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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)

Identity

Alias (NCBI)RNX
HOX11L2
HGNC (Hugo) TLX3
HGNC Alias symbRNX
HGNC Previous nameHOX11L2
HGNC Previous namehomeo box 11-like 2
 T-cell leukemia, homeobox 3
 T-cell leukemia homeobox 3
LocusID (NCBI) 30012
Atlas_Id 398
Location 5q35.1  [Link to chromosome band 5q35]
Location_base_pair Starts at 171309248 and ends at 171312139 bp from pter ( according to GRCh38/hg38-Dec_2013)  [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)

DNA/RNA

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

Protein

 
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

Note
  
Entity 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 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)
  

Breakpoints

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

Bibliography

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
 

Citation

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 ]


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 10 ]
  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;14)(q35;q11) TRD::TLX3


External links

 

Nomenclature
HGNC (Hugo)TLX3   13532
Cards
AtlasTLX3ID398
Entrez_Gene (NCBI)TLX3    T cell leukemia homeobox 3
AliasesHOX11L2; RNX
GeneCards (Weizmann)TLX3
Ensembl hg19 (Hinxton)ENSG00000164438 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000164438 [Gene_View]  ENSG00000164438 [Sequence]  chr5:171309248-171312139 [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  -     chr5:171309248-171312139 +  5q35.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)TLX3  -     5q35.1   [Description]    (hg19-Feb_2009)
GoldenPathTLX3 - 5q35.1 [CytoView hg19]  TLX3 - 5q35.1 [CytoView hg38]
ImmunoBaseENSG00000164438
Genome Data Viewer NCBITLX3 [Mapview hg19]  
OMIM604640   
Gene and transcription
Genbank (Entrez)BC017291
RefSeq transcript (Entrez)NM_021025
Consensus coding sequences : CCDS (NCBI)TLX3
Gene ExpressionTLX3 [ NCBI-GEO ]   TLX3 [ EBI - ARRAY_EXPRESS ]   TLX3 [ SEEK ]   TLX3 [ MEM ]
Gene Expression Viewer (FireBrowse)TLX3 [ Firebrowse - Broad ]
GenevisibleExpression of TLX3 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
PhosPhoSitePlusO43711
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Homeobox-like_sf    Homeobox_CS    Homeobox_dom    Homeobox_metazoa    TLX1/2/3   
Domain families : Pfam (Sanger)Homeodomain (PF00046)   
Domain families : Pfam (NCBI)pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  
Conserved Domain (NCBI)TLX3
SuperfamilyO43711
AlphaFold pdb e-kbO43711   
Human Protein Atlas [tissue]ENSG00000164438-TLX3 [tissue]
HPRD06868
Protein Interaction databases
DIP (DOE-UCLA)O43711
IntAct (EBI)O43711
BioGRIDTLX3
STRING (EMBL)TLX3
ZODIACTLX3
Ontologies - Pathways
QuickGOO43711
Ontology : AmiGOchromatin  RNA polymerase II cis-regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  neuron migration  regulation of respiratory gaseous exchange by nervous system process  protein binding  nucleus  nucleoplasm  regulation of transcription by RNA polymerase II  central nervous system development  respiratory gaseous exchange by respiratory system  negative regulation of neuron differentiation  animal organ development  neuron fate specification  sequence-specific double-stranded DNA binding  
Ontology : EGO-EBIchromatin  RNA polymerase II cis-regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription factor activity, RNA polymerase II-specific  neuron migration  regulation of respiratory gaseous exchange by nervous system process  protein binding  nucleus  nucleoplasm  regulation of transcription by RNA polymerase II  central nervous system development  respiratory gaseous exchange by respiratory system  negative regulation of neuron differentiation  animal organ development  neuron fate specification  sequence-specific double-stranded DNA binding  
Pathways : KEGGTranscriptional misregulation in cancer   
NDEx NetworkTLX3
Atlas of Cancer Signalling NetworkTLX3
Wikipedia pathwaysTLX3
Orthology - Evolution
OrthoDB30012
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]  
Fusion : MitelmanTLX3::RANBP17 [5q35.1/5q35.1]  
Fusion : MitelmanTRD::TLX3 [-/5q35.1]  
Fusion : QuiverTLX3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTLX3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TLX3
dbVarTLX3
ClinVarTLX3
MonarchTLX3
1000_GenomesTLX3 
Exome Variant ServerTLX3
GNOMAD BrowserENSG00000164438
Varsome BrowserTLX3
ACMGTLX3 variants
VarityO43711
Genomic Variants (DGV)TLX3 [DGVbeta]
DECIPHERTLX3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisTLX3 
Mutations
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]  
Somatic Mutations in Cancer : COSMIC3DTLX3
Mutations and Diseases : HGMDTLX3
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaTLX3
DgiDB (Drug Gene Interaction Database)TLX3
DoCM (Curated mutations)TLX3
CIViC (Clinical Interpretations of Variants in Cancer)TLX3
OncoKBTLX3
NCG (London)TLX3
Cancer3DTLX3
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604640   
Orphanet14434   
DisGeNETTLX3
MedgenTLX3
Genetic Testing Registry TLX3
NextProtO43711 [Medical]
GENETestsTLX3
Target ValidationTLX3
Huge Navigator TLX3 [HugePedia]
ClinGenTLX3
Clinical trials, drugs, therapy
MyCancerGenomeTLX3
Protein Interactions : CTDTLX3
Pharm GKB GenePA37797
PharosO43711
Clinical trialTLX3
Miscellaneous
canSAR (ICR)TLX3
HarmonizomeTLX3
DataMed IndexTLX3
Probes
Litterature
PubMed39 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXTLX3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Oct 8 21:29:38 CEST 2021

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