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IMGT allele nomenclature for sequence polymorphisms

References to be quoted for IMGT description of allele polymorphisms and somatic hypermutations:
Lefranc, M.-P. "IMGT Locus on Focus: A new section of Experimental and Clinical Immunogenetics", Exp. Clin. Immunogenet., 15, 1-7 (1998) pdf
Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999)
Lefranc M-P. Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics. Front Immunol. 2014 Feb 05;5:22. doi: 10.3389/fimmu.2014.00022. Open access PMID: 24600447

IMGT allele name nomenclature for IG and TR of all vertebrates

IMGT general rules

Alleles are described, exhaustively and in a standardized way, for the four "core" coding regions, that is the germline V-REGION, D-REGION, and J-REGION, and for the C-REGION, from IG and TR of all vertebrate species with jaws (gnathostomata). These alleles refer to sequence polymorphisms, with mutations described at the sequence level.

Polymorphic sequence mutations which concern parts of the gene (including untranslated exons) are not studied systematically and are only reported in the sequence flat files.
IMGT allele names

IMGT allele description and representations

Allele mutation description and numbering

Allele polymorphism mutations are described according to IMGT description of mutations.

Allele representations

Two representations of alleles are available :

Definitive allele designation

Definitive allele designation, confirmed by genetic studies and/or different sources of data is indicated by "+" in the Tables of alleles.

IMGT reference directory

The IMGT reference directory is constituted by sets of sequences which contain the V-REGION, D-REGION and J-REGION alleles, isolated from the Functional and ORF IMGT reference sequences.

By definition, these sets contain one sequence for each allele. Allele names of these sequences are shown in red in Alignments of alleles.

The IMGT reference directory is used to analyse the IG and TR sequences and is crucial for the high quality of IMGT/V-QUEST results (See also IMGT/V-QUEST Documentation). To download the IMGT reference directory in FASTA format, click here

Somatic hypermutations

Somatic hypermutations of the rearranged variable regions can be described when the corresponding germline V-REGION, D-REGION and J-REGION alleles have been identified.

The IMGT unique numbering allows a standardized description of somatic hypermutations of rearranged variable genes.

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