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In pharmacogenomics it is very common to identify genetic variants with a special nomenclature, which is not elsewhere used in genetics. It is the so-called star allele nomenclature. In this nomenclature, alleles with a pharmacogenomic relevance aren't identified with their cDNA or genomic position as usual (HGVS nomenclature), but through the means of numbers and letters separated from the gene name by a star (that's why this is called star allele nomenclature). For example: CYP3A5*2 identifies the genetic variant in genomic position g.27289C>A leading to the amino acid substitution p.T398N in the protein chain. The star allele nomenclature is therefore useful to identify a certain allele in a fast and easy way, whereas the standard HGVS nomenclature could be less comprehensible (and more subject to transcription mistakes) by not specialized personnel.
The star allele nomenclature has been firstly used to identify alleles within the cytochrome P450 (CYP) gene family. From that it spread to all genes that have been studied in pharmacogenomics. Of note, the star allele nomenclature is used only do identify pharmacogenomic markers and it is not elsewhere used in genetics.
The list of the star alleles of the cytochrome P450 gene family and of the POR gene is available at http://www.cypalleles.ki.se.
However the star allele nomenclature has some defects. First of all it does not indicate the mutation type, i.e. if it is a missense, nonsense or splice mutation or again a large deletion/duplication. Moreover, despite the possibility it has to identify even a group of alleles under one single number (to know how the star allele nomenclature works you can read here), it is not flexible enough to express the complexity and the enormous amount of data as produced by high-throughput sequencing (e.g exome sequencing and genome sequencing). Nevertheless the star allele nomenclature remains the gold-standard in the identification of pharmacogenomic markers in the scientific literature and in the official documents of the drug agencies.
