Variant: VIP

rs1799853 in CYP2C9

Alleles (on + chromosomal strand)
  1. C > T

Clinical Annotations

PharmGKB clinical annotations provide information about variant-drug pairs based on a summary of the individual variant annotations in the database. Therefore, each clinical annotation could represent information from a single paper or multiple papers. The rating system used to assign "Strength of Evidence" levels is described here. The individual variant annotations, including the PMID for each supporting PubMed publication, can be found on the "PGx Research" tab above.

This information is manually curated by PharmGKB. All alleles are displayed on the positive chromosomal strand.

Variant Annotations

PharmGKB variant annotations provide information about variant-drug pairs or variant-disease pairs based on individual PubMed publications. Each annotation represents information from a single paper and the goal is to report the information that the author states, not an interpretation of the paper. The PMID for supporting PubMed publications is found in the "Evidence" field.

Information presented, including study size, allele frequencies and statistics is taken directly from the publication. However, if the author does not correct p-values in cases of multiple hypotheses, curators may apply a Bonferroni correction. Curators attempt to report study size based on the actual number of participants used for the calculation of the association statistics, so the number may vary slightly from what is reported in the abstract of the paper. OMB Race Category information is derived from the paper and mapped to standardized categories. Category definitions may be found by clicking on the "OMB Race Category" link.

List of all variant annotations for this variant.

There are 54 annotations for this variant. Register or sign in to see them.

Variant Overview

PharmGKB Accession ID: PA166153972
Type: SNP
Class: Missense
Clinical Significance: Not reported
Genes: CYP2C9

Primary Locus

Name:
[GRCh37]chr10:96702047
Location:
NC_000010.10 96702047 - 96702047
  • C > T
Sequence Type:
genomic
Source:
dbSnp

Alternate Locations

  1. Name:
    NP_000762.2:p.R144C
    Location:
    NP_000762.2 144 - 144
    • R > C
    Sequence Type:
    protein
    Source:
    dbSnp

Variant Frequencies

Population variation data is sourced from HapMap 3.

Alternate Names

  • NC_000010.10:g.96702047C=
  • NC_000010.10:g.96702047C>T
  • NC_000010.11:g.94942290C=
  • NC_000010.11:g.94942290C>T
  • NG_008385.1:g.8633C=
  • NG_008385.1:g.8633C>T
  • NM_000771.3:c.430C=
  • NM_000771.3:c.430C>T
  • NP_000762.2:p.Arg144=
  • NP_000762.2:p.Arg144Cys
  • XM_005269575.1:c.430C=
  • XM_005269575.1:c.430C>T
  • XP_005269632.1:p.Arg144=
  • XP_005269632.1:p.Arg144Cys
  • rs17110268
  • rs28371674
  • rs33968134
  • rs60690363

VIP Variant in CYP2C9

This variant in exon 3 is the defining allele for the CYP2C9*2 haplotype. Other variant positions delineate between haplotypes in the *2 series (see http://www.imm.ki.se/CYPalleles for defining website), but a T allele at this position defines a CYP2C9*2 haplotype. For further information about the CYP2C9*2 haplotype see the Haplotype page.

According to most in-vitro data, substrate affinity is not affected substantially by the *2 haplotype, but the maximum rate of metabolism (Vmax) is reduced to approximately 50% of that for CYP2C9*1 (wild-type) [Articles:11927841, 15637526, 14597963, 11337938].
Individuals homozygous for this variant have been found to have much lower clearance values for S-acenocoumarol, S-warfarin, phenytoin, tolbutamide, ibuprofen, nateglinide, fluvastatin, phenprocoumon when compared to individuals homozygous for R (Arg) [Articles:15637526, 16863464]. Homozygotes for this variant also have a lower clearance as compared to individuals homozygous for R (Arg) (68-90%) for the following drugs: phenytoin, tolbutamide, ibuprofen, nateglinide, fluvastatin, phenprocoumon [Article:15637526]. The R144C variant has been genotyped in various populations. The variant exists in about 10-20% of the Caucasian population, and is rare in the tested Asian and African-American populations [Articles:19151603, 15469410].

PopulationN subjectsAllele Frequency of "T"PMID
Chinese (Shanghai)3940.001[Article:12803577]
Korean5740.000[Article:11298075]
Japanese1470.000[Article:16111713]
Japanese1400.000[Article:9631918]
Japanese640.000[Article:16424822]
Vietnamese (Kinh)1570.000[Article:15795654]
Iranian2000.128[Article:17201743]
Turkish4990.106[Article:10510154]
Ashekenazi Jew1000.085[Article:16111713]
Yemenite Jew990.051[Article:16111713]
Moroccan Jew1000.095[Article:16111713]
Libyan Jew890.152[Article:16111713]
Egyptian2470.120[Article:12047484]
Ethiopian1500.040[Article:11678789]
African-American660.000[Article:16424822]
Caucasian1150.143[Article:16424822]
Russian2900.105[Article:12879168]
Croatian2000.165[Article:12950145]
French Caucasians1510.150[Article:12803577]
German1180.140[Article:12445031]
Swedish4300.107[Article:9920790]
Spanish1570.143[Article:11372590]
Italian1570.110[Article:11678789]
Citation Cytochrome P450 2C9-CYP2C9. Pharmacogenetics and genomics. 2010. Van Booven Derek, Marsh Sharon, McLeod Howard, Carrillo Michelle Whirl, Sangkuhl Katrin, Klein Teri E, Altman Russ B. PubMed
Reviewed 11/18/2009
Drugs / Other Molecules

Appendix

CYP2C9: 144Arg>Cys

Genomic Variant & GenBank ID:15450573 C>T on NT_030059 
mRNA Variant & GenBank ID:430 C>T on NM_000771 
Protein Variant & GenBank ID:144Arg>Cys on NP_000762 
Key Haplotypes:CYP2C9*2
gp Positionchr10:96692037(hg18)

Connected Chemicals and Chemical Classes

Evidence Drug

Connected Diseases

Evidence Disease

Related Publications

Evidence Publication