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 SLC19A1
Note: The SLC19A1 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 may differ (in a complementary manner) from those in this VIP summary that are given on the minus strand as reported in the literature.
This common variant in the 5'-UTR region of SLC19A1 is found in all HapMap populations. A clinical study involving 106 rheumatoid arthritis patients who received methotrexate treatment has found this variant is associated with lower RFC1 protein expression [Article:17404734] and it is predicted that this regulatory region shows putative consensus sequence of the AP1 transcription factor. This variant is also associated with red blood cell folate levels, with the C allele associated with low red blood cell folate levels. However, this regulatory variant is not sufficient to predict patient response to MTX therapy or toxicity [Article:17404734].
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Appendix
2. SLC19A1:5'-UTR variant, -43T>C (rs1131596)
| Genomic Variant & GenBank ID: | 3952357G>A on NT_011515.12 |
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| mRNA Variant & GenBank ID: | -43C>T on NM_194255.1 |
| Protein Variant & GenBank ID: | NA |
| GoldenPath Position: | chr21:45782344 (hg18) |
Publications related to rs1131596 at chr21:46957916: 1
| Transcription regulatory polymorphism -43T>C in the 5'-flanking region of SLC19A1 gene could affect rheumatoid arthritis patient response to methotrexate therapy. Rheumatology international. 2007. Chatzikyriakidou Anthoula, et al. [Article:17404734@PubMed] |