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AFF4 (ALL1 fused gene from chromosome 5q31)

Written2003-06Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France
This article is an update of :
2000-04Jean-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 (NCBI)AF5q31 (ALL1 fused gene from chromosome 5q31)
HGNC (Hugo) AFF4
HGNC Alias symbAF5Q31
MCEF
HGNC Alias nameALL1 fused gene from 5q31
HGNC Previous nameAF4/FMR2 family, member 4
LocusID (NCBI) 27125
Atlas_Id 230
Location 5q31.1  [Link to chromosome band 5q31]
Location_base_pair Starts at 132875396 and ends at 132963634 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping AFF4.png]
 
  AF5q31 (5q31) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
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)
SKP1 (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 in, LAF4, FMR2

Implicated in

Note
  
Entity acute lymphoblastic leukemia (ALL) --> KMT2A-AFF4
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 ]
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) [ 7 ]
  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)
t(5;5)(q31;q31) SKP1/AFF4
t(5;12)(q31;q24) KDM2B/AFF4


External links

Nomenclature
HGNC (Hugo)AFF4   17869
Cards
AtlasAF5q31ID230
Entrez_Gene (NCBI)AFF4    AF4/FMR2 family member 4
AliasesAF5Q31; CHOPS; MCEF
GeneCards (Weizmann)AFF4
Ensembl hg19 (Hinxton)ENSG00000072364 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000072364 [Gene_View]  ENSG00000072364 [Sequence]  chr5:132875396-132963634 [Contig_View]  AFF4 [Vega]
ICGC DataPortalENSG00000072364
TCGA cBioPortalAFF4
AceView (NCBI)AFF4
Genatlas (Paris)AFF4
SOURCE (Princeton)AFF4
Genetics Home Reference (NIH)AFF4
Genomic and cartography
GoldenPath hg38 (UCSC)AFF4  -     chr5:132875396-132963634 -  5q31.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)AFF4  -     5q31.1   [Description]    (hg19-Feb_2009)
GoldenPathAFF4 - 5q31.1 [CytoView hg19]  AFF4 - 5q31.1 [CytoView hg38]
ImmunoBaseENSG00000072364
genome Data Viewer NCBIAFF4 [Mapview hg19]  
OMIM604417   616368   
Gene and transcription
Genbank (Entrez)AA706988 AB209547 AF161355 AF173886 AF197927
RefSeq transcript (Entrez)NM_014423
Consensus coding sequences : CCDS (NCBI)AFF4
Alternative Splicing GalleryENSG00000072364
Gene ExpressionAFF4 [ NCBI-GEO ]   AFF4 [ EBI - ARRAY_EXPRESS ]   AFF4 [ SEEK ]   AFF4 [ MEM ]
Gene Expression Viewer (FireBrowse)AFF4 [ Firebrowse - Broad ]
GenevisibleExpression of AFF4 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)27125
GTEX Portal (Tissue expression)AFF4
Human Protein AtlasENSG00000072364-AFF4 [pathology]   [cell]   [tissue]
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
PhosPhoSitePlusQ9UHB7
Domains : Interpro (EBI)AF4/FMR2    AF4/FMR2_CHD    AF4_int   
Domain families : Pfam (Sanger)AF-4_C (PF18876)    AF4_int (PF18875)   
Domain families : Pfam (NCBI)pfam18876    pfam18875   
Conserved Domain (NCBI)AFF4
PDB (RSDB)4IMY    4OGR    4OR5    5JW9    5L1Z    6CYT    6K7P    6KN5    6R80   
PDB Europe4IMY    4OGR    4OR5    5JW9    5L1Z    6CYT    6K7P    6KN5    6R80   
PDB (PDBSum)4IMY    4OGR    4OR5    5JW9    5L1Z    6CYT    6K7P    6KN5    6R80   
PDB (IMB)4IMY    4OGR    4OR5    5JW9    5L1Z    6CYT    6K7P    6KN5    6R80   
Structural Biology KnowledgeBase4IMY    4OGR    4OR5    5JW9    5L1Z    6CYT    6K7P    6KN5    6R80   
SCOP (Structural Classification of Proteins)4IMY    4OGR    4OR5    5JW9    5L1Z    6CYT    6K7P    6KN5    6R80   
CATH (Classification of proteins structures)4IMY    4OGR    4OR5    5JW9    5L1Z    6CYT    6K7P    6KN5    6R80   
SuperfamilyQ9UHB7
AlphaFold pdb e-kbQ9UHB7   
Human Protein Atlas [tissue]ENSG00000072364-AFF4 [tissue]
HPRD09187
Protein Interaction databases
DIP (DOE-UCLA)Q9UHB7
IntAct (EBI)Q9UHB7
BioGRIDAFF4
STRING (EMBL)AFF4
ZODIACAFF4
Ontologies - Pathways
QuickGOQ9UHB7
Ontology : AmiGOfibrillar center  protein binding  nucleoplasm  nucleoplasm  transcription by RNA polymerase II  transcription elongation from RNA polymerase II promoter  spermatid development  transcription elongation factor complex  regulation of gene expression  super elongation complex  transcriptionally active chromatin  
Ontology : EGO-EBIfibrillar center  protein binding  nucleoplasm  nucleoplasm  transcription by RNA polymerase II  transcription elongation from RNA polymerase II promoter  spermatid development  transcription elongation factor complex  regulation of gene expression  super elongation complex  transcriptionally active chromatin  
REACTOMEQ9UHB7 [protein]
REACTOME PathwaysR-HSA-75955 [pathway]   
NDEx NetworkAFF4
Atlas of Cancer Signalling NetworkAFF4
Wikipedia pathwaysAFF4
Orthology - Evolution
OrthoDB27125
GeneTree (enSembl)ENSG00000072364
Phylogenetic Trees/Animal Genes : TreeFamAFF4
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]  
Fusion : MitelmanAFF4/SNTG2 [5q31.1/2p25.3]  
Fusion : MitelmanSEPT8/AFF4 [5q31.1/5q31.1]  
Fusion : COSMICSEPT8 [AFF4]  -  5q31.1 [677]  
Fusion PortalAFF4 5q31.1 FSTL4 5q31.1 BRCA
Fusion PortalAFF4 5q31.1 SNTG2 2p25.3 PRAD
Fusion : QuiverAFF4
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerAFF4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)AFF4
dbVarAFF4
ClinVarAFF4
MonarchAFF4
1000_GenomesAFF4 
Exome Variant ServerAFF4
GNOMAD BrowserENSG00000072364
Varsome BrowserAFF4
Genomic Variants (DGV)AFF4 [DGVbeta]
DECIPHERAFF4 [patients]   [syndromes]   [variants]   [genes]  
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]  
Somatic Mutations in Cancer : COSMIC3DAFF4
Mutations and Diseases : HGMDAFF4
intOGen PortalAFF4
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
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)
OncoKBAFF4
NCG6 (London) select AFF4
Cancer3DAFF4(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604417    616368   
Orphanet23479   
DisGeNETAFF4
MedgenAFF4
Genetic Testing Registry AFF4
NextProtQ9UHB7 [Medical]
GENETestsAFF4
Target ValidationAFF4
Huge Navigator AFF4 [HugePedia]
ClinGenAFF4
Clinical trials, drugs, therapy
MyCancerGenomeAFF4
Protein Interactions : CTDAFF4
Pharm GKB GenePA142672641
PharosQ9UHB7
Clinical trialAFF4
Miscellaneous
canSAR (ICR)AFF4
HarmonizomeAFF4
DataMed IndexAFF4
Probes
Litterature
PubMed80 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXAFF4
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Sep 15 23:39:43 CEST 2021

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