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.
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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.
Similarly to rs1051296, this variant in the 3'-UTR region of SLC19A1 (rs1051298) showed high allele frequencies (40 - 50%) in all HapMap populations. An analog of methotrexate called pemetrexed, which is transported into the cells by SLC19A1, has recently been approved for its indication in non-small cell lung cancer. Forty-eight patients enrolled in the Phase II clinical trial (NCCTG and SWOG study N0426) for pemetrexed plus bevacizumab in advanced non-small cell lung cancer, were genotyped for the this SNP in SLC19A1 as well as other drug metabolizing enzymes [Article:19841321]. The result from this study showed that the variant T allele is correlated with 3-month progression-free status (P=0.01) and with median progression-free survival (CC v CT v TT: 5.7 v 2.8 v 4.7 months, respectively; log-rank test, P=0.05).
| Key Publications: |
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Appendix
5. SLC19A1: 3'-UTR; 2522C>T (rs1051298)
| Genomic Variant & GenBank ID: | 3929267G>A on NT_011515.12 |
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| mRNA Variant & GenBank ID: | 2522C>T on NM_19455.1 |
| Protein Variant & GenBank ID: | NA |
| GoldenPath Position: | chr21:45759254 (hg18) |
Publications related to rs1051298 at chr21:46934826: 1
| Phase II trial of pemetrexed plus bevacizumab for second-line therapy of patients with advanced non-small-cell lung cancer: NCCTG and SWOG study N0426. Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 2010. Adjei Alex A, et al. [Article:19841321@PubMed] |
Cross-References
- UCSC Golden Path:
- chr21:46934826
- dbSNP:
- rs1051298
- HapMap:
- rs1051298
- JSNP:
- IMS-JST006716