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 2 annotations for this variant. Register or sign in to see them.
VIP Variant in UGT1A1
UGT1A1:*60
Identified in 2002 by Sugatani et al., rs4124874, -3279T>G (*60; also referred to as -3263T>G) is a common variant that is located in the Phenobarbital Response Enhancer Module (PBREM), a regulatory element positioned 3kb upstream of the UGT1A1 gene [Article:11906189]. The allele frequency of -3279T in Caucasians ranges from 0.39-0.55, while the -3279T allele frequency is much lower in the African-American population (0.15) [Articles:12464801, 15007088]. The allele frequency of -3279T in a Japanese population was estimated to be 0.83, while a Japanese population with Gilbert syndrome had a -3279T allele frequency of 0.42 [Article:11906189]. The functional significance of the -3279T>G variant requires further investigation, but genotyping of the -3279T>G variant has been proposed, in combination with the -3156G>A PBREM variant, to improve the prediction of UGT1A1 status in individuals being treated with irinotecan [Articles:15864130, 15007088, 15179405].
| Key Publications: | |
|---|---|
| Drugs / Other Molecules |
Drug (6)
|
| Diseases | Hyperbilirubinemia 11 12 |
| Phenotype |
|
| Phenotype Datasets | Irinotecan Clinical Data |
Appendix
gp position: chr2:234330398(hg18)
Genomic Variant & GenBank ID: 598413G>T on NT_005120
Connected Drugs
| Evidence | Drug |
|---|---|
| atazanavir | |
| etoposide | |
| irinotecan | |
| tranilast |
Connected Drug Classes
| Evidence | Drug Class |
|---|---|
| VIP Annotation | estrogens |
| VIP Annotation | thyroid hormones |
Publications related to rs4124874 at chr2:234665659: 5
Cross-References
- UCSC Golden Path:
- chr2:234665659
- dbSNP:
- rs4124874
- HapMap:
- rs4124874
Platform Availability
- Illumina