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MLLT3 (myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3)

Written1997-12Jean-Loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)


Alias_namesmyeloid/lymphoid or mixed-lineage leukemia
Alias_symbol (synonym)AF-9
Other aliasLTG9
AF9 (ALL1 fused gene from chromosome 9)
LocusID (NCBI) 4300
Atlas_Id 5
Location 9p21.3  [Link to chromosome band 9p21]
Location_base_pair Starts at 20341663 and ends at 20621986 bp from pter ( according to hg19-Feb_2009)  [Mapping MLLT3.png]
  AF9 (9p22) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.
Fusion genes
(updated 2016)
ALL1 () / MLLT3 (9p21.3)KMT2A (11q23.3) / MLLT3 (9p21.3)KMT2B (19q13.12) / MLLT3 (9p21.3)
MLLT3 (9p21.3) / CISD3 (17q12)MLLT3 (9p21.3) / IZUMO3 (9p21.3)MLLT3 (9p21.3) / KMT2A (11q23.3)
MLLT3 (9p21.3) / SLC28A3 (9q21.32)PAX5 (9p13.2) / MLLT3 (9p21.3)SCFD1 (14q12) / MLLT3 (9p21.3)


Transcription 5 kb mRNA; coding sequence: 1.7 kb


Description 568 amino acids; 63 kDa; serine and proline rich in many places; possesses a nuclear targeting sequence
Localisation nuclear
Function transcription activator
Homology with ENL (human)

Implicated in

Entity t(9;11) (p22;q23)/AML -->MLL -AF9
Disease M5/M4 de novo and therapy related AML
Prognosis the prognosis may not be as poor as in other 11q23 leukaemias in de novo cases; very poor prognosis in secondary AML cases
Cytogenetics may be overlooked; often as a sole anomaly
Hybrid/Mutated Gene variable breakpoints on both genes
Abnormal Protein N-term -- AT hook and DNA methyltransferase from MLL fused to the 192 C-term amino acids from AF9 (as breakpoints are variable, this is only an exemple)


Implication of prior treatment with drug combinations including inhibitors of topoisomerase II in therapy-related monocytic leukemia with a 9;11 translocation.
Albain KS, Le Beau MM, Ullirsch R, Schumacher H
Genes, chromosomes & cancer. 1990 ; 2 (1) : 53-58.
PMID 2177642
Molecular basis of 11q23 rearrangements in hematopoietic malignant proliferations.
Bernard OA, Berger R
Genes, chromosomes & cancer. 1995 ; 13 (2) : 75-85.
PMID 7542910
Identification of MLL and chimeric MLL gene products involved in 11q23 translocation and possible mechanisms of leukemogenesis by MLL truncation.
Joh T, Kagami Y, Yamamoto K, Segawa T, Takizawa J, Takahashi T, Ueda R, Seto M
Oncogene. 1996 ; 13 (9) : 1945-1953.
PMID 8934541
11q23 rearrangements in acute leukemia.
Rubnitz JE, Behm FG, Downing JR
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 1996 ; 10 (1) : 74-82.
PMID 8558942
Chromosome abnormalities in leukaemia: the 11q23 paradigm.
Young BD, Saha V
Cancer surveys. 1996 ; 28 : 225-245.
PMID 8977038


This paper should be referenced as such :
Huret, JL
AF9 (ALL1 fused gene from chromosome 9)
Atlas Genet Cytogenet Oncol Haematol. 1997;1(2):58-58.
Free journal version : [ pdf ]   [ DOI ]
On line version :

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 7 ]
  11q23 rearrangements (KMT2A) in de novo childhood acute myeloid leukemia
11q23 rearrangements (KMT2A) in leukaemia
11q23 rearrangements (KMT2A) in therapy related leukaemias
del(9p) in Acute Lymphoblastic Leukemia
Infant leukaemias::Congenital leukaemias::Neonatal leukaemias
t(9;11)(p21;q23) KMT2A/MLLT3
t(11;16)(q23;p13.3) KMT2A/CREBBP

External links

HGNC (Hugo)MLLT3   7136
Entrez_Gene (NCBI)MLLT3  4300  myeloid/lymphoid or mixed-lineage leukemia; translocated to, 3
AliasesAF9; YEATS3
GeneCards (Weizmann)MLLT3
Ensembl hg19 (Hinxton)ENSG00000171843 [Gene_View]  chr9:20341663-20621986 [Contig_View]  MLLT3 [Vega]
Ensembl hg38 (Hinxton)ENSG00000171843 [Gene_View]  chr9:20341663-20621986 [Contig_View]  MLLT3 [Vega]
ICGC DataPortalENSG00000171843
TCGA cBioPortalMLLT3
Genatlas (Paris)MLLT3
SOURCE (Princeton)MLLT3
Genetics Home Reference (NIH)MLLT3
Genomic and cartography
GoldenPath hg19 (UCSC)MLLT3  -     chr9:20341663-20621986 -  9p22   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)MLLT3  -     9p22   [Description]    (hg38-Dec_2013)
EnsemblMLLT3 - 9p22 [CytoView hg19]  MLLT3 - 9p22 [CytoView hg38]
Mapping of homologs : NCBIMLLT3 [Mapview hg19]  MLLT3 [Mapview hg38]
Gene and transcription
Genbank (Entrez)AK128222 AK225957 AK297587 AK301474 AK312914
RefSeq transcript (Entrez)NM_001286691 NM_004529
RefSeq genomic (Entrez)NC_000009 NC_018920 NT_008413 NW_004929342
Consensus coding sequences : CCDS (NCBI)MLLT3
Cluster EST : UnigeneHs.591085 [ NCBI ]
CGAP (NCI)Hs.591085
Alternative Splicing GalleryENSG00000171843
Gene ExpressionMLLT3 [ NCBI-GEO ]   MLLT3 [ EBI - ARRAY_EXPRESS ]   MLLT3 [ SEEK ]   MLLT3 [ MEM ]
Gene Expression Viewer (FireBrowse)MLLT3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)4300
GTEX Portal (Tissue expression)MLLT3
Protein : pattern, domain, 3D structure
UniProt/SwissProtP42568   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP42568  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP42568
Splice isoforms : SwissVarP42568
Domaine pattern : Prosite (Expaxy)YEATS (PS51037)   
Domains : Interpro (EBI)YEATS   
Domain families : Pfam (Sanger)YEATS (PF03366)   
Domain families : Pfam (NCBI)pfam03366   
Conserved Domain (NCBI)MLLT3
DMDM Disease mutations4300
Blocks (Seattle)MLLT3
PDB (SRS)2LM0    2MV7    4TMP   
PDB (PDBSum)2LM0    2MV7    4TMP   
PDB (IMB)2LM0    2MV7    4TMP   
PDB (RSDB)2LM0    2MV7    4TMP   
Structural Biology KnowledgeBase2LM0    2MV7    4TMP   
SCOP (Structural Classification of Proteins)2LM0    2MV7    4TMP   
CATH (Classification of proteins structures)2LM0    2MV7    4TMP   
Human Protein AtlasENSG00000171843
Peptide AtlasP42568
IPIIPI01015721   IPI00000033   IPI00644625   IPI00478977   
Protein Interaction databases
IntAct (EBI)P42568
Ontologies - Pathways
Ontology : AmiGOprotein binding  nucleus  transcription, DNA-templated  regulation of transcription, DNA-templated  segment specification  transcription elongation factor complex  anterior/posterior pattern specification  extracellular exosome  negative regulation of canonical Wnt signaling pathway  negative regulation of canonical Wnt signaling pathway  positive regulation of Wnt signaling pathway, planar cell polarity pathway  
Ontology : EGO-EBIprotein binding  nucleus  transcription, DNA-templated  regulation of transcription, DNA-templated  segment specification  transcription elongation factor complex  anterior/posterior pattern specification  extracellular exosome  negative regulation of canonical Wnt signaling pathway  negative regulation of canonical Wnt signaling pathway  positive regulation of Wnt signaling pathway, planar cell polarity pathway  
Pathways : KEGGTranscriptional misregulation in cancer   
REACTOMEP42568 [protein]
REACTOME Pathways112382 [pathway]   112387 [pathway]   674695 [pathway]   75955 [pathway]   
NDEx NetworkMLLT3
Atlas of Cancer Signalling NetworkMLLT3
Wikipedia pathwaysMLLT3
Orthology - Evolution
GeneTree (enSembl)ENSG00000171843
Phylogenetic Trees/Animal Genes : TreeFamMLLT3
Homologs : HomoloGeneMLLT3
Homology/Alignments : Family Browser (UCSC)MLLT3
Gene fusions - Rearrangements
Fusion : MitelmanMLLT3/CISD3 [9p21.3/17q12]  
Fusion : MitelmanMLLT3/IZUMO3 [9p21.3/9p21.3]  [t(9;9)(p21;p21)]  
Fusion : MitelmanMLLT3/SLC28A3 [9p21.3/9q21.32]  [t(9;9)(p21;q21)]  
Fusion : COSMICKMT2A [11q23.3]  -  MLLT3 [9p21.3]  [fusion_1856]  [fusion_1857]  [fusion_1858]  [fusion_1861]  [fusion_1983]  [fusion_1985]  [fusion_1986]  
[fusion_1987]  [fusion_2081]  [fusion_2082]  [fusion_2083]  [fusion_2084]  [fusion_2085]  [fusion_2086]  [fusion_2087]  [fusion_2088]  [fusion_2089]  
Fusion : COSMICMLLT3 [9p21.3]  -  KMT2A [11q23.3]  [fusion_1984]  
Fusion: TCGAMLLT3 9p21.3 CISD3 17q12 BRCA
Fusion: TCGAMLLT3 9p21.3 IZUMO3 9p21.3 GBM
Fusion: TCGAMLLT3 9p21.3 SLC28A3 9q21.32 BRCA
Fusion: TCGAMLL MLLT3 9p21.3 LAML
Fusion : TICdbKMT2A [11q23.3]  -  MLLT3 [9p21.3]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerMLLT3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)MLLT3
Exome Variant ServerMLLT3
ExAC (Exome Aggregation Consortium)MLLT3 (select the gene name)
Genetic variants : HAPMAP4300
Genomic Variants (DGV)MLLT3 [DGVbeta]
DECIPHER (Syndromes)9:20341663-20621986  ENSG00000171843
CONAN: Copy Number AnalysisMLLT3 
ICGC Data PortalMLLT3 
TCGA Data PortalMLLT3 
Broad Tumor PortalMLLT3
OASIS PortalMLLT3 [ Somatic mutations - Copy number]
Cancer Gene: CensusMLLT3 
Somatic Mutations in Cancer : COSMICMLLT3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDMLLT3
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 MLLT3
DgiDB (Drug Gene Interaction Database)MLLT3
DoCM (Curated mutations)MLLT3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)MLLT3 (select a term)
NCG5 (London)MLLT3
Cancer3DMLLT3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Genetic Testing Registry MLLT3
NextProtP42568 [Medical]
Huge Navigator MLLT3 [HugePedia]
snp3D : Map Gene to Disease4300
BioCentury BCIQMLLT3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD4300
Chemical/Pharm GKB GenePA30852
Drug Sensitivity MLLT3
Clinical trialMLLT3
canSAR (ICR)MLLT3 (select the gene name)
PubMed66 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
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 : Wed Apr 12 11:27:28 CEST 2017

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