The main purpose of the Human Cytochrome P450 (CYP) Allele Nomenclature
website is the management of an official and unified allele designation
system, as well as the provision of a database of CYP alleles and their
associated effects.
The nomenclature system
adheres to the guidelines provided in Shows et al (1987), Daly et al (1996), Antonarakis and the Nomenclature Working
Group (1998), den Dunnen and Antonarakis (2001) and Kalman et al 2016.
GUIDELINES:
- On this website only human CYP and POR
alleles are considered.
- The gene and the allele name
is separated by an asterisk followed by Arabic numerals designating the
specific allele (e.g. CYP1A1*3).
- For allele designation, sequence
information of at least all exons and exon-intron borders must be
submitted.
- To be assigned a unique
allele name, the sequence should contain at least one nucleotide change
that has been shown to affect transcription, splicing, translation,
posttranscriptional or posttranslational modifications or result in at
least one amino acid change. So-called sub-alleles containing
additional non-functional variations in addition to the functional ones
described (e.g. CYP2D6*10B) are not be designated.
5.
If a new sequence variation causing functional consequences is shown
to exist in different combinations with other sequence variations not causing
functional effects, the sequence with the lowest number of additional
variations will be chosen for allele designation.
- If sequence variations causing
functional effects of similar magnitude (e.g. amino acid substitutions)
are found to exist together as well as on their own, the combination
allele will be given a new allele name (see e.g. CYP2D6*102 and *103).
- For extra gene copies (n) placed in
tandem on the same chromosome the entire allelic arrangement should be
referred to as e.g. CYP2D6*2Xn.
- Nucleotides are numbered according to
the base A in the initiation codon ATG as +1 and the base before A as
-1.
- The names for the corresponding proteins
have a period between the name of the gene product and the allele number
(e.g. CYP2D6.2). If the allele is unable to produce full length protein,
no protein name will be assigned.
- Novel sequence variations
causing functional consequences that have an unclear linkage with other
variations causing functional effects will not be assigned.
- All submissions are kept confidential
and new allele names are on request kept confidential until publication.
Authors are encouraged to submit their novel allele to the CYP-allele
website prior to submission to a journal, especially since many Editors
request naming of new alleles by the CYP-allele website prior to
publication. Journal publication is however not a requirement for
publication on the CYP-allele website.
12.
Usage of star (*) allele designations resembling those officially
designated by the CYP-allele Nomenclature committee is highly discouraged due
to the apparent risk of confusion.
13.
Further information on in vitro
or in vivo activity analyses for
known CYP alleles can at any time be submitted to
the CYP-allele website for inclusion with the respective allele.
- All variants identified through
Next Generation Sequencing (NGS) techniques must be confirmed through
Sanger sequencing or another independent method. Furthermore, NGS
sequence data must at a minimum have 100% coverage over exons and
exon-flanking regions to be considered for allele name assignments.