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 variant in the 3'-UTR region of SLC19A1 showed high allele frequencies (40 - 50%) in all HapMap populations. Potentially, a SNP located within the 3'-untranslated region (UTR), which contains regulatory sequences and binding sites for other molecules that could alter the stability of the mRNA transcript of the gene. However, this SNP has not been functionally characterized although this SNP has been genotyped and assessed for its effect on non-Hodgkin lymphoma (NHL) among over 1000 cases and 949 population-based controls [Article:17119116]. There is no significant association of this variant with risk of NHL.
| Key Publications: |
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Appendix
4. SLC19A1: 3'-UTR ; 2606G>T (rs1051296)
| Genomic Variant & GenBank ID: | 3929302A>C on NT_011515.12 |
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| mRNA Variant & GenBank ID: | 2606G>T on NM_19455.1 |
| Protein Variant & GenBank ID: | NA |
| GoldenPath Position: | chr21:45759289 (hg18) |
Publications related to rs1051296 at chr21:46934861: 1
| 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] |
Cross-References
- UCSC Golden Path:
- chr21:46934861
- dbSNP:
- rs1051296
- HapMap:
- rs1051296
- JSNP:
- IMS-JST006715
Platform Availability
- Illumina