Clinical Annotations
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Variant Annotations
PharmGKB variant annotations provide information about variant-drug 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.
There are 12 annotations for this variant.
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There are 1 disease-related annotations for this variant.
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VIP Variant
in VKORC1
Note: The VKORC1 gene is found on the minus chromosomal strand. Please note that for standardization, the PharmGKB presents all allele base pairs on the positive chromosomal strand, therefore the alleles within our variant annotations and haplotypes may differ (in a complementary manner) from those in this VIP summary that are given on the minus strand as reported in the literature.
C6484T, or 1173C>T, is a SNP in the first intron of VKORC1, and is in near perfect linkage disequilibrium with G3673A. C6484T was the first SNP associated with the low dose warfarin phenotype [Article:15358623], and although it is believed to be functionally inert, C6484T is still very commonly used as a marker SNP for G3673A and haplotypes containing this variant. Below is a table that shows the frequency of C6484T in several different populations. Comparison of this table with that of the frequencies in G3673A will reveal that the two polymorphisms are very closely linked. Some of the studies genotyped both SNPs with similar if not identical frequency results.
| Population | N | Allele Frequency of ""T"" | PMID |
|---|
| Japanese | 93 | 93% | [Article:17049586] |
| Swedish | 169 | 38% | [Article:17048007] |
| Japanese | 31 | 91% | [Article:17031720] |
| Japanese (anticoagulated) | 250 | 89% | [Article:16890578] |
| Japanese (healthy) | 228 | 94% | [Article:16890578] |
| Swedish (anticoagulated) | 92 | 36% | [Article:16879214] |
| Swedish (healthy) | 180 | 39% | [Article:16879214] |
| Dutch | 231 | 41% | [Article:16815313] |
| Han Chinese | 390 | 92% | [Article:16700826] |
| Slovenian | 165 | 44% | [Article:16676068] |
| Caucasians (anticoagulated) | 93 | 45% | [Article:16611750] |
| African Americans | 64 | 9% | [Article:16424822] |
| Caucasians | 115 | 42% | [Article:16424822] |
| Japanese | 64 | 89% | [Article:16424822] |
| Germans | 200 | 42% | [Article:16270629] |
| Dutch (bleeders) | 109 | 45% | [Article:16201835] |
| Dutch (non-bleeders) | 216 | 36% | [Article:16201835] |
| Swedish | 201 | 39% | [Article:15883587] |
| French | 263 | 42% | [Article:15790782] |
| Italian | 147 | 40% | [Article:15358623] |
| Utah (anticoagulated) | 213 | 38% | [Article:17111199] |
| Japanese | 828 | 91% | [Article:16432637] |
Appendix
| gp position | chr16:31012379(hg18) |
|---|
Publications related to rs9934438 at chr16:31104878: 21
The following icons indicate that data of a certain type is available:
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DG
Dosing Guideline information is available
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DL
Drug Label information is available
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CA
High-level Clinical Annotation is available
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VA
Variant Annotation is available
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VIP
VIP information is available
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PW
Pathway is available
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Genetic polymorphisms are associated with variations in warfarin maintenance dose in Han Chinese patients with venous thromboembolism. Pharmacogenomics. 2012. Zhang Wei, et al. [Article:22248286@PubMed] |
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Warfarin pharmacogenetics: a single VKORC1 polymorphism is predictive of dose across 3 racial groups. Blood. 2010. Limdi Nita A, et al. [Article:20203262@PubMed] |
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Pharmacogenetic relevance of CYP4F2 V433M polymorphism on acenocoumarol therapy. Blood. 2009. Pérez-Andreu Virginia, et al. [Article:19270263@PubMed] |
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Warfarin response and vitamin K epoxide reductase complex 1 in African Americans and Caucasians. Clinical pharmacology and therapeutics. 2007. Schelleman H, et al. [Article:17329985@PubMed] |
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Association of warfarin dose with genes involved in its action and metabolism. Human genetics. 2007. Wadelius Mia, et al. [Article:17048007@PubMed] |
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Genotypes of vitamin K epoxide reductase, gamma-glutamyl carboxylase, and cytochrome P450 2C9 as determinants of daily warfarin dose in Japanese patients. Thrombosis research. 2007. Kimura Rina, et al. [Article:17049586@PubMed] |
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Genetic polymorphism of vitamin K epoxide reductase (VKORC1) 1173C>T in a Chinese and a Caucasian population. Basic & clinical pharmacology & toxicology. 2006. Larramendy-Gozalo Claire, et al. [Article:16700826@PubMed] |
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VKORC1 and CYP2C9 genotypes and acenocoumarol anticoagulation status: interaction between both genotypes affects overanticoagulation. Clinical pharmacology and therapeutics. 2006. Schalekamp Tom, et al. [Article:16815313@PubMed] |
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VKORC1 gene variations are the major contributors of variation in warfarin dose in Japanese patients. Clinical pharmacology and therapeutics. 2006. Obayashi Kyoko, et al. [Article:16890578@PubMed] |
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Association of VKORC1 and CYP2C9 polymorphisms with warfarin dose requirements in Japanese patients. Journal of human genetics. 2006. Mushiroda Taisei, et al. [Article:16432637@PubMed] |
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Polymorphisms in the VKORC1 gene are strongly associated with warfarin dosage requirements in patients receiving anticoagulation. Journal of medical genetics. 2006. Li T, et al. [Article:16611750@PubMed] |
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Main haplotypes and mutational analysis of vitamin K epoxide reductase (VKORC1) in a Swedish population: a retrospective analysis of case records. Journal of thrombosis and haemostasis : JTH. 2006. Osman A, et al. [Article:16879214@PubMed] |
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Genotypes of the cytochrome p450 isoform, CYP2C9, and the vitamin K epoxide reductase complex subunit 1 conjointly determine stable warfarin dose: a prospective study. Journal of thrombosis and thrombolysis. 2006. Carlquist John F, et al. [Article:17111199@PubMed] |
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1173C>T polymorphism in VKORC1 modulates the required warfarin dose. Pediatric cardiology. 2006. Kosaki K, et al. [Article:17031720@PubMed] |
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Different contributions of polymorphisms in VKORC1 and CYP2C9 to intra- and inter-population differences in maintenance dose of warfarin in Japanese, Caucasians and African-Americans. Pharmacogenetics and genomics. 2006. Takahashi Harumi, et al. [Article:16424822@PubMed] |
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The influence of sequence variations in factor VII, gamma-glutamyl carboxylase and vitamin K epoxide reductase complex genes on warfarin dose requirement. Thrombosis and haemostasis. 2006. Herman Darja, et al. [Article:16676068@PubMed] |
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A polymorphism in the VKORC1 gene is associated with an interindividual variability in the dose-anticoagulant effect of warfarin. Blood. 2005. D'Andrea Giovanna, et al. [Article:15358623@PubMed] |
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Cytochrome P450 2C9 (CYP2C9) and vitamin K epoxide reductase (VKORC1) genotypes as determinants of acenocoumarol sensitivity. Blood. 2005. Bodin Laurent, et al. [Article:15790782@PubMed] |
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A C1173T dimorphism in the VKORC1 gene determines coumarin sensitivity and bleeding risk. PLoS medicine. 2005. Reitsma Pieter H, et al. [Article:16201835@PubMed] |
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Common VKORC1 and GGCX polymorphisms associated with warfarin dose. The pharmacogenomics journal. 2005. Wadelius M, et al. [Article:15883587@PubMed] |
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VKORC1 haplotypes and their impact on the inter-individual and inter-ethnical variability of oral anticoagulation. Thrombosis and haemostasis. 2005. Geisen Christof, et al. [Article:16270629@PubMed] |
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