IMGT®, the international ImMunoGeneTics information system®

Clan

Citing this page:
Elemento, O. and Lefranc, M.-P. "IMGT/PhyloGene: an online software package for phylogenetic analysis of immunoglobulin and T cell receptor genes", Dev. Comp. Immunol., 27, 763-779 (2003) PMID: 12818634
Lefranc, M.-P. and Lefranc, G. "The Immunoglobulin FactsBook" Academic Press, London, UK (458 pages) (2001) ISBN: 012441351X

Definition

A clan is a set of subgroups, eventually from different species, which appear related on phylogenetic trees (IGHV, IGKV, IGLV clans).
The 'clan' concept is part of the 'CLASSIFICATION' concept of IMGT-ONTOLOGY [10].

IMGT clans correspond to the categorization of variable gene subgroups based on nucleotide sequences similarity of the FR-IMGT [1].

IMGT/PhyloGene allows to perform directly clan analysis for the human and mouse genes [2] or for any variable nucleotide region provided with gaps according to the IMGT unique numbering.

IMGT/PhyloGene analysis does not include pseudogenes for which FR-IMGT and CDR-IMGT delimitations are not defined.

IGHV clans

IGHV clans, first defined for human IGHV genes [3], comprise the following human [1,4,5] and mouse IGHV subgroup genes:

• clan I: Homo sapiens IGHV1, IGHV5 and IGHV7 subgroup genes; Mus musculus IGHV1, IGHV9, IGHV14 and IGHV15 subgroup genes
• clan II: Homo sapiens IGHV2, IGHV4 and IGHV6 subgroup genes; Mus musculus IGHV2, IGHV3, IGHV8, IGHV12 subgroup genes
• clan III: Homo sapiens IGHV3 subgroup genes; Mus musculus IGHV4, IGHV5, IGHV6, IGHV7, IGHV10, IGHV11, IGHV13, IGHV16 subgroup genes.

IGKV clans

IGKV clans comprise the following human [1,5,6] and mouse [7] IGKV subgroup genes:

• clan I: Homo sapiens IGKV1 subgroup genes; Mus musculus IGKV9, IGKV10, IGKV11, IGKV12, IGKV13, IGKV14, IGKV15, IGKV16, IGKV19 subgroup genes
• clan II: Homo sapiens IGKV2 , IGKV3, IGKV4 and IGKV6 subgroup genes; Mus musculus IGKV1, IGKV2, IGKV5, IGKV6, IGKV7, IGKV8 and IGKV18 subgroup genes
• clan III: Homo sapiens IGKV5 and IGKV7 subgroup genes; Mus musculus IGKV3, IGKV4 and IGKV17 subgroup genes

IGLV clans

IGLV clans comprise the following human [1,5,8,9] and mouse [9] subgroup genes:

• clan I: Homo sapiens IGLV1, IGLV2, IGLV6 and IGLV10 subgroup genes, and pseudogenes IGLV(I)-20, -38, -42, -56, -63, -68 and -70; Mus musculus IGLV3 subgroup (IGLV4 to IGLV8 genes)
• clan II: Homo sapiens IGLV3 subgroup genes;
• clan III: Homo sapiens IGLV7 and IGLV8 subgroup genes; Mus musculus IGLV1 subgroup (IGLV1 and IGLV2 genes)
• clan IV: Homo sapiens IGLV5 and IGLV11 subgroup genes, and pseudogenes IGLV(IV)-53, -59, -64, -65 and -66-1
• clan V: Homo sapiens IGLV4 and IGLV9 subgroup genes, and pseudogenes IGLV(V)-58 and -66; Mus musculus IGLV2 subgroup (IGLV3 gene)
• clan VI: Homo sapiens pseudogenes IGLV(VI)-22-1 and -25-1
• clan VII: Homo sapiens pseudogene IGLV(VII)-41-1

References:

[1] Lefranc, M.-P. and Lefranc, G., "The Immunoglobulin FactsBook", Academic Press, London, UK (458 pages) (2001) ISBN: 012441351X
[2] Elemento, O. and Lefranc, M.-P., Dev. Comp. Immunol., 27, 763-779 (2003) PMID: 12818634 LIGM:273
[3] Kirkham, P.M. et al., EMBO J., 11, 603-609 (1992). PMID: 1537339
[4] Lefranc, M.-P., Exp. Clin. Immunogenet., 18, 100-116 (2001) PMID: 11340299 LIGM:246
[5] Scaviner, D. et al., Exp. Clin. Immunogenet., 16, 234-240 (1999) PMID: 10575277 LIGM:218
[6] Lefranc, M.-P., Exp. Clin. Immunogenet., 18, 161-174 (2001) PMID: 11549845 LIGM:251
[7] Martinez-Jean, C. et al., Exp. Clin. Immunogenet., 18, 255-279 (2001) PMID: 11872956 LIGM:256
[8] Lefranc, M.-P., Exp. Clin. Immunogenet., 18, 242-254 (2001) PMID: 11872955 LIGM:254
[9] Lefranc, M.-P. and Lefranc, G., "Immunoglobulin lambda (IGL) genes of human and mouse", In: Molecular Biology of B cells (Honjo T., Alt, F. W. and Neuberger, M. S. eds), Academic Press, Elsevier Science, pp. 37-59 (2004) ISBN: 0120536412
[10] Giudicelli, V. and Lefranc, M.-P., Bioinformatics, 15, 1047-1054 (1999) PMID: 10745995 LIGM:221