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TLX3 (T-cell leukemia, homeobox protein 3)

Written2004-03Roderick AF MacLeod, Stefan Nagel
DSMZ-Deutsche Sammlung von, Mikroorganismen und Zellkulturen, Inhoffenstr. 7B, D-38124 Braunschweig, Germany

(Note : for Links provided by Atlas : click)


homeo box 11-like 2
T-cell leukemia, homeobox 3
Alias_symbol (synonym)RNX
Other alias
HGNC (Hugo) TLX3
LocusID (NCBI) 30012
Atlas_Id 398
Location 5q35.1  [Link to chromosome band 5q35]
Location_base_pair Starts at 171309284 and ends at 171312134 bp from pter ( according to hg19-Feb_2009)  [Mapping TLX3.png]
  TLX3 (5q35.1): FISH with BAC clone ctb-45L16 (red) showing a breakpoint signal in the consensus breakpoint region split between der(5) and der(14) partners. Analysis was performed on the pediatric T-ALL cell line HPB-ALL (DSMZ ACC-483) which carries t(5;14)(q35.1;q32.2) as part of a complex 4-way rearrangement involving chromosomes 1 and 16. Normally (in the absence of secondary translocations) the breakpoints on both partners lie closely equidistant to the q-arm telomeres rendering the translocation cryptic and difficult to detect even with chromosome painting.
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
BCL11B (14q32.2) / TLX3 (5q35.1)C2CD5 (12p12.1) / TLX3 (5q35.1)CDK6 (7q21.2) / TLX3 (5q35.1)
STIL (1p33) / TLX3 (5q35.1)TLX3 (5q35.1) / BCL11B (14q32.2)TLX3 (5q35.1) / NKX2-5 (5q35.1)
TLX3 (5q35.1) / RANBP17 (5q35.1)TLX3 (5q35.1) / TLX3 (5q35.1)


Description 3 exons on 2.23 kb
Transcription In a centromeric --> telomeric orientation; 876 bp mRNA (coding)


Description 291 amino acids, 31.8 kDa; contains one homeobox domain (residues 166-221)
Expression Narrowly restricted to brain.
Localisation Probably nuclear
Function Murine Tlx-3 and Tlx-1 together sustain expression of Drg-11, and control development of somatic and visceral relay sensory neurons.
Homology With homeobox genes, especially with those of the NK-like family.

Implicated in

Entity t(5;14)(q35;q32) in T-ALL-->TLX3 - BCL11B
Disease T-cell acute lymphocytic leukemia (T-ALL)
Prognosis TLX3 expression may denote poor prognosis.
Cytogenetics Cryptic translocation detectable by locus specific FISH. t(5;14) may exclude del(1)(p32) SIL-TAL1 fusion.
Hybrid/Mutated Gene 5' TLX3-3' BCL11B on der(14).
Oncogenesis Ectopic expression in T-cells
Entity t(5;14)(q35;q11) in T-ALL --> TLX3 - TCRD
Disease T-cell acute lymphocytic leukemia (T-ALL)
Cytogenetics Apparent variant of t(5;14)
Hybrid/Mutated Gene 5' TLX3-TCRD on der(14)


Note Within the upstream region or within the neighboring gene RanBP17.


HOX11L2 expression defines a clinical subtype of pediatric T-ALL associated with poor prognosis.
Ballerini P, Blaise A, Busson-Le Coniat M, Su XY, Zucman-Rossi J, Adam M, van den Akker J, Perot C, Pellegrino B, Landman-Parker J, Douay L, Berger R, Bernard OA
Blood. 2002 ; 100 (3) : 991-997.
PMID 12130513
t(5;14)/HOX11L2-positive T-cell acute lymphoblastic leukemia. A collaborative study of the Groupe Français de Cytogénétique Hématologique (GFCH).
Berger R, Dastugue N, Busson M, Van Den Akker J, Pérot C, Ballerini P, Hagemeijer A, Michaux L, Charrin C, Pages MP, Mugneret F, Andrieux J, Talmant P, Hélias C, Mauvieux L, Lafage-Pochitaloff M, Mozziconacci MJ, Cornillet-Lefebvre P, Radford I, Asnafi V, Bilhou-Nabera C, Nguyen Khac F, Léonard C, Speleman F, Poppe B, Bastard C, Taviaux S, Quilichini B, Herens C, Grégoire MJ, Cavé H, Groupe Français de Cytogénétique Hématologique (GFCH), Bernard OA
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2003 ; 17 (9) : 1851-1857.
PMID 12970786
A new recurrent and specific cryptic translocation, t(5;14)(q35;q32), is associated with expression of the Hox11L2 gene in T acute lymphoblastic leukemia.
Bernard OA, Busson-LeConiat M, Ballerini P, Mauchauffé M, Della Valle V, Monni R, Nguyen Khac F, Mercher T, Penard-Lacronique V, Pasturaud P, Gressin L, Heilig R, Daniel MT, Lessard M, Berger R
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2001 ; 15 (10) : 1495-1504.
PMID 11587205
Clinical significance of HOX11L2 expression linked to t(5;14)(q35;q32), of HOX11 expression, and of SIL-TAL fusion in childhood T-cell malignancies: results of EORTC studies 58881 and 58951.
Cavé H, Suciu S, Preudhomme C, Poppe B, Robert A, Uyttebroeck A, Malet M, Boutard P, Benoit Y, Mauvieux L, Lutz P, Méchinaud F, Grardel N, Mazingue F, Dupont M, Margueritte G, Pages MP, Bertrand Y, Plouvier E, Brunie G, Bastard C, Plantaz D, Vande Velde I, Hagemeijer A, Speleman F, Lessard M, Otten J, Vilmer E, EORTC-CLG, Dastugue N
Blood. 2004 ; 103 (2) : 442-450.
PMID 14504110
Assignment of the HOX11L2 gene to human chromosome band 5q35.1 and of its murine homolog to mouse chromosome bands 11A4-A5 by in situ hybridization.
Cinti R, Fava M, Sancandi M, Matera I, Ravazzolo R, Ceccherini I
Cytogenetics and cell genetics. 2001 ; 92 (3-4) : 354-355.
PMID 11435716
Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia.
Ferrando AA, Neuberg DS, Staunton J, Loh ML, Huard C, Raimondi SC, Behm FG, Pui CH, Downing JR, Gilliland DG, Lander ES, Golub TR, Look AT
Cancer cell. 2002 ; 1 (1) : 75-87.
PMID 12086890
Disruption of the RanBP17/Hox11L2 region by recombination with the TCRdelta locus in acute lymphoblastic leukemias with t(5;14)(q34;q11).
Hansen-Hagge TE, Schäfer M, Kiyoi H, Morris SW, Whitlock JA, Koch P, Bohlmann I, Mahotka C, Bartram CR, Janssen JW
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2002 ; 16 (11) : 2205-2212.
PMID 12399963
Assignment of the human homeobox 11-like 2 gene (HOX11L2) to chromosome 5q34-->q35 by radiation hybrid mapping.
Lee-Kirsch MA, Engel K, Paditz E, Rösen-Wolff A, Lee YA, Gahr M
Cytogenetics and cell genetics. 2001 ; 92 (3-4) : page 358.
PMID 11435718
Activation of HOX11L2 by juxtaposition with 3'-BCL11B in an acute lymphoblastic leukemia cell line (HPB-ALL) with t(5;14)(q35;q32.2).
MacLeod RA, Nagel S, Kaufmann M, Janssen JW, Drexler HG
Genes, chromosomes & cancer. 2003 ; 37 (1) : 84-91.
PMID 12661009
High incidence of Hox11L2 expression in children with T-ALL.
Mauvieux L, Leymarie V, Helias C, Perrusson N, Falkenrodt A, Lioure B, Lutz P, Lessard M
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2002 ; 16 (12) : 2417-2422.
PMID 12454747
The cardiac homeobox gene NKX2-5 is deregulated by juxtaposition with BCL11B in pediatric T-ALL cell lines via a novel t(5;14)(q35.1;q32.2).
Nagel S, Kaufmann M, Drexler HG, MacLeod RA
Cancer research. 2003 ; 63 (17) : 5329-5334.
PMID 14500364


This paper should be referenced as such :
MacLeod, RAF ; Nagel, S
TLX3 (T-cell leukemia, homeobox protein 3)
Atlas Genet Cytogenet Oncol Haematol. 2004;8(2):69-71.
Free journal version : [ pdf ]   [ DOI ]
On line version :

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 12 ]
  NUP214/ABL1 fusion gene on amplified episomes
Pediatric T-Cell Acute Lymphoblastic Leukemia
t(5;7)(q35;q21) TLX3/CDK6
t(5;14)(q35;q11) RANBP17 (or TLX3)/TRD
t(5;14)(q35;q32) BCL11B/TLX3
t(5;14)(q35;q32.2) BCL11B/TLX3 and NKX2-5
t(7;12)(q34;p13) TRB/CCND2::t(12;14)(p13;q11) TRA or TRD/CCND2
t(7;19)(q34;p13) TRB/LYL1
T-lineage acute lymphoblastic leukemia (T-ALL)
t(5;7)(q35;q21) CDK6/TLX3
t(5;14)(q35;q11) TRD/TLX3
t(5;14)(q35;q32) TLX3/BCL11B

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(5;5)(q35;q35) TLX3/RANBP17

External links

HGNC (Hugo)TLX3   13532
Entrez_Gene (NCBI)TLX3  30012  T cell leukemia homeobox 3
AliasesHOX11L2; RNX
GeneCards (Weizmann)TLX3
Ensembl hg19 (Hinxton)ENSG00000164438 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000164438 [Gene_View]  ENSG00000164438 [Sequence]  chr5:171309284-171312134 [Contig_View]  TLX3 [Vega]
ICGC DataPortalENSG00000164438
TCGA cBioPortalTLX3
AceView (NCBI)TLX3
Genatlas (Paris)TLX3
SOURCE (Princeton)TLX3
Genetics Home Reference (NIH)TLX3
Genomic and cartography
GoldenPath hg38 (UCSC)TLX3  -     chr5:171309284-171312134 +  5q35.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)TLX3  -     5q35.1   [Description]    (hg19-Feb_2009)
EnsemblTLX3 - 5q35.1 [CytoView hg19]  TLX3 - 5q35.1 [CytoView hg38]
Mapping of homologs : NCBITLX3 [Mapview hg19]  TLX3 [Mapview hg38]
Gene and transcription
Genbank (Entrez)BC017291
RefSeq transcript (Entrez)NM_021025
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)TLX3
Cluster EST : UnigeneHs.249125 [ NCBI ]
CGAP (NCI)Hs.249125
Alternative Splicing GalleryENSG00000164438
Gene ExpressionTLX3 [ NCBI-GEO ]   TLX3 [ EBI - ARRAY_EXPRESS ]   TLX3 [ SEEK ]   TLX3 [ MEM ]
Gene Expression Viewer (FireBrowse)TLX3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)30012
GTEX Portal (Tissue expression)TLX3
Human Protein AtlasENSG00000164438-TLX3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO43711   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO43711  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO43711
Splice isoforms : SwissVarO43711
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Homeobox-like    Homeobox_CS    Homeobox_dom    Homeobox_metazoa   
Domain families : Pfam (Sanger)Homeobox (PF00046)   
Domain families : Pfam (NCBI)pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  
Conserved Domain (NCBI)TLX3
DMDM Disease mutations30012
Blocks (Seattle)TLX3
Human Protein Atlas [tissue]ENSG00000164438-TLX3 [tissue]
Peptide AtlasO43711
Protein Interaction databases
IntAct (EBI)O43711
Ontologies - Pathways
Ontology : AmiGOneuron migration  regulation of respiratory gaseous exchange by neurological system process  protein binding  nucleoplasm  regulation of transcription, DNA-templated  central nervous system development  respiratory gaseous exchange  sequence-specific DNA binding  negative regulation of neuron differentiation  neuron fate specification  
Ontology : EGO-EBIneuron migration  regulation of respiratory gaseous exchange by neurological system process  protein binding  nucleoplasm  regulation of transcription, DNA-templated  central nervous system development  respiratory gaseous exchange  sequence-specific DNA binding  negative regulation of neuron differentiation  neuron fate specification  
NDEx NetworkTLX3
Atlas of Cancer Signalling NetworkTLX3
Wikipedia pathwaysTLX3
Orthology - Evolution
GeneTree (enSembl)ENSG00000164438
Phylogenetic Trees/Animal Genes : TreeFamTLX3
Homologs : HomoloGeneTLX3
Homology/Alignments : Family Browser (UCSC)TLX3
Gene fusions - Rearrangements
Fusion : MitelmanBCL11B/TLX3 [14q32.2/5q35.1]  [t(5;14)(q35;q32)]  
Fusion : MitelmanTLX3/RANBP17 [5q35.1/5q35.1]  [t(5;5)(q35;q35)]  
Fusion : MitelmanTRD/TLX3 [-/5q35.1]  [t(5;14)(q35;q11)]  
Fusion : QuiverTLX3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTLX3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TLX3
Exome Variant ServerTLX3
ExAC (Exome Aggregation Consortium)ENSG00000164438
GNOMAD BrowserENSG00000164438
Genetic variants : HAPMAP30012
Genomic Variants (DGV)TLX3 [DGVbeta]
DECIPHERTLX3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisTLX3 
ICGC Data PortalTLX3 
TCGA Data PortalTLX3 
Broad Tumor PortalTLX3
OASIS PortalTLX3 [ Somatic mutations - Copy number]
Cancer Gene: CensusTLX3 
Somatic Mutations in Cancer : COSMICTLX3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDTLX3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch TLX3
DgiDB (Drug Gene Interaction Database)TLX3
DoCM (Curated mutations)TLX3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)TLX3 (select a term)
NCG5 (London)TLX3
Cancer3DTLX3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Genetic Testing Registry TLX3
NextProtO43711 [Medical]
Target ValidationTLX3
Huge Navigator TLX3 [HugePedia]
snp3D : Map Gene to Disease30012
BioCentury BCIQTLX3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD30012
Chemical/Pharm GKB GenePA37797
Clinical trialTLX3
canSAR (ICR)TLX3 (select the gene name)
PubMed33 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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indexed on : Mon Jul 16 10:02:39 CEST 2018

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