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.
In a study which involved 122 lung cancer cases and 122 matched controls in Xuan Wei, China, where the incidence of lung cancer mortality is high due to indoor smoky coal emissions [Article:15922487], the group found that the synonymous variant in SLC19A1 Pro232Pro (rs12659) is associated with an increased risk of lung cancer in this population (OR=1.83, 95% CI = 1.02 - 3.28). The effect of this variant Pro232Pro, as well as other polymorphisms in genes involved in one-carbon metabolic pathway which controls nucleotide synthesis and DNA methylation [Article:17119116], was assessed for their effect on non-Hodgkin lymphoma (NHL) among over 1000 cases and 949 population-based controls. However, the variant Pro232Pro did not show any protective association. A positive association of this variant Pro232Pro is implicated in a study involving cervical carcinoma patients where platinum-based chemotherapy was used for their treatment [Article:16875718]. In this study, the probability of response was higher in patients with the variant allele T (P=0.032).
| Key Publications: |
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Appendix
3. SLC19A1: Pro232Pro; 6318C>T (rs12659)
| Key PubMed IDs: | PMIDs: 15922487, 17119116, 16875718 |
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| Genomic Variant & GenBank ID: | 3945997A>G on NT_011515.12 |
| mRNA Variant & GenBank ID: | 6318C>T on NM_19455.1 |
| Protein Variant & GenBank ID: | NA |
| GoldenPath Position: | chr21:45775984 (hg18) |
Publications related to rs12659 at chr21:46951556: 3
| Gene-nutrient interactions among determinants of folate and one-carbon metabolism on the risk of non-Hodgkin lymphoma: NCI-SEER case-control study. Blood. 2007. Lim Unhee, et al. [Article:17119116@PubMed] | |
| XRCC1 R399Q polymorphism is associated with response to platinum-based neoadjuvant chemotherapy in bulky cervical cancer. Gynecologic oncology. 2006. Chung Hyun Hoon, et al. [Article:16875718@PubMed] | |
| Polymorphisms in folate metabolic genes and lung cancer risk in Xuan Wei, China. Lung cancer (Amsterdam, Netherlands). 2005. Shen Min, et al. [Article:15922487@PubMed] |