The recommended nomenclature for the human polymorphic UGT genes*.
On this website only human UGT alleles are considered. We encourage scientists worldwide to use this nomenclature guidelines to avoid « home-made » allelic designations that can confuse the nomenclature system and the scientific literature.
- The gene and allele is separated by an asterisk followed by Arabic numerals and upper-case Roman letters with less than four characters to name the allele (e.g. UGT1A1*2 , UGT1A7*2B ).
- A gene is considered as the sequence from 5 kb upstream from the transcription start site to 500 bp downstream of the last exon. However, if a regulatory element has been characterised at a more distant part of the gene, also this area belongs to the gene.
- To be assigned as a unique allele it should contain nucleotide changes that result in at least one amino acid change.
- Additional nucleotide changes and combinations of nucleotide changes in the gene will be given letters (e.g. *2A , *1B ). Thus, in cases where silent mutations occur or mutations are present in regulatory parts or introns, the allelic name will be given letters and should adhere to the closest allele by subgroup assignments.
- Allelic variants can be defined as combinations of up to three letters (e.g. UGT1A1*1ABC ), thereby allowing room for 22 x 22 x 22 = 10,648 different variants for each allelic number. The letters I, O, X and Y are excluded because of indexing problems.
- For extra gene copies (n) placed in tandem the entire allelic arrangement should be referred to as e.g. UGT1A1*2Xn.
- Numbering of nucleotides in the allele should be as described in Antonarakis and the Nomenclature Working Group (1998) . The base A in the initiation codon ATG is denoted +1 and the base before A is numbered -1.
- For reasons of indexing, the names for proteins should have a period between the name of the gene product and number (e.g. UGT1A1.1).
- The wild type allele is defined as the sequence of the first alleles sequenced and should be designated as *1 (or *1A and *1B in case of slightly variant sequences).
- Allele names will be assign based on the haplotypes. Submission of new alleles should be done with information sufficient to fulfil the criteria to be assigned a unique allele as under # 4 above or a letter as described under # 5 above. For incorporation into the Web page as a unique allele, known polymorphisms ( those on the UGT alleles site) in this gene should have been sequenced as well as exon-intron borders. For polymorphism to be present in only one sample, a duplicate PCR reaction followed by sequencing from the original DNA sample would be needed to confirm its presence.
- SNPs that are not easily assigned to a specific allele, will be listed at the bottom of the corresponding nomenclature page with relevant literature references.
- If a new allele has been detected on the cDNA level, verification of the mutation(s) on the genomic level is required. For acceptance of a new SNP given a separate letter, evidence for its presence on the genomic level is required.
- No temporary allelic numbers or letters are provided, and information about any new allele submitted, will continuously be published on the web Page. In case an author does not want to release the information on the web page before publication, the Webmaster can usually provide him or her with an allelic designation but not release the information on the web page until the manuscript has been accepted or published.
*Based on the existing criteria of CYP ( http://www.imm.ki.se/CYPalleles/criteria.htm )