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CDX2 (caudal-related homeobox 2)

Written2000-04Nick CP Cross
Wessex Regional Genetics Laboratory Salisbury District Hospital Salisbury, SP2 8BJ, UK

(Note : for Links provided by Atlas : click)

Identity

Other namesCDX3
HGNC (Hugo) CDX2
LocusID (NCBI) 1045
Atlas_Id 326
Location 13q12.2  [Link to chromosome band 13q12]
Location_base_pair Starts at 28536205 and ends at 28543505 bp from pter ( according to hg19-Feb_2009)  [Mapping CDX2.png]
Local_order IPF1-CDX2- FLT3 -FLT1
 
  CDX2 (13q12) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics.
Fusion genes
(updated 2016)
CDX2 (13q12.2) / ETV6 (12p13.2)ETV6 (12p13.2) / CDX2 (13q12.2)

DNA/RNA

Description Three exons transcribed from telomere to centromere.

Protein

Description 311 amino acid protein of MW 33kDa. Class I homeobox gene related to Drosophila caudal.
Expression Nuclear protein normally expressed almost exclusively in the intestine, where it plays a role in the proliferation and differentiation of intestinal epithelial cells.

Mutations

Somatic Found to be mutated in rare cases of colorectal carcinoma

Implicated in

Note
Entity t(12;13)(p13;q12) acute myeloid leukemia --> ETV6/ CDX2
Abnormal Protein Fusion of ETV6 exon 2 to CDX2 exon 2. The predicted protein contains the N-terminal region of ETV6 38 fused to the entire homeobox of CDX2. The single case described that harbours this fusion also expressed normal CDX2, which is not normally expressed in haemopoietic cells.
  

Bibliography

Fusion of ETV6 to the caudal-related homeobox gene CDX2 in acute myeloid leukemia with the t(12;13)(p13;q12).
Chase A, Reiter A, Burci L, Cazzaniga G, Biondi A, Pickard J, Roberts IA, Goldman JM, Cross NC
Blood. 1999 ; 93 (3) : 1025-1031.
PMID 9920852
 
Cloning and chromosome assignment of the human CDX2 gene.
Drummond F, Putt W, Fox M, Edwards YH
Annals of human genetics. 1997 ; 61 (Pt 5) : 393-400.
PMID 9459001
 
CDX2, a human homologue of Drosophila caudal, is mutated in both alleles in a replication error positive colorectal cancer.
Wicking C, Simms LA, Evans T, Walsh M, Chawengsaksophak K, Beck F, Chenevix-Trench G, Young J, Jass J, Leggett B, Wainwright B
Oncogene. 1998 ; 17 (5) : 657-659.
PMID 9704932
 
CDX2 is mutated in a colorectal cancer with normal APC/beta-catenin signaling.
da Costa LT, He TC, Yu J, Sparks AB, Morin PJ, Polyak K, Laken S, Vogelstein B, Kinzler KW
Oncogene. 1999 ; 18 (35) : 5010-5014.
PMID 10490837
 

Citation

This paper should be referenced as such :
Cross, NCP
CDX2 (caudal-related homeobox 2)
Atlas Genet Cytogenet Oncol Haematol. 2000;4(2):60-61.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/CDX2ID326.html


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  12p rearrangements in CLL
t(12;13)(p12;q12-14) ETV6/CDX2
t(12;13)(p13;q12) ETV6/FLT3

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 0 ]
  Esophagus: Barrett's esophagus, dysplasia and adenocarcinoma

External links

Nomenclature
HGNC (Hugo)CDX2   1806
Cards
AtlasCDX2ID326
Entrez_Gene (NCBI)CDX2  1045  caudal type homeobox 2
AliasesCDX-3; CDX2/AS; CDX3
GeneCards (Weizmann)CDX2
Ensembl hg19 (Hinxton)ENSG00000165556 [Gene_View]  chr13:28536205-28543505 [Contig_View]  CDX2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000165556 [Gene_View]  chr13:28536205-28543505 [Contig_View]  CDX2 [Vega]
ICGC DataPortalENSG00000165556
TCGA cBioPortalCDX2
AceView (NCBI)CDX2
Genatlas (Paris)CDX2
WikiGenes1045
SOURCE (Princeton)CDX2
Genomic and cartography
GoldenPath hg19 (UCSC)CDX2  -     chr13:28536205-28543505 -  13q12.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)CDX2  -     13q12.2   [Description]    (hg38-Dec_2013)
EnsemblCDX2 - 13q12.2 [CytoView hg19]  CDX2 - 13q12.2 [CytoView hg38]
Mapping of homologs : NCBICDX2 [Mapview hg19]  CDX2 [Mapview hg38]
OMIM600297   
Gene and transcription
Genbank (Entrez)BC014461 BI085425 DQ893626 EU176674 KJ081251
RefSeq transcript (Entrez)NM_001265
RefSeq genomic (Entrez)NC_000013 NC_018924 NT_024524 NW_004929388
Consensus coding sequences : CCDS (NCBI)CDX2
Cluster EST : UnigeneHs.740844 [ NCBI ]
CGAP (NCI)Hs.740844
Alternative Splicing GalleryENSG00000165556
Gene ExpressionCDX2 [ NCBI-GEO ]   CDX2 [ EBI - ARRAY_EXPRESS ]   CDX2 [ SEEK ]   CDX2 [ MEM ]
Gene Expression Viewer (FireBrowse)CDX2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)1045
GTEX Portal (Tissue expression)CDX2
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ99626 (Uniprot)
NextProtQ99626  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ99626
Splice isoforms : SwissVarQ99626 (Swissvar)
PhosPhoSitePlusQ99626
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Caudal_activation_dom    Homeobox_CS    Homeobox_dom    Homeobox_metazoa    Homeodomain-like    HTH_motif   
Domain families : Pfam (Sanger)Caudal_act (PF04731)    Homeobox (PF00046)   
Domain families : Pfam (NCBI)pfam04731    pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  
DMDM Disease mutations1045
Blocks (Seattle)CDX2
SuperfamilyQ99626
Human Protein AtlasENSG00000165556
Peptide AtlasQ99626
HPRD02622
IPIIPI00016928   IPI01024878   
Protein Interaction databases
DIP (DOE-UCLA)Q99626
IntAct (EBI)Q99626
FunCoupENSG00000165556
BioGRIDCDX2
STRING (EMBL)CDX2
ZODIACCDX2
Ontologies - Pathways
QuickGOQ99626
Ontology : AmiGOnegative regulation of transcription from RNA polymerase II promoter  condensed nuclear chromosome  RNA polymerase II distal enhancer sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  blood vessel development  trophectodermal cell differentiation  transcription factor activity, sequence-specific DNA binding  transcription corepressor activity  nucleus  nucleoplasm  transcription from RNA polymerase II promoter  positive regulation of cell proliferation  endosome to lysosome transport  organ morphogenesis  anterior/posterior axis specification  regulation of somitogenesis  transcriptional repressor complex  cell differentiation  somatic stem cell population maintenance  establishment or maintenance of epithelial cell apical/basal polarity  positive regulation of cell differentiation  positive regulation of transcription, DNA-templated  intestinal epithelial cell differentiation  labyrinthine layer development  
Ontology : EGO-EBInegative regulation of transcription from RNA polymerase II promoter  condensed nuclear chromosome  RNA polymerase II distal enhancer sequence-specific DNA binding  transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding  blood vessel development  trophectodermal cell differentiation  transcription factor activity, sequence-specific DNA binding  transcription corepressor activity  nucleus  nucleoplasm  transcription from RNA polymerase II promoter  positive regulation of cell proliferation  endosome to lysosome transport  organ morphogenesis  anterior/posterior axis specification  regulation of somitogenesis  transcriptional repressor complex  cell differentiation  somatic stem cell population maintenance  establishment or maintenance of epithelial cell apical/basal polarity  positive regulation of cell differentiation  positive regulation of transcription, DNA-templated  intestinal epithelial cell differentiation  labyrinthine layer development  
REACTOMEQ99626 [protein]
REACTOME PathwaysR-HSA-381771 Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) [pathway]
NDEx NetworkCDX2
Atlas of Cancer Signalling NetworkCDX2
Wikipedia pathwaysCDX2
Orthology - Evolution
OrthoDB1045
GeneTree (enSembl)ENSG00000165556
Phylogenetic Trees/Animal Genes : TreeFamCDX2
Homologs : HomoloGeneCDX2
Homology/Alignments : Family Browser (UCSC)CDX2
Gene fusions - Rearrangements
Fusion : MitelmanETV6/CDX2 [12p13.2/13q12.2]  [t(12;13)(p13;q12)]  
Fusion : TICdbETV6 [12p13.2]  -  CDX2 [13q12.2]
Polymorphisms : SNP, variants
NCBI Variation ViewerCDX2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)CDX2
dbVarCDX2
ClinVarCDX2
1000_GenomesCDX2 
Exome Variant ServerCDX2
ExAC (Exome Aggregation Consortium)CDX2 (select the gene name)
Genetic variants : HAPMAP1045
Genomic Variants (DGV)CDX2 [DGVbeta]
Mutations
ICGC Data PortalCDX2 
TCGA Data PortalCDX2 
Broad Tumor PortalCDX2
OASIS PortalCDX2 [ Somatic mutations - Copy number]
Cancer Gene: CensusCDX2 
Somatic Mutations in Cancer : COSMICCDX2 
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 CDX2
DgiDB (Drug Gene Interaction Database)CDX2
DoCM (Curated mutations)CDX2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)CDX2 (select a term)
intoGenCDX2
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)13:28536205-28543505  ENSG00000165556
CONAN: Copy Number AnalysisCDX2 
Mutations and Diseases : HGMDCDX2
OMIM600297   
MedgenCDX2
Genetic Testing Registry CDX2
NextProtQ99626 [Medical]
TSGene1045
GENETestsCDX2
Huge Navigator CDX2 [HugePedia]
snp3D : Map Gene to Disease1045
BioCentury BCIQCDX2
ClinGenCDX2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD1045
Chemical/Pharm GKB GenePA26352
Clinical trialCDX2
Miscellaneous
canSAR (ICR)CDX2 (select the gene name)
Probes
Litterature
PubMed249 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineCDX2
EVEXCDX2
GoPubMedCDX2
iHOPCDX2
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Oct 1 16:34:35 CEST 2016

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