Clinical Annotations
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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 13 annotations for this variant. Register or sign in to see them.
There are 3 disease-related annotations for this variant. Register or sign in to see them.
VIP Variant in CYP2D6
CYP2D6 1846G>A (also seen as 1934G>A in the literature) is diagnostic for the non-functional CYP2D6*4 haplotype [Article:10634130]. CYP2D6 1846G>A causes a splicing defect that results in a non-functional protein [Articles:2211621, 1978251, 1978565]. This variant is responsible for the majority of the PMs found in Caucasian populations [Article:9241659], and is also found at much lower frequencies in other populations, such as Koreans [Article:9895131].
Note: The CYP2D6 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.
Appendix
CYP2D6: 1846G>A
| Genomic Variant & GenBank ID: | G3465A on M33388 |
|---|---|
| mRNA Variant & GenBank ID: | N/A |
| Protein Variant & GenBank ID: | splicing defect |
| GoldenPath Position: | chr22:40854891 on hg 18 |
| DNA Source Containing *Homozygous Reference* *Allele(Coriell Lines):* | GM17201 |
| DNA Source Containing *Heterozygous* *Reference* *Allele* (Coriell Lines): | GM17203 |
| DNA Source Containing *Homozygous Minor* *Allele(Coriell Lines):* | GM17225 |
| Key Haplotypes: | CYP2D6*4 |
Connected Drugs
Connected Diseases
Publications related to rs3892097 at chr22:42524947: 15
Cross-References
- UCSC Golden Path:
- chr22:42524947
- dbSNP:
- rs3892097
- ALFRED:
- SI015494X
Platform Availability
- Illumina