Variant: VIP

rs9934438 in PRSS53,VKORC1

Alleles (on + chromosomal strand)
  1. G > A

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.

Clinical Annotation for rs9934438 (VKORC1), warfarin, Arteriosclerosis, Heart Diseases, Hemorrhage, Intracranial Hemorrhages, Myocardial Infarction, Peripheral Vascular Diseases, Pulmonary Embolism, Stroke, Thromboembolism, venous thromboembolism and Venous Thrombosis (level 1B Dosage)

Level of Evidence
Level 1B
Type
Dosage
Variant
rs9934438
Genes
VKORC1
Phenotypes
Arteriosclerosis, Heart Diseases, Hemorrhage, Intracranial Hemorrhages, Myocardial Infarction, Peripheral Vascular Diseases, Pulmonary Embolism, Stroke, Thromboembolism, venous thromboembolism, Venous Thrombosis
OMB Race
Mixed Population
Race Notes
White,Black or African American, Asian

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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 90 annotations for this variant. Register or sign in to see them.

Variant Overview

PharmGKB Accession ID: PA166155096
Type: SNP
Class: Intronic
Clinical Significance: Not reported
Genes: PRSS53, VKORC1

Primary Locus

Name:
[GRCh37]chr16:31104878
Location:
NC_000016.9 31104878 - 31104878
  • G > A
Sequence Type:
genomic
Source:
dbSnp

Alternate Locations

None specified

Variant Frequencies

Population variation data is sourced from HapMap 3.

Alternate Names

  • NC_000016.10:g.31093557G>A
  • NC_000016.9:g.31104878G>A
  • NG_011564.1:g.6399C>T
  • NM_001311311.1:c.174-136C>T
  • NM_024006.5:c.174-136C>T
  • NM_206824.2:c.173+1000C>T
  • XM_005255568.1:c.174-136C>T
  • XM_011545943.1:c.174-136C>T
  • XM_011545944.1:c.174-136C>T
  • XM_011545945.1:c.173+1000C>T
  • XR_243303.1:n.823-236C>T
  • XR_950848.1:n.962-136C>T
  • rs17641219

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.

PopulationNAllele Frequency of ""T""PMID
Japanese9393%[Article:17049586]
Swedish16938%[Article:17048007]
Japanese3191%[Article:17031720]
Japanese (anticoagulated)25089%[Article:16890578]
Japanese (healthy)22894%[Article:16890578]
Swedish (anticoagulated)9236%[Article:16879214]
Swedish (healthy)18039%[Article:16879214]
Dutch23141%[Article:16815313]
Han Chinese39092%[Article:16700826]
Slovenian16544%[Article:16676068]
Caucasians (anticoagulated)9345%[Article:16611750]
African Americans649%[Article:16424822]
Caucasians11542%[Article:16424822]
Japanese6489%[Article:16424822]
Germans20042%[Article:16270629]
Dutch (bleeders)10945%[Article:16201835]
Dutch (non-bleeders)21636%[Article:16201835]
Swedish20139%[Article:15883587]
French26342%[Article:15790782]
Italian14740%[Article:15358623]
Utah (anticoagulated)21338%[Article:17111199]
Japanese82891%[Article:16432637]
Citation VKORC1 pharmacogenomics summary. Pharmacogenetics and genomics. 2010. Owen Ryan P, Gong Li, Sagreiya Hersh, Klein Teri E, Altman Russ B. PubMed
Key Publications:
Drugs / Other Molecules

Appendix

gp positionchr16:31012379(hg18)

Connected Chemicals and Chemical Classes

Evidence Drug

Connected Diseases

Evidence Disease

Related Publications

Evidence Publication