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Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
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TLX3 (T-cell leukemia, homeobox protein 3)


Other namesRNX
HGNC (Hugo) TLX3
LocusID (NCBI) 30012
Location 5q35.1
Location_base_pair Starts at 170736288 and ends at 170739138 bp from pter ( according to hg19-Feb_2009)  [Mapping]
  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.


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.

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

Leukemias 11q23ChildAMLID1615 11q23ID1030 11q23secondLeukID1131 t1119ELLID1029 t0812q24q22ID2057

External links

HGNC (Hugo)TLX3   13532
Entrez_Gene (NCBI)TLX3  30012  T-cell leukemia homeobox 3
GeneCards (Weizmann)TLX3
Ensembl hg19 (Hinxton)ENSG00000164438 [Gene_View]  chr5:170736288-170739138 [Contig_View]  TLX3 [Vega]
Ensembl hg38 (Hinxton)ENSG00000164438 [Gene_View]  chr5:170736288-170739138 [Contig_View]  TLX3 [Vega]
ICGC DataPortalENSG00000164438
AceView (NCBI)TLX3
Genatlas (Paris)TLX3
SOURCE (Princeton)TLX3
Genomic and cartography
GoldenPath hg19 (UCSC)TLX3  -     chr5:170736288-170739138 +  5q35.1   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)TLX3  -     5q35.1   [Description]    (hg38-Dec_2013)
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 DQ892654 DQ895893 DQ896085
RefSeq transcript (Entrez)NM_021025
RefSeq genomic (Entrez)NC_000005 NC_018916 NT_023133 NW_004929325
Consensus coding sequences : CCDS (NCBI)TLX3
Cluster EST : UnigeneHs.249125 [ NCBI ]
CGAP (NCI)Hs.249125
Alternative Splicing : Fast-db (Paris)GSHG0024461
Alternative Splicing GalleryENSG00000164438
Gene ExpressionTLX3 [ NCBI-GEO ]     TLX3 [ SEEK ]   TLX3 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO43711 (Uniprot)
NextProtO43711  [Medical]
With graphics : InterProO43711
Splice isoforms : SwissVarO43711 (Swissvar)
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Homeobox_CS    Homeobox_dom    Homeobox_metazoa    Homeodomain-like   
Related proteins : CluSTrO43711
Domain families : Pfam (Sanger)Homeobox (PF00046)   
Domain families : Pfam (NCBI)pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  
DMDM Disease mutations30012
Blocks (Seattle)O43711
Human Protein AtlasENSG00000164438
Peptide AtlasO43711
Protein Interaction databases
IntAct (EBI)O43711
Ontologies - Pathways
Ontology : AmiGOneuron migration  regulation of respiratory gaseous exchange by neurological system process  protein binding  nucleus  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  nucleus  regulation of transcription, DNA-templated  central nervous system development  respiratory gaseous exchange  sequence-specific DNA binding  negative regulation of neuron differentiation  neuron fate specification  
Pathways : KEGGTranscriptional misregulation in cancer   
Protein Interaction DatabaseTLX3
DoCM (Curated mutations)TLX3
Wikipedia pathwaysTLX3
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerTLX3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TLX3
Exome Variant ServerTLX3
SNP (GeneSNP Utah)TLX3
Genetic variants : HAPMAPTLX3
Genomic Variants (DGV)TLX3 [DGVbeta]
ICGC Data PortalENSG00000164438 
Somatic Mutations in Cancer : COSMICTLX3 
CONAN: Copy Number AnalysisTLX3 
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
DECIPHER (Syndromes)5:170736288-170739138
Mutations and Diseases : HGMDTLX3
NextProtO43711 [Medical]
Disease Genetic AssociationTLX3
Huge Navigator TLX3 [HugePedia]  TLX3 [HugeCancerGEM]
snp3D : Map Gene to Disease30012
DGIdb (Drug Gene Interaction db)TLX3
General knowledge
Homologs : HomoloGeneTLX3
Homology/Alignments : Family Browser (UCSC)TLX3
Phylogenetic Trees/Animal Genes : TreeFamTLX3
Chemical/Protein Interactions : CTD30012
Chemical/Pharm GKB GenePA37797
Clinical trialTLX3
Cancer Resource (Charite)ENSG00000164438
Other databases
PubMed30 Pubmed reference(s) in Entrez


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
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, Rˆsen-Wolff A, Lee YA, Gahr M
Cytogenetics and cell genetics. 2001 ; 92 (3-4) : page 358.
PMID 11435718
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, Mauchauffˆ© 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
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
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
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, Schˆ§fer 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
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
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
t(5;14)/HOX11L2-positive T-cell acute lymphoblastic leukemia. A collaborative study of the Groupe Franˆßais de Cytogˆ©nˆ©tique Hˆ©matologique (GFCH).
Berger R, Dastugue N, Busson M, Van Den Akker J, Pˆ©rot C, Ballerini P, Hagemeijer A, Michaux L, Charrin C, Pages MP, Mugneret F, Andrieux J, Talmant P, Hˆ©lias C, Mauvieux L, Lafage-Pochitaloff M, Mozziconacci MJ, Cornillet-Lefebvre P, Radford I, Asnafi V, Bilhou-Nabera C, Nguyen Khac F, Lˆ©onard C, Speleman F, Poppe B, Bastard C, Taviaux S, Quilichini B, Herens C, Grˆ©goire MJ, Cavˆ© H, Groupe Franˆßais de Cytogˆ©nˆ©tique Hˆ©matologique (GFCH), Bernard OA
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2003 ; 17 (9) : 1851-1857.
PMID 12970786
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
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.
Cavˆ© H, Suciu S, Preudhomme C, Poppe B, Robert A, Uyttebroeck A, Malet M, Boutard P, Benoit Y, Mauvieux L, Lutz P, Mˆ©chinaud 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
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Written03-2004Roderick AF MacLeod, Stefan Nagel


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 ]

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