You need to go to the star allele nomenclature website - http://www.cypalleles.ki.se/ - this then gives you the rs# for each star allele and links to the original article; you can then work out what the effect allele is. I think some of this information is in my PhD thesis (there's a table of cyp2c19 and the corresponding rs#)

cheers

M

It depends on purpose - a proper nomenclature requres rsID or position; however "CYP2C19*2" is the one what mostly used by people from genetics/pharmacogenetics. The most common variants like CYP have the databases as Michael posted, bunch of them you can find by OMIM - ncbi too or....in papers... It`s good for understanding, however if you want to publish it in future., be aware that most of the journals require HGVS nomenclature (rs..../chromos pos.), especially when using GWAS, it`s a must.

Go to:

http://www.cypalleles.ki.se/

Methods Mol Biol. 2013;987:251-9. doi: 10.1007/978-1-62703-321-3_21.

Update on allele nomenclature for human cytochromes P450 and the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Database.

Sim SC1, Ingelman-Sundberg M.

Dear Sander,

I think the best way to answer your question is to get the web site Pharmacogenomics knowledge database: https://www.pharmgkb.org/index.jsp

The PharmGKB is a pharmacogenomics knowledge resource that encompasses clinical information including dosing guidelines and drug labels, potentially clinically actionable gene-drug associations and genotype-phenotype relationships.

I am sure that this database will be very helpful for you to resolve this and many other related tasks on pharmacogenomics research.

All you need is just to register on the site. In this case you will have an access to all databases where you will find all you need and much more interesting information.

Regarding your current answer, for example, you can explore the following link:

https://www.pharmgkb.org/haplotype/PA165816528?previousQuery=CYP2C19*2#tabview=tab2&subtab=

I hope my reply will help you not only to answer this question but also provide substantially more information on the impact of human genetic variation on drug responses.  

Best wishes,

Alexey

What you mention here, "CYP2C19*2," is only the haplotype.  A full genotype and in order to establish a patient's phenotype, there would have to be two "*" numbers.  Thus a phenotype would show CYP2C19 *1/*2 as an example. (Genes are italicized by convention.  Without italics, the gene designation is actually referring to the protein encoded by the gene.)

Many of the sites above will give you more information about the individual substitutions (e.g. *1, *17) but a clinical report from a lab, at a minimum, should give you the phenotype that the individual genotype represents.  As examples, a phenotype in the pharmacogenomic sense would be something like "Normal Metabolizer," "Intermediate Metabolizer," "Ultra" or "Rapid Metabolizer."  A good report will also list various medications (at least the meds the patient is taking) and give you an idea of how the metabolism of that drug (or drugs) is affected in that particular patient.  Note than while a gene may have dozens of genotypes, they are all usually grouped into no more than 2, 3 or 4 phenotypes.

There are several formats for nomenclature, but the "*" system is the easiest to use in Pgx reports.  Each * number represents a substitution at a particular position on the gene.  The majority of the time, "*1" represents the "normal" or most common configuration.  That means that a CYP2D6 *1/*1 is what is most commonly considered normal.  A number of sites such as uswest.ensemblr.com will give the frequencies in the general population as well as break it down into a number of demographic groups.  True, the "rs" number (e.g. rs1801133) indicates a particular configuration at a particular site on a gene, but these are too cumbersome to use on clinical lab reports, thus the "*" nomenclature is usually used.  But again, a good lab report should make these "rs" numbers available somewhere.  But you can Google either the "rs" number or the "*" + the gene name and bring up more sites and information than you will ever want to know about any particular configuration.

Message me back if you would like additional information.

www.MolecularTestingLabs.com

Hi,

Can someone please explain me, how do you come from the e.g.CYP3A5 rs776746 designation of AA genotype, which I get from the TaqMan testing to the star nomencalture *1/*1.

Thank you

https://www.pharmvar.org/