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AFF3 (lymphoid nuclear protein related to AF4)

Identity

Other namesLAF4 (lymphoid nuclear protein related to AF4)
MLLT2-related protein, lymphoid nuclear protein 4
HGNC (Hugo) AFF3
LocusID (NCBI) 3899
Location 2q11.2
Location_base_pair Starts at 100163716 and ends at 100722045 bp from pter ( according to hg19-Feb_2009)  [Mapping]

DNA/RNA

Description at least 17 exons.
Transcription in a telomere to centromere direction; 3857 bp mRNA; 3684 bp open reading frame.

Protein

Description 1227 amino acids; 133734 Da.
Expression Preferentially expressed in lymphoid tissues, highest levels being found in the thymus. Lower expression in brain and lung.
Localisation Nuclear
Function Putative transcription activator that may function in lymphoid development and oncogenesis. Binds in vitro to double-stranded DNA
Homology Belongs to the AF4/LAF4/FMR2/AF5q31 family.

Implicated in

Entity t(2;11)(q11;q23) . --> MLL-LAF4
Note MLL fusion partner at chromosome 2 in infant ALL
Disease The three cases reported to date were all infant-ALL with proB phenotype
Prognosis Prognosis is poor, although based on only three cases.
Cytogenetics The three reported cases harboured different rearrangements involving chromosomes 2 and 11: t(2;11)(q11;q23), t(2;11)(p15;p14), and ins(11;2)(q23;q11.2q11.2).
Abnormal Protein The MLL-LAF4 fusion protein includes the transactivation domain of LAF4 that is part of the AF4/LAF4/FMR2 homology domain.
 
Coding sequence of LAF4 compared to AF4 and site of fusion. Schematic representation of MLL, LAF4, AF4, and the putative MLL-LAF4 fusion protein. Domains in MLL are shaded: MT, DNA methyltransferase homology region; TRX, Drosophila trithorax homology. The percentage of amino acid homology between corresponding regions of LAF4 and AF4 is indicated: NHD, N-terminal homology domain; ALF, AF4/LAF4/FMR2 homology domain; TAD, transactivation domain; NLS, nuclear localization sequence; CHD, C-terminal homology domain. Arrows indicate the fusion sites with MLL. The breakpoint in LAF4 corresponds to one of the known breakpoints in AF4.
  

Breakpoints

 

Other Leukemias implicated (Data extracted from papers in the Atlas)

Leukemias t0817q24q22ID1494 t1119q23p13ID1540 t614p25q32IRF4IGHID1175

External links

Nomenclature
HGNC (Hugo)AFF3   6473
Cards
AtlasLAF4ID315
Entrez_Gene (NCBI)AFF3  3899  AF4/FMR2 family, member 3
GeneCards (Weizmann)AFF3
Ensembl (Hinxton)ENSG00000144218 [Gene_View]  chr2:100163716-100722045 [Contig_View]  AFF3 [Vega]
ICGC DataPortalENSG00000144218
cBioPortalAFF3
AceView (NCBI)AFF3
Genatlas (Paris)AFF3
WikiGenes3899
SOURCE (Princeton)NM_001025108 NM_002285
Genomic and cartography
GoldenPath (UCSC)AFF3  -  2q11.2   chr2:100163716-100722045 -  2q11.2-q12   [Description]    (hg19-Feb_2009)
EnsemblAFF3 - 2q11.2-q12 [CytoView]
Mapping of homologs : NCBIAFF3 [Mapview]
OMIM601464   
Gene and transcription
Genbank (Entrez)AB209634 AK055117 AK091320 AK092327 AK290468
RefSeq transcript (Entrez)NM_001025108 NM_002285
RefSeq genomic (Entrez)AC_000134 NC_000002 NC_018913 NT_022171 NW_001838818 NW_004929303
Consensus coding sequences : CCDS (NCBI)AFF3
Cluster EST : UnigeneHs.444414 [ NCBI ]
CGAP (NCI)Hs.444414
Alternative Splicing : Fast-db (Paris)GSHG0017858
Alternative Splicing GalleryENSG00000144218
Gene ExpressionAFF3 [ NCBI-GEO ]     AFF3 [ SEEK ]   AFF3 [ MEM ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP51826 (Uniprot)
NextProtP51826  [Medical]
With graphics : InterProP51826
Splice isoforms : SwissVarP51826 (Swissvar)
Domains : Interpro (EBI)TF_AF4/FMR2 [organisation]  
Related proteins : CluSTrP51826
Domain families : Pfam (Sanger)AF-4 (PF05110)   
Domain families : Pfam (NCBI)pfam05110   
DMDM Disease mutations3899
Blocks (Seattle)P51826
Human Protein AtlasENSG00000144218 [gene] [tissue] [antibody] [cell] [cancer]
Peptide AtlasP51826
HPRD03272
IPIIPI00515069   IPI00916518   IPI00917755   IPI00915807   IPI00020918   IPI00917160   IPI00917446   IPI00917619   IPI00916078   IPI00917889   IPI00917500   IPI00916649   
Protein Interaction databases
DIP (DOE-UCLA)P51826
IntAct (EBI)P51826
FunCoupENSG00000144218
BioGRIDAFF3
InParanoidP51826
Interologous Interaction database P51826
IntegromeDBAFF3
STRING (EMBL)AFF3
Ontologies - Pathways
Ontology : AmiGOdouble-stranded DNA binding  nucleus  nucleolus  transcription, DNA-templated  regulation of transcription, DNA-dependent  response to tumor necrosis factor  embryonic hindlimb morphogenesis  
Ontology : EGO-EBIdouble-stranded DNA binding  nucleus  nucleolus  transcription, DNA-templated  regulation of transcription, DNA-dependent  response to tumor necrosis factor  embryonic hindlimb morphogenesis  
Protein Interaction DatabaseAFF3
Wikipedia pathwaysAFF3
Gene fusion - rearrangments
Rearrangement : TICdbAFF3 [2q11.2]  -  BCL2 [2p23.2]
Rearrangement : TICdbKMT2A [11q23.3]  -  AFF3 [17q12]
Rearrangement : TICdbRUNX1 [21q22.12]  -  AFF3 [9q34.12]
Polymorphisms : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)AFF3
snp3D : Map Gene to Disease3899
SNP (GeneSNP Utah)AFF3
SNP : HGBaseAFF3
Genetic variants : HAPMAPAFF3
Exome VariantAFF3
1000_GenomesAFF3 
ICGC programENSG00000144218 
Cancer Gene: CensusAFF3 
Somatic Mutations in Cancer : COSMICAFF3 
CONAN: Copy Number AnalysisAFF3 
Mutations and Diseases : HGMDAFF3
Genomic VariantsAFF3  AFF3 [DGVbeta]
dbVarAFF3
ClinVarAFF3
Pred. of missensesPolyPhen-2  SIFT(SG)  SIFT(JCVI)  Align-GVGD  MutAssessor  Mutanalyser  
Pred. splicesGeneSplicer  Human Splicing Finder  MaxEntScan  
Diseases
OMIM601464   
MedgenAFF3
GENETestsAFF3
Disease Genetic AssociationAFF3
Huge Navigator AFF3 [HugePedia]  AFF3 [HugeCancerGEM]
General knowledge
Homologs : HomoloGeneAFF3
Homology/Alignments : Family Browser (UCSC)AFF3
Phylogenetic Trees/Animal Genes : TreeFamAFF3
Chemical/Protein Interactions : CTD3899
Chemical/Pharm GKB GenePA30264
Clinical trialAFF3
Cancer Resource (Charite)ENSG00000144218
Other databases
Probes
Litterature
PubMed29 Pubmed reference(s) in Entrez
CoreMineAFF3
iHOPAFF3

Bibliography

LAF-4 encodes a lymphoid nuclear protein with transactivation potential that is homologous to AF-4, the gene fused to MLL in t(4;11) leukemias.
Ma C, Staudt LM
Blood. 1996 ; 87 (2) : 734-745.
PMID 8555498
 
LAF4, an AF4-related gene, is fused to MLL in infant acute lymphoblastic leukemia.
von Bergh AR, Beverloo HB, Rombout P, van Wering ER, van Weel MH, Beverstock GC, Kluin PM, Slater RM, Schuuring E
Genes, chromosomes & cancer. 2002 ; 35 (1) : 92-96.
PMID 12203795
 
Occurrence of an MLL/LAF4 fusion gene caused by the insertion ins(11;2)(q23;q11.2q11.2) in an infant with acute lymphoblastic leukemia.
Bruch J, Wilda M, Teigler-Schlegel A, Harbott J, Borkhardt A, Metzler M
Genes, chromosomes & cancer. 2003 ; 37 (1) : 106-109.
PMID 12661012
 
Fusion of an AF4-related gene, LAF4, to MLL in childhood acute lymphoblastic leukemia with t(2;11)(q11;q23).
Hiwatari M, Taki T, Taketani T, Taniwaki M, Sugita K, Okuya M, Eguchi M, Ida K, Hayashi Y
Oncogene. 2003 ; 22 (18) : 2851-2855.
PMID 12743608
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written08-2003Anne RM von Bergh

Citation

This paper should be referenced as such :
von Bergh, ARM
LAF4 (lymphoid nuclear protein related to AF4)
Atlas Genet Cytogenet Oncol Haematol. 2003;7(4):226-227.
Free online version   Free pdf version   [Bibliographic record ]
URL : http://AtlasGeneticsOncology.org/Genes/LAF4ID315.html

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indexed on : Fri Jul 11 17:26:24 CEST 2014
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