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AFF4 (ALL1 fused gene from chromosome 5q31)

Written2000-04Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France
Updated2003-06Jean-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_namesAF4/FMR2 family
Alias_symbol (synonym)AF5Q31
MCEF
HGNC (Hugo) AFF4
LocusID (NCBI) 27125
Atlas_Id 230
Location 5q31.1  [Link to chromosome band 5q31]
Location_base_pair Starts at 132211071 and ends at 132299354 bp from pter ( according to hg19-Feb_2009)  [Mapping AFF4.png]
 
  AF5q31 (5q31) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.
Fusion genes
(updated 2016)
AFF4 (5q31.1) / FSTL4 (5q31.1)AFF4 (5q31.1) / KMT2A (11q23.3)AFF4 (5q31.1) / LAMC3 (9q34.12)
AFF4 (5q31.1) / SNTG2 (2p25.3)COX6C (8q22.2) / AFF4 (5q31.1)FAM129B (9q33.3) / AFF4 (5q31.1)
KDM2B (12q24.31) / AFF4 (5q31.1)KMT2A (11q23.3) / AFF4 (5q31.1)SEPT8 (5q31.1) / AFF4 (5q31.1)

DNA/RNA

Description at least 16 exons
Transcription in a telomere to centromere direction; 4235 bp mRNA; open reading frame: 3491 bp

Protein

Description 1163 amino acids; 127 kDa
Expression mostly in fetal tissues (heart, lung, brain, liver); at a low level in adult tissues; therefore, AF5q31 may play a critical role in the fetal development
Homology with AF4-related proteins: AF4, the gene involved int(4;11)(q21;q23), LAF4, FMR2

Implicated in

Note
Entity ins(5;11)(q31;q13q23)acute lymphoblastic leukemia (ALL) --> MLL-AF5q31
Note poorly defined: only 2 cases to date, infants with CD19+ ALL; complete remission, relapse and death
Hybrid/Mutated Gene AF5Q31 and MLL are transcribed in opposite directions, and inverted insertion is required
  

Bibliography

Insertion of MLL sequences into chromosome band 5q31 results in an MLL-AF5Q31 fusion and is a rare but recurrent abnormality associated with infant leukemia.
Deveney R, Chervinsky DS, Jani-Sait SN, Grossi M, Aplan PD
Genes, chromosomes & cancer. 2003 ; 37 (3) : 326-331.
PMID 12759932
 
AF5q31, a newly identified AF4-related gene, is fused to MLL in infant acute lymphoblastic leukemia with ins(5;11)(q31;q13q23).
Taki T, Kano H, Taniwaki M, Sako M, Yanagisawa M, Hayashi Y
Proceedings of the National Academy of Sciences of the United States of America. 1999 ; 96 (25) : 14535-14540.
PMID 10588740
 

Citation

This paper should be referenced as such :
Huret, JL
AF5q31 (ALL1 fused gene from chromosome 5q31)
Atlas Genet Cytogenet Oncol Haematol. 2003;7(3):165-165.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/AF5q31ID230.html
History of this paper:
Huret, JL. AF5q31 (ALL1 fused gene from chromosome 5q31). Atlas Genet Cytogenet Oncol Haematol. 2000;4(2):57-57.
http://documents.irevues.inist.fr/bitstream/handle/2042/37610/04-2000-AF5q31ID230.pdf


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 5 ]
  11q23 rearrangements (KMT2A) in leukaemia
ins(5;11)(q31;q13q23) KMT2A/AFF4
t(2;11)(q11;q23) KMT2A/AFF3
t(2;18)(q11;q21) AFF3/BCL2
t(2;21)(q11;q22)


External links

Nomenclature
HGNC (Hugo)AFF4   17869
Cards
AtlasAF5q31ID230
Entrez_Gene (NCBI)AFF4  27125  AF4/FMR2 family member 4
AliasesAF5Q31; CHOPS; MCEF
GeneCards (Weizmann)AFF4
Ensembl hg19 (Hinxton)ENSG00000072364 [Gene_View]  chr5:132211071-132299354 [Contig_View]  AFF4 [Vega]
Ensembl hg38 (Hinxton)ENSG00000072364 [Gene_View]  chr5:132211071-132299354 [Contig_View]  AFF4 [Vega]
ICGC DataPortalENSG00000072364
TCGA cBioPortalAFF4
AceView (NCBI)AFF4
Genatlas (Paris)AFF4
WikiGenes27125
SOURCE (Princeton)AFF4
Genetics Home Reference (NIH)AFF4
Genomic and cartography
GoldenPath hg19 (UCSC)AFF4  -     chr5:132211071-132299354 -  5q31   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)AFF4  -     5q31   [Description]    (hg38-Dec_2013)
EnsemblAFF4 - 5q31 [CytoView hg19]  AFF4 - 5q31 [CytoView hg38]
Mapping of homologs : NCBIAFF4 [Mapview hg19]  AFF4 [Mapview hg38]
OMIM604417   616368   
Gene and transcription
Genbank (Entrez)AA706988 AB209547 AF161355 AF173886 AF197927
RefSeq transcript (Entrez)NM_014423
RefSeq genomic (Entrez)NC_000005 NC_018916 NG_030340 NT_034772 NW_004929323
Consensus coding sequences : CCDS (NCBI)AFF4
Cluster EST : UnigeneHs.664840 [ NCBI ]
CGAP (NCI)Hs.664840
Alternative Splicing GalleryENSG00000072364
Gene ExpressionAFF4 [ NCBI-GEO ]   AFF4 [ EBI - ARRAY_EXPRESS ]   AFF4 [ SEEK ]   AFF4 [ MEM ]
Gene Expression Viewer (FireBrowse)AFF4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)27125
GTEX Portal (Tissue expression)AFF4
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9UHB7   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9UHB7  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9UHB7
Splice isoforms : SwissVarQ9UHB7
PhosPhoSitePlusQ9UHB7
Domains : Interpro (EBI)TF_AF4/FMR2   
Domain families : Pfam (Sanger)AF-4 (PF05110)   
Domain families : Pfam (NCBI)pfam05110   
Conserved Domain (NCBI)AFF4
DMDM Disease mutations27125
Blocks (Seattle)AFF4
PDB (SRS)4IMY    4OGR    4OR5   
PDB (PDBSum)4IMY    4OGR    4OR5   
PDB (IMB)4IMY    4OGR    4OR5   
PDB (RSDB)4IMY    4OGR    4OR5   
Structural Biology KnowledgeBase4IMY    4OGR    4OR5   
SCOP (Structural Classification of Proteins)4IMY    4OGR    4OR5   
CATH (Classification of proteins structures)4IMY    4OGR    4OR5   
SuperfamilyQ9UHB7
Human Protein AtlasENSG00000072364
Peptide AtlasQ9UHB7
HPRD09187
IPIIPI00004344   IPI00383219   IPI00658213   IPI00384917   IPI00789165   IPI00965337   
Protein Interaction databases
DIP (DOE-UCLA)Q9UHB7
IntAct (EBI)Q9UHB7
FunCoupENSG00000072364
BioGRIDAFF4
STRING (EMBL)AFF4
ZODIACAFF4
Ontologies - Pathways
QuickGOQ9UHB7
Ontology : AmiGOtranscription factor activity, sequence-specific DNA binding  protein binding  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  spermatid development  transcription elongation factor complex  transcriptionally active chromatin  
Ontology : EGO-EBItranscription factor activity, sequence-specific DNA binding  protein binding  regulation of transcription, DNA-templated  transcription from RNA polymerase II promoter  spermatid development  transcription elongation factor complex  transcriptionally active chromatin  
NDEx NetworkAFF4
Atlas of Cancer Signalling NetworkAFF4
Wikipedia pathwaysAFF4
Orthology - Evolution
OrthoDB27125
GeneTree (enSembl)ENSG00000072364
Phylogenetic Trees/Animal Genes : TreeFamAFF4
HOVERGENQ9UHB7
HOGENOMQ9UHB7
Homologs : HomoloGeneAFF4
Homology/Alignments : Family Browser (UCSC)AFF4
Gene fusions - Rearrangements
Fusion : MitelmanAFF4/FSTL4 [5q31.1/5q31.1]  
Fusion : MitelmanAFF4/LAMC3 [5q31.1/9q34.12]  [t(5;9)(q31;q34)]  
Fusion : MitelmanAFF4/SNTG2 [5q31.1/2p25.3]  [t(2;5)(p25;q31)]  
Fusion : MitelmanSEPT8/AFF4 [5q31.1/5q31.1]  [del(5)(q31q31)]  
Fusion : COSMICKMT2A [11q23.3]  -  AFF4 [5q31.1]  [fusion_1797]  [fusion_1798]  [fusion_1815]  [fusion_1824]  [fusion_1825]  
Fusion : COSMICSEPT8 [5q31.1]  -  AFF4 [5q31.1]  [fusion_677]  [fusion_678]  
Fusion: TCGAAFF4 5q31.1 FSTL4 5q31.1 BRCA
Fusion: TCGAAFF4 5q31.1 SNTG2 2p25.3 PRAD
Fusion : TICdbKMT2A [11q23.3]  -  AFF4 [5q31.1]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerAFF4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)AFF4
dbVarAFF4
ClinVarAFF4
1000_GenomesAFF4 
Exome Variant ServerAFF4
ExAC (Exome Aggregation Consortium)AFF4 (select the gene name)
Genetic variants : HAPMAP27125
Genomic Variants (DGV)AFF4 [DGVbeta]
DECIPHER (Syndromes)5:132211071-132299354  ENSG00000072364
CONAN: Copy Number AnalysisAFF4 
Mutations
ICGC Data PortalAFF4 
TCGA Data PortalAFF4 
Broad Tumor PortalAFF4
OASIS PortalAFF4 [ Somatic mutations - Copy number]
Cancer Gene: CensusAFF4 
Somatic Mutations in Cancer : COSMICAFF4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDAFF4
intOGen PortalAFF4
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch AFF4
DgiDB (Drug Gene Interaction Database)AFF4
DoCM (Curated mutations)AFF4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)AFF4 (select a term)
intoGenAFF4
NCG5 (London)AFF4
Cancer3DAFF4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604417    616368   
Orphanet23479   
MedgenAFF4
Genetic Testing Registry AFF4
NextProtQ9UHB7 [Medical]
TSGene27125
GENETestsAFF4
Huge Navigator AFF4 [HugePedia]
snp3D : Map Gene to Disease27125
BioCentury BCIQAFF4
ClinGenAFF4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD27125
Chemical/Pharm GKB GenePA142672641
Clinical trialAFF4
Miscellaneous
canSAR (ICR)AFF4 (select the gene name)
Probes
Litterature
PubMed51 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineAFF4
EVEXAFF4
GoPubMedAFF4
iHOPAFF4
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri Nov 18 20:09:36 CET 2016

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