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IGK (Immunoglobulin Kappa)

Written2000-07Marie-Paule Lefranc
IMGT, LIGM, IGH, UPR CNRS 1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France

(Note : for Links provided by Atlas : click)

Identity

Alias_namesIGK@
Other aliasIGK@ (Immunoglobulin Kappa)
HGNC (Hugo) IGK
LocusID (NCBI) 50802
Atlas_Id 17
Location 2p11.2  [Link to chromosome band 2p11]
Location_base_pair Starts at 88810151 and ends at 90250363 bp from pter
 
  for complete Figure, see: chromosome 2, IMGT (The International ImMunoGeneTics information system ®) © Copyright 1995-2017 IMGT, IMGT is a CNRS trademark
Fusion genes
(updated 2016)
IGK (2p11.2) / BCL10 (1p22.3)IGK (2p11.2) / BCL2 (18q21.33)IGK (2p11.2) / BCL3 (19q13.32)
IGK (2p11.2) / BCL6 (3q27.3)IGK (2p11.2) / CCND1 (11q13.3)IGK (2p11.2) / CCND2 (12p13.32)
IGK (2p11.2) / CDK6 (7q21.2)IGK (2p11.2) / FVT1 ()IGK (2p11.2) / KDSR (18q21.33)
IGK (2p11.2) / MYC (8q24.21)IGK (2p11.2) / PVT1 (8q24.21)IGK (2p11.2) / TPD52 (8q21.13)
IGK (2p11.2) / ZC3H12D (6q25.1)KDSR (18q21.33) / IGK (2p11.2)MYC (8q24.21) / IGK (2p11.2)
Note The human IGK locus is located on chromosome 2 on the short arm, at band 2p12. The orientation of the locus has been determined by the analysis of translocations, involving the IGK locus, in leukemia and lymphoma.

DNA/RNA

 
  IGK
V-GENE: Green box: Functional; Yellow box: Open reading frame; Red: Pseudogene.
J-GENE: Grey: Functional .
C-GENE: Blue: Functional.
for complete Figure, see: locus IGK, IMGT (The International ImMunoGeneTics information system ®) © Copyright 1995-2017 IMGT, IMGT is a CNRS trademark
Description
  • The human IGK locus at 2p12 spans 1820 kb. It consists of 76 IGKV genes belonging to 7 subgroups, 5 IGKJ segments, and a unique IGKC gene
  • The 76 IGKV genes are organized in two clusters separated by 800 kb. The IGKV distal cluster (the most 5' from IGKC and in the most centromeric position) spans 400 kb and comprises 36 genes. The IGKV proximal cluster (in 3' of the locus, closer to IGKC, and in the most telomeric position) spans 600 kb and comprises 40 genes.
  • The potential genomic IGK repertoire comprises 31 to 35 functional IGKV genes belonging to 5 subgroups, the 5 IGKJ segments, and the unique IGKC gene.
  • One rare IGKV haplotype has been described which contains only the proximal cluster. This haplotype comprises the 40 proximal IGKV genes belonging to 7 subgroups, of which 17 to 19 are functional and belong to 5 subgroups.
  • Twenty-eight IGKV orphons have been identified and sequenced: 3 on the short arm of chromosome 2 but outside of the main IGK locus, 13 on the long arm of chromosome 2, 6 on chromosome 22, one on chromosome 1, one on chromosome 15, and 4 outside of chromosome 2
  • If both the proximal and distal IGKV clusters are present, the total number of human IGK genes per haploid genome is 82 (110 genes, if the orphons are included) of which 37-41 are functional. If only the proximal IGKV cluster is present, the total number of genes per haploid genome is 46 (74 genes, if the orphons are included) of which 23-25 genes are functional.
  • List of the human IGK genes
  • Protein

    Description
  • Proteins encoded by the IGK locus are the immunoglobulin kappa chains. They result from the recombination (or rearrangement), at the DNA level, of two genes: IGKV and IGKJ, with deletion of the intermediary DNA to create a rearranged IGKV-J gene. The rearranged IGKV-J gene is transcribed with the IGKC gene and translated into an immunoglobulin kappa chain.
  • Translation of the variable germline genes involved in the IGKV-J rearrangements are available at IMGT Repertoire Protein displays. Compared to the germline genes, the rearranged variable genes will acquire somatic mutations during the B cell differentiation in the lymph nodes, which will considerably increase their diversity. These somatic mutations can be analysed using IMGT/V-QUEST tool
  • Mutations

    Note Mutations which correspond to allelic polymorphisms of the functional germline IGKV, IGKJ and IGKC genes are described in the IMGT database: (IMGT Repertoire> Alignments of alleles)

    Implicated in

    Note
      
    Entity Translocations which frequently result from errors of the recombinase enzyme complexe (RAG1, RAG2, etc.), which is responsable of the Immunoglobulin and T cell receptor V-J and V-D-J rearrangements. IGKV or IGKJ recombination signals or isolated heptamer are observed at the breakpoints
     
    c-Immunoglobulin genes IgK at 2p12, in normal cells: PAC 1117G4 - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.
      
      
    Entity t(2;3;)(p12;q27); involve BCL6 in 3q27
    Disease B-cell non-Hodgkin lymphomas (NHL), mainly diffuse large cell lymphoma; adult aggressive lymphoma
    Prognosis controversial
      
      
    Entity t(2;8)(p12;q24); involve C-MYC in 8q24
    Disease B-cell acute lymphoblastic leukemia (ALL3) and non-Hodgkin lymphomas (NHL), especially in the Burkitt lymphoma
    Prognosis the prognosis has evolved with new treatments
      

    Breakpoints

     

    Bibliography

    The human immunoglobulin kappa variable (IGKV) genes and joining (IGKJ) segments.
    Barbié V, Lefranc MP
    Experimental and clinical immunogenetics. 1998 ; 15 (3) : 171-183.
    PMID 9813414
     
    Duration of effect of botulinum toxin type A in adult patients with cervical dystonia: a retrospective chart review.
    Brashear A, Watts MW, Marchetti A, Magar R, Lau H, Wang L
    Clinical therapeutics. 2000 ; 22 (12) : 1516-1524.
    PMID 11192142
     
    A directory of human germ-line V kappa segments reveals a strong bias in their usage.
    Cox JP, Tomlinson IM, Winter G
    European journal of immunology. 1994 ; 24 (4) : 827-836.
    PMID 8149953
     
    Cloned human and mouse kappa immunoglobulin constant and J region genes conserve homology in functional segments.
    Hieter PA, Max EE, Seidman JG, Maizel JV Jr, Leder P
    Cell. 1980 ; 22 (1 Pt 1) : 197-207.
    PMID 6775818
     
    The V kappa genes of the L regions and the repertoire of V kappa gene sequences in the human germ line.
    Huber C, Schäble KF, Huber E, Klein R, Meindl A, Thiebe R, Lamm R, Zachau HG
    European journal of immunology. 1993 ; 23 (11) : 2868-2875.
    PMID 8223863
     
    Nomenclature of the human immunoglobulin kappa (IGK) genes.
    Lefranc MP
    Experimental and clinical immunogenetics. 2001 ; 18 (3) : 161-174.
    PMID 11549845
     
    The Immunoglobulin FactsBook (Review)
    Lefranc MP and Lefranc G
    Academic Press, London, UK (458 pages), 2001. ISBN: 012441351X
     
    Localization of human immunoglobulin kappa light chain variable region genes to the short arm of chromosome 2 by in situ hybridization.
    Malcolm S, Barton P, Murphy C, Ferguson-Smith MA, Bentley DL, Rabbitts TH
    Proceedings of the National Academy of Sciences of the United States of America. 1982 ; 79 (16) : 4957-4961.
    PMID 6812058
     
    Protein displays of the human immunoglobulin heavy, kappa and lambda variable and joining regions.
    Scaviner D, Barbié V, Ruiz M, Lefranc MP
    Experimental and clinical immunogenetics. 1999 ; 16 (4) : 234-240.
    PMID 10575277
     
    The human immunoglobulin kappa locus: pseudogenes, unique and repetitive sequences.
    Schäble K, Thiebe R, Flügel A, Meindl A, Zachau HG
    Biological chemistry Hoppe-Seyler. 1994 ; 375 (3) : 189-199.
    PMID 8011175
     
    The immunoglobulin kappa locus-or-what has been learned from looking closely at one-tenth of a percent of the human genome.
    Zachau HG
    Gene. 1993 ; 135 (1-2) : 167-173.
    PMID 8276255
     

    Citation

    This paper should be referenced as such :
    Lefranc, MP
    IGK (immunoglobulin kappa)
    Atlas Genet Cytogenet Oncol Haematol. 2000;4(3):111-1113.
    Free journal version : [ pdf ]   [ DOI ]
    On line version : http://AtlasGeneticsOncology.org/Genes/IgKID17.html


    Other Leukemias implicated (Data extracted from papers in the Atlas) [ 11 ]
      3q27 rearrangements (BCL6) in non Hodgkin lymphoma::t(3;Var)(q27;Var) in non Hodgkin lymphoma
    Double Hit Lymphoma (DHL)::Triple Hit Lymphoma (THL)
    Plasmablastic lymphoma (PBL)
    t(2;7)(p11;q21) IGK/CDK6::t(7;14)(q21;q32) IGH/CDK6::t(7;22)(q21;q11) IGL/CDK6
    t(8;14)(q24;q32) IGH/MYC::t(2;8)(p12;q24) IGK/MYC::t(8;22)(q24;q11) IGL/MYC
    t(1;2)(p22;p12) IGK/BCL10::t(1;14)(p22;q32) IGH/BCL10
    t(2;12)(p12;p13) IGK/CCND2::t(12;14)(p13;q32) IGH/CCND2::t(12;22)(p13;q11) IGL/CCND2
    t(14;18)(q32;q21) IGH/BCL2::t(2;18)(p11;q21) IGK/BCL2::t(18;22)(q21;q11) IGL/BCL2
    t(2;19)(p12;q13.3) IGK/BCL3::t(14;19)(q32;q13.3) IGH/BCL3::t(19;22)(q13.3;q11) BCL3/IGL
    t(14;22)(q32;q11) IGH/IGL
    t(3;14)(q27;q32) IGH/BCL6::t(2;3)(p12;q27) IGK/BCL6::t(3;22)(q27;q11) IGL/BCL6


    External links

    Nomenclature
    HGNC (Hugo)IGK   5715
    Cards
    AtlasIgKID17
    Entrez_Gene (NCBI)IGK  50802  immunoglobulin kappa locus
    AliasesIGK@
    GeneCards (Weizmann)IGK
    Ensembl hg19 (Hinxton) [Gene_View]
    Ensembl hg38 (Hinxton) [Gene_View]  chr2:88810151-90250363 [Contig_View]  IGK [Vega]
    TCGA cBioPortalIGK
    AceView (NCBI)IGK
    Genatlas (Paris)IGK
    WikiGenes50802
    SOURCE (Princeton)IGK
    Genetics Home Reference (NIH)IGK
    Genomic and cartography
    GoldenPath hg38 (UCSC)IGK  -     chr2:88810151-90250363 2p11.2  hg19-Feb_2009   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)IGK  -     hg19-Feb_2009   [Description]    (hg19-Feb_2009)
    EnsemblIGK - hg19-Feb_2009 [CytoView hg19]  IGK - hg19-Feb_2009 [CytoView hg38]
    Mapping of homologs : NCBIIGK [Mapview hg19]  IGK [Mapview hg38]
    Gene and transcription
    Genbank (Entrez)AF103353 AJ239369 AK129807 BC016380 BC030813
    RefSeq transcript (Entrez)
    RefSeq genomic (Entrez)
    Consensus coding sequences : CCDS (NCBI)IGK
    Cluster EST : UnigeneHs.719895 [ NCBI ]
    CGAP (NCI)Hs.719895
    Gene ExpressionIGK [ NCBI-GEO ]   IGK [ EBI - ARRAY_EXPRESS ]   IGK [ SEEK ]   IGK [ MEM ]
    Gene Expression Viewer (FireBrowse)IGK [ Firebrowse - Broad ]
    SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
    BioGPS (Tissue expression)50802
    GTEX Portal (Tissue expression)IGK
    Protein : pattern, domain, 3D structure
    Domain families : Pfam (Sanger)
    Domain families : Pfam (NCBI)
    Conserved Domain (NCBI)IGK
    DMDM Disease mutations50802
    Blocks (Seattle)IGK
    IPIIPI00784865   IPI00784985   
    Protein Interaction databases
    BioGRIDIGK
    STRING (EMBL)IGK
    ZODIACIGK
    Ontologies - Pathways
    Huge Navigator IGK [HugePedia]
    snp3D : Map Gene to Disease50802
    BioCentury BCIQIGK
    ClinGenIGK
    Clinical trials, drugs, therapy
    Chemical/Protein Interactions : CTD50802
    Chemical/Pharm GKB GenePA35310
    Clinical trialIGK
    Miscellaneous
    canSAR (ICR)IGK (select the gene name)
    Other databaseIGK@ - IMGT
    Probes
    Litterature
    PubMed23 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    CoreMineIGK
    EVEXIGK
    GoPubMedIGK
    iHOPIGK
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

    Search in all EBI   NCBI

    © Atlas of Genetics and Cytogenetics in Oncology and Haematology
    indexed on : Tue Aug 1 17:28:32 CEST 2017

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