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Inclusion criteria
The main function of this Web page is to encourage scientists worldwide to
speak the same language and to avoid "home-made" allelic
designations that can confuse the nomenclature system and the scientific
literature, and it contains the recommended nomenclature for the human
polymorphic CYP genes. It adheres to the guidelines provided in Shows
et al (1987), Daly
et al (1996), Antonarakis and the Nomenclature Working Group (1998)
and den
Dunnen and Antonarakis
(2001) as detailed below:
- On this website only
human CYP alleles are considered.
- 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. CYP1A1*3,
CYP1B1*22, CYP2D6*10B).
- 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 have been shown
to affect transcription, splicing, translation, posttranscriptional or
posttranslational modifications or 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. *21A, *21B). Thus, in cases
where silent mutations occur or mutations are present in regulatory
parts or introns with unclear function, the
allelic name should adhere to the closest functionally characterised allele by subgroup assignments such as
CYP2D6*4A. Allelic variants can be defined as combinations of up
to three letters (e.g. CYP2D6*2ABC), 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. CYP2D6*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. CYP2D6.2A).
- 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.
- 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, all exons and exon-intron
borders should have been sequenced. 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.
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