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 5 annotations for this variant. Register or sign in to see them.
There are 1 disease-related annotations for this variant. Register or sign in to see them.
VIP Variant in KCNH2
Note: The KCNH2 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.
This variant has altered biophysics [Article:14975928] and has been associated both prolongation [Articles:15746444, 14499861, 17709632] and a shortening of the QT interval [Articles:10862094, 12829173, 19019189]. It has been shown to create a phosphorylation site that inhibited channel activity, independent of drug binding [Article:18791070]. The K897 allele has been associated with higher incidence of atrial fibrillation. [Article:18222980]. All studies were conducted without drugs. Allele frequencies for minor allele for those with aLQTS 14%; without aLQTS 16%; TN-control 12%; NHGRI-control 13% [Article:11997281]. Allele frequencies for minor allele: SIDS African American 5.9%; African American-control 4%; SIDS Caucasian 17.8%; Caucasian control 24% [Article:14975928].
| Key Publications: | |
|---|---|
| Diseases | Atrial Fibrillation Long QT Syndrome |
Appendix
| Genomic Variant & GenBank ID: | T>G 11221550 on NT_007914.14 |
|---|---|
| mRNA Variant & GenBank ID: | 1670A>C on NM_172057.1 |
| Protein Variant & GenBank ID: | K897T on NP_000229.1 |
| DNA Source Containing *Homozygous Reference* *Allele(Coriell Lines):* | CC Sample PA126745233(GM15036) |
| DNA Source Containing * Heterozygous* *Reference* * Allele(Coriell Lines):* | AC Sample PA126745261 (GM15330) |
| DNA Source Containing * Homozygous Minor* *Allele(Coriell Lines):* | not found in PharmGKB; |
Connected Drug Classes
| Evidence | Drug Class |
|---|---|
| Variant Annotation | antiarrhythmics, class i and iii |
Connected Diseases
| Evidence | Disease |
|---|---|
| Acquired Long QT Syndrome (aLQTS) | |
| Atrial Fibrillation | |
| Long QT Syndrome |
Publications related to rs1805123 at chr7:150645534: 7
Cross-References
- UCSC Golden Path:
- chr7:150645534
- dbSNP:
- rs1805123
- HapMap:
- rs1805123
Platform Availability
- Illumina