mar 09, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Affected status: yes
Allele origin: germline
GeneDx
Accession: SCV000730664.1
First in ClinVar: Apr 09, 2018
Last updated: Apr 09, 2018
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
drug response
(Feb 11, 2019)
criteria provided, single submitter
Method: curation
Flurbiprofen response
Drug used for Pain , Inflammation , Osteoarthritis , Rheumatoid Arthritis , Bursitis , and Tendinitis
Affected status: yes
Allele origin: germline
Medical Genetics Summaries
Accession: SCV000926948.1
First in ClinVar: Jul 21, 2019
Last updated: Jul 21, 2019
Publications:
PubMed (5)
Other databases
https://dailymed.nlm.nih.gov/dai… https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=4e5c06f1-f279-4f2f-b10d-0f70005a27e6
Comment:
The dose of flurbiprofen should be reduced in individuals with 2 decreased function alleles (CYP2C9 poor metabolizers) to avoid abnormally high plasma levels due to … (more)
drug response
(Feb 11, 2019)
criteria provided, single submitter
Method: curation
Lesinurad response
Drug used for Gout
Affected status: yes
Allele origin: germline
Medical Genetics Summaries
Accession: SCV000927091.1
First in ClinVar: Jul 24, 2019
Last updated: Jul 24, 2019
Publications:
PubMed (1)
PubMed: 30742400
Other databases
https://dailymed.nlm.nih.gov/dai… https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=ef9e7711-f478-4e35-bf4e-6021c8457e3b
Comment:
Lesinurad should be used with caution in individuals with 2 decreased function alleles (CYP2C9 poor metabolizers) because of increased exposure and an increased risk of … (more)
drug response
(Feb 11, 2019)
criteria provided, single submitter
Method: curation
Piroxicam response
Drug used for Pain , Inflammation , Osteoarthritis , and Rheumatoid arthritis
Affected status: yes
Allele origin: germline
Medical Genetics Summaries
Accession: SCV000927097.1
First in ClinVar: Jul 24, 2019
Last updated: Jul 24, 2019
Publications:
PubMed (6)
Other databases
https://dailymed.nlm.nih.gov/dai… https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=6039e036-c0aa-4249-af50-115f49ad758a
Comment:
Individuals with 2 decreased function alleles (CYP2C9 poor metabolizers) have reduced clearance of piroxicam. Because the standard recommended dose of piroxicam may cause abnormally high … (more)
drug response
(Aug 09, 2018)
no assertion criteria provided
Method: literature only
WARFARIN SENSITIVITY
Affected status: not provided
Allele origin: germline
OMIM
Accession: SCV000029130.2
First in ClinVar: Apr 04, 2013
Last updated: Aug 11, 2018
Publications:
PubMed (5)
Comment on evidence:
The arg144-to-cys (R144C) substitution results from a 430C-T transition in the CYP2C9 gene and is also known as rs1799853 and CYP2C9*2. The variant leads to … (more)
drug response
(Sep 24, 2020)
no assertion criteria provided
Method: case-control
Phenytoin response
Drug used for status epilepticus
Affected status: yes
Allele origin: germline
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne
Accession: SCV001441533.1
First in ClinVar: Nov 06, 2020
Last updated: Nov 06, 2020
Publications:
PubMed (2)
PubMed: 2509916432779747
Comment:
May cause toxicity/ADR and poor metabolism/PK

Functional evidence

Help
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

Help
Title Author Journal Year Link
Clinical Pharmacogenetics Implementation Consortium (CPIC) Guideline for CYP2C9 and HLA-B Genotypes and Phenytoin Dosing: 2020 Update. Karnes JH Clinical pharmacology and therapeutics 2021 PMID: 32779747
Piroxicam Therapy and CYP2C9 Genotype. Pratt VM - 2019 PMID: 30742401
Lesinurad Therapy and CYP2C9 Genotype. Pratt VM - 2019 PMID: 30742400
Flurbiprofen Therapy and CYP2C9 Genotype. Pratt VM - 2019 PMID: 30742399
Efficacy of piroxicam for postoperative pain after lower third molar surgery associated with CYP2C8*3 and CYP2C9. Calvo AM Journal of pain research 2017 PMID: 28740425
CYP2C9 genotype vs. metabolic phenotype for individual drug dosing--a correlation analysis using flurbiprofen as probe drug. Vogl S PloS one 2015 PMID: 25775139
Effects of CYP2C9*1/*3 genotype on the pharmacokinetics of flurbiprofen in Korean subjects. Lee YJ Archives of pharmacal research 2015 PMID: 25712887
Clinical pharmacogenetics implementation consortium guidelines for CYP2C9 and HLA-B genotypes and phenytoin dosing. Caudle KE Clinical pharmacology and therapeutics 2014 PMID: 25099164
Worldwide allele frequency distribution of four polymorphisms associated with warfarin dose requirements. Ross KA Journal of human genetics 2010 PMID: 20555338
Genetically based impairment in CYP2C8- and CYP2C9-dependent NSAID metabolism as a risk factor for gastrointestinal bleeding: is a combination of pharmacogenomics and metabolomics required to improve personalized medicine? Agúndez JA Expert opinion on drug metabolism & toxicology 2009 PMID: 19422321
Genetic susceptibility to nonsteroidal anti-inflammatory drug-related gastroduodenal bleeding: role of cytochrome P450 2C9 polymorphisms. Pilotto A Gastroenterology 2007 PMID: 17681167
Impact of CYP2C9*3/*3 genotype on the pharmacokinetics and pharmacodynamics of piroxicam. Perini JA Clinical pharmacology and therapeutics 2006 PMID: 17112811
Polymorphisms in the VKORC1 gene are strongly associated with warfarin dosage requirements in patients receiving anticoagulation. Li T Journal of medical genetics 2006 PMID: 16611750
Influence of CYP2C9 genotypes on the pharmacokinetics and pharmacodynamics of piroxicam. Perini JA Clinical pharmacology and therapeutics 2005 PMID: 16198655
CYP2C9 gene variants, drug dose, and bleeding risk in warfarin-treated patients: a HuGEnet systematic review and meta-analysis. Sanderson S Genetics in medicine : official journal of the American College of Medical Genetics 2005 PMID: 15714076
Upstream and coding region CYP2C9 polymorphisms: correlation with warfarin dose and metabolism. King BP Pharmacogenetics 2004 PMID: 15608560
Differences in flurbiprofen pharmacokinetics between CYP2C9*1/*1, *1/*2, and *1/*3 genotypes. Lee CR European journal of clinical pharmacology 2003 PMID: 12698304
Association of polymorphisms in the cytochrome P450 CYP2C9 with warfarin dose requirement and risk of bleeding complications. Aithal GP Lancet (London, England) 1999 PMID: 10073515
DailyMed Drug Label, FLURBIPROFEN, 2021 - - - -
DailyMed Drug Label, ZURAMPIC, 2018 - - - -
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CYP2C9 - - - -
https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=4e5c06f1-f279-4f2f-b10d-0f70005a27e6 - - - -
https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=6039e036-c0aa-4249-af50-115f49ad758a - - - -
https://dailymed.nlm.nih.gov/dailymed/drugInfo.cfm?setid=ef9e7711-f478-4e35-bf4e-6021c8457e3b - - - -

Text-mined citations for rs1799853...

Help
These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 03, 2022