Atlas of Genetics and Cytogenetics in Oncology and Haematology


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IKZF1 (Ikaros family zinc finger 1)

Written2000-08Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias_namesregulatory subunit 92
ZNFN1A1
Alias_symbol (synonym)hIk-1
LyF-1
Hs.54452
IKAROS
PPP1R92
Other aliasIK1
LYF1
ZNFN1A1 (zinc finger protein, subfamily 1A, 1)
HGNC (Hugo) IKZF1
LocusID (NCBI) 10320
Atlas_Id 258
Location 7p12.2  [Link to chromosome band 7p12]
Location_base_pair Starts at 50304669 and ends at 50405100 bp from pter ( according to hg19-Feb_2009)  [Mapping IKZF1.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
BCL6 (3q27.3) / IKZF1 (7p12.2)CREB3L2 (7q33) / IKZF1 (7p12.2)ENTPD1 (10q24.1) / IKZF1 (7p12.2)
IKZF1 (7p12.2) / ABCA13 (7p12.3)IKZF1 (7p12.2) / B2M (15q21.1)IKZF1 (7p12.2) / BCL6 (3q27.3)
IKZF1 (7p12.2) / CDK2 (12q13.2)IKZF1 (7p12.2) / ETV6 (12p13.2)IKZF1 (7p12.2) / IKZF1 (7p12.2)
IKZF1 (7p12.2) / LRBA (4q31.3)IKZF1 (7p12.2) / NUTM1 (15q14)IKZF1 (7p12.2) / POLR2A (17p13.1)
IKZF1 (7p12.2) / PRDM16 (1p36.32)IKZF1 (7p12.2) / SETD5 (3p25.3)IKZF1 (7p12.2) / TRPV2 (17p11.2)
IKZF1 (7p12.2) / ZEB2 (2q22.3)SETD5 (3p25.3) / IKZF1 (7p12.2)STIM2 (4p15.2) / IKZF1 (7p12.2)

DNA/RNA

Transcription 3629 bp mRNA; coding sequence: 1559 bp; 6 different splicings (--> 6 isoform proteins: ik1-ik6)

Protein

Description 519 amino acids; 58 kDa; possesses 2 Zinc-finger (C2H2-type) domains: one with 4 ZnF, the second with2 ZnF; DNA binding
Expression specificity for hematopoietic organs in the foetus and in the adult as well
Localisation nuclear
Function transcription regulator; can repress transcription through the recruitment of histone deacetylase complexes; role in conjunction with Aiolos; hemopoietic-specific zinc finger protein regulator of B and T-cell differentiation

Implicated in

Note
  
Entity t(3;7)(q27;p12) diffuse large B-cell lymphoma (DLCL) --> BCL6 / IKZF1
Note only 2 cases to date
Hybrid/Mutated Gene 5' Ikaros - 3' BCL6 fusion transcript; it is supposed that substitution of the promoter of BCL6 may be responsible for BCL6 deregulation
  

Bibliography

Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin.
Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, Fisher AG
Cell. 1997 ; 91 (6) : 845-854.
PMID 9413993
 
The role of the Ikaros gene in lymphocyte development and homeostasis.
Georgopoulos K, Winandy S, Avitahl N
Annual review of immunology. 1997 ; 15 : 155-176.
PMID 9143685
 
The Ikaros gene, a central regulator of lymphoid differentiation, fuses to the BCL6 gene as a result of t(3;7)(q27;p12) translocation in a patient with diffuse large B-cell lymphoma.
Hosokawa Y, Maeda Y, Ichinohasama R, Miura I, Taniwaki M, Seto M
Blood. 2000 ; 95 (8) : 2719-2721.
PMID 10753856
 
Ikaros interactions with CtBP reveal a repression mechanism that is independent of histone deacetylase activity.
Koipally J, Georgopoulos K
The Journal of biological chemistry. 2000 ; 275 (26) : 19594-19602.
PMID 10766745
 
Defects in hemopoietic stem cell activity in Ikaros mutant mice.
Nichogiannopoulou A, Trevisan M, Neben S, Friedrich C, Georgopoulos K
The Journal of experimental medicine. 1999 ; 190 (9) : 1201-1214.
PMID 10544193
 
Pre-T cell receptor (TCR) and TCR-controlled checkpoints in T cell differentiation are set by Ikaros.
Winandy S, Wu L, Wang JH, Georgopoulos K
The Journal of experimental medicine. 1999 ; 190 (8) : 1039-1048.
PMID 10523602
 
Identification of heterologous translocation partner genes fused to the BCL6 gene in diffuse large B-cell lymphomas: 5'-RACE and LA - PCR analyses of biopsy samples.
Yoshida S, Kaneita Y, Aoki Y, Seto M, Mori S, Moriyama M
Oncogene. 1999 ; 18 (56) : 7994-7999.
PMID 10637510
 

Citation

This paper should be referenced as such :
Huret, JL
IKZF1 (Ikaros family zinc finger 1)
Atlas Genet Cytogenet Oncol Haematol. 2000;4(4):179-180.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/IkarosID258.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 15 ]
  3q27 rearrangements (BCL6) in non Hodgkin lymphoma::t(3;Var)(q27;Var) in non Hodgkin lymphoma
Blastic Plasmacytoid Dendritic Cell Neoplasm (BPDCN)
Chronic myelogenous leukaemia (CML)
del(5)(q32q33) EBF1/PDGFRB
del(9p) in Acute Lymphoblastic Leukemia
del(X)(p22p22) P2RY8/CRLF2::del(Y)(p11p11) P2RY8/CRLF2
Early T-cell precursor acute lymphoblastic leukemia
i(7)(q10)
Acute lymphoblastic leukemia in Down syndrome
Mixed phenotype acute leukemia (MPAL)
Myeloid proliferations in Down syndrome
t(1;7)(p36;p12) IKZF1/PRDM16
t(3;7)(q27;p12) IKZF1/BCL6
t(5;9)(q14.1;p24) SSBP2/JAK2
t(7;8)(p12;q24) /MYC


External links

Nomenclature
HGNC (Hugo)IKZF1   13176
Cards
AtlasIkarosID258
Entrez_Gene (NCBI)IKZF1  10320  IKAROS family zinc finger 1
AliasesCVID13; Hs.54452; IK1; IKAROS; 
LYF1; LyF-1; PPP1R92; PRO0758; ZNFN1A1
GeneCards (Weizmann)IKZF1
Ensembl hg19 (Hinxton)ENSG00000185811 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000185811 [Gene_View]  chr7:50304669-50405100 [Contig_View]  IKZF1 [Vega]
ICGC DataPortalENSG00000185811
TCGA cBioPortalIKZF1
AceView (NCBI)IKZF1
Genatlas (Paris)IKZF1
WikiGenes10320
SOURCE (Princeton)IKZF1
Genetics Home Reference (NIH)IKZF1
Genomic and cartography
GoldenPath hg38 (UCSC)IKZF1  -     chr7:50304669-50405100 +  7p12.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)IKZF1  -     7p12.2   [Description]    (hg19-Feb_2009)
EnsemblIKZF1 - 7p12.2 [CytoView hg19]  IKZF1 - 7p12.2 [CytoView hg38]
Mapping of homologs : NCBIIKZF1 [Mapview hg19]  IKZF1 [Mapview hg38]
OMIM603023   616873   
Gene and transcription
Genbank (Entrez)AF116605 AF180297 AF432219 AK303586 AK308411
RefSeq transcript (Entrez)
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)IKZF1
Cluster EST : UnigeneHs.731495 [ NCBI ]
CGAP (NCI)Hs.731495
Alternative Splicing GalleryENSG00000185811
Gene ExpressionIKZF1 [ NCBI-GEO ]   IKZF1 [ EBI - ARRAY_EXPRESS ]   IKZF1 [ SEEK ]   IKZF1 [ MEM ]
Gene Expression Viewer (FireBrowse)IKZF1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)10320
GTEX Portal (Tissue expression)IKZF1
Human Protein AtlasENSG00000185811-IKZF1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13422   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ13422  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13422
Splice isoforms : SwissVarQ13422
PhosPhoSitePlusQ13422
Domaine pattern : Prosite (Expaxy)ZINC_FINGER_C2H2_1 (PS00028)    ZINC_FINGER_C2H2_2 (PS50157)   
Domains : Interpro (EBI)Znf_C2H2    Znf_C2H2-like    Znf_C2H2/integrase_DNA-bd   
Domain families : Pfam (Sanger)zf-C2H2 (PF00096)   
Domain families : Pfam (NCBI)pfam00096   
Domain families : Smart (EMBL)ZnF_C2H2 (SM00355)  
Conserved Domain (NCBI)IKZF1
DMDM Disease mutations10320
Blocks (Seattle)IKZF1
SuperfamilyQ13422
Human Protein Atlas [tissue]ENSG00000185811-IKZF1 [tissue]
Peptide AtlasQ13422
HPRD04318
IPIIPI00013232   IPI00216387   IPI00216388   IPI00216389   IPI00216390   IPI00216391   IPI00216392   IPI00782995   IPI01011333   IPI00152529   IPI00926847   
Protein Interaction databases
DIP (DOE-UCLA)Q13422
IntAct (EBI)Q13422
FunCoupENSG00000185811
BioGRIDIKZF1
STRING (EMBL)IKZF1
ZODIACIKZF1
Ontologies - Pathways
QuickGOQ13422
Ontology : AmiGODNA binding  transcription factor activity, sequence-specific DNA binding  protein binding  nucleus  nucleoplasm  nucleolus  cytoplasm  transcription, DNA-templated  cell cycle  mesoderm development  covalent chromatin modification  protein domain specific binding  lymphocyte differentiation  erythrocyte differentiation  nuclear pericentric heterochromatin  intracellular membrane-bounded organelle  protein complex  protein complex  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  metal ion binding  protein heterooligomerization  
Ontology : EGO-EBIDNA binding  transcription factor activity, sequence-specific DNA binding  protein binding  nucleus  nucleoplasm  nucleolus  cytoplasm  transcription, DNA-templated  cell cycle  mesoderm development  covalent chromatin modification  protein domain specific binding  lymphocyte differentiation  erythrocyte differentiation  nuclear pericentric heterochromatin  intracellular membrane-bounded organelle  protein complex  protein complex  transcription regulatory region DNA binding  negative regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  metal ion binding  protein heterooligomerization  
NDEx NetworkIKZF1
Atlas of Cancer Signalling NetworkIKZF1
Wikipedia pathwaysIKZF1
Orthology - Evolution
OrthoDB10320
GeneTree (enSembl)ENSG00000185811
Phylogenetic Trees/Animal Genes : TreeFamIKZF1
HOVERGENQ13422
HOGENOMQ13422
Homologs : HomoloGeneIKZF1
Homology/Alignments : Family Browser (UCSC)IKZF1
Gene fusions - Rearrangements
Fusion : MitelmanIKZF1/ABCA13 [7p12.2/7p12.3]  
Fusion : MitelmanIKZF1/BCL6 [7p12.2/3q27.3]  [t(3;7)(q27;p12)]  
Fusion : MitelmanIKZF1/LRBA [7p12.2/4q31.3]  [t(4;7)(q31;p12)]  
Fusion : MitelmanIKZF1/PRDM16 [7p12.2/1p36.32]  [t(1;7)(p36;p12)]  
Fusion: TCGA_MDACCIKZF1 7p12.2 LRBA 4q31.3 BRCA
Tumor Fusion PortalIKZF1
Fusion : TICdbIKZF1 [7p12.2]  -  BCL6 [3q27.3]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerIKZF1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)IKZF1
dbVarIKZF1
ClinVarIKZF1
1000_GenomesIKZF1 
Exome Variant ServerIKZF1
ExAC (Exome Aggregation Consortium)ENSG00000185811
GNOMAD BrowserENSG00000185811
Genetic variants : HAPMAP10320
Genomic Variants (DGV)IKZF1 [DGVbeta]
DECIPHERIKZF1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisIKZF1 
Mutations
ICGC Data PortalIKZF1 
TCGA Data PortalIKZF1 
Broad Tumor PortalIKZF1
OASIS PortalIKZF1 [ Somatic mutations - Copy number]
Cancer Gene: CensusIKZF1 
Somatic Mutations in Cancer : COSMICIKZF1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDIKZF1
LOVD (Leiden Open Variation Database)**PUBLIC** CCHMC Molecular Genetics Laboratory Mutation Database
BioMutasearch IKZF1
DgiDB (Drug Gene Interaction Database)IKZF1
DoCM (Curated mutations)IKZF1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)IKZF1 (select a term)
intoGenIKZF1
NCG5 (London)IKZF1
Cancer3DIKZF1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603023    616873   
Orphanet21584    10430    14433   
DisGeNETIKZF1
MedgenIKZF1
Genetic Testing Registry IKZF1
NextProtQ13422 [Medical]
TSGene10320
GENETestsIKZF1
Target ValidationIKZF1
Huge Navigator IKZF1 [HugePedia]
snp3D : Map Gene to Disease10320
BioCentury BCIQIKZF1
ClinGenIKZF1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD10320
Chemical/Pharm GKB GenePA37748
Clinical trialIKZF1
Miscellaneous
canSAR (ICR)IKZF1 (select the gene name)
Probes
Litterature
PubMed215 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineIKZF1
EVEXIKZF1
GoPubMedIKZF1
iHOPIKZF1
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 Nov 21 14:53:08 CET 2017

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For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.