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 SCN5A
R34C was observed with a minor allelic frequency of 9.2% among blacks and 1.7% among Hispanics [Article:15851227]. The frequency of this common nonsynonymous coding region polymorphism was no different between patients with drug-induced long QT syndrome and control subjects, 3% versus 3% [Article:11997281].
Note: The SCN5A 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 will differ (in a complementary manner) from those in this VIP summary that are given on the minus strand as reported in the literature.
| Key Publications: |
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Appendix
1. SCN5A:R34C
| Genomic Variant & GenBank ID: | 38,614,703 G>A on NT_022517 |
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| mRNA Variant & GenBank ID: | 294 C>T on NM_000335 (transcript variant 2); 294 C>T on NM_198056 (transcript variant 1) |
| Protein Variant & GenBank ID: | 34 Arg>Cys on NP_000326; 34 Arg>Cys on NP_932173(the two sequences are for the two wild-type splice variants.) |
| DNA Source Containing Homzygous Reference Allele(Coriell Lines): | NA15362 (PA126721293) |
| *DNA Source Containing Heterozygous Reference Allele(Coriell Lines): | NA15369 (PA126721271) |
| *DNA Source Containing Homozygous Minor Allele(Coriell Lines): | NA15380 (PA126721294) |
| GoldenPath Position: | chr3:38649703 (hg18) |
Publications related to rs6791924 at chr3:38674699: 3
| Common human SCN5A polymorphisms have altered electrophysiology when expressed in Q1077 splice variants. Heart rhythm : the official journal of the Heart Rhythm Society. 2005. Tan Bi-Hua, et al. [Article:15992732@PubMed] | |
| Spectrum and prevalence of cardiac sodium channel variants among black, white, Asian, and Hispanic individuals: implications for arrhythmogenic susceptibility and Brugada/long QT syndrome genetic testing. Heart rhythm : the official journal of the Heart Rhythm Society. 2004. Ackerman Michael J, et al. [Article:15851227@PubMed] | |
| Allelic variants in long-QT disease genes in patients with drug-associated torsades de pointes. Circulation. 2002. Yang Ping, et al. [Article:11997281@PubMed] |
Cross-References
- UCSC Golden Path:
- chr3:38674699
- dbSNP:
- rs6791924
- HapMap:
- rs6791924
Platform Availability
- Illumina