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HOXA9 (homeobox A9)

Written1998-01Jean-loup Huret
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)HOX1G (homeobox-1G);
HGNC (Hugo) HOXA9
HGNC Previous nameHOX1G
 HOX1
HGNC Previous namehomeo box A9
LocusID (NCBI) 3205
Atlas_Id 61
Location 7p15.2  [Link to chromosome band 7p15]
Location_base_pair Starts at 27162438 and ends at 27165537 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping HOXA9.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
C2CD5 (12p12.1)::HOXA9 (7p15.2)GATA2 (3q21.3)::HOXA9 (7p15.2)HOXA9 (7p15.2)::MSI2 (17q22)
HOXA9 (7p15.2)::NUP98 (11p15.4)MED12 (Xq13.1)::HOXA9 (7p15.2)MSI2 (17q22)::HOXA9 (7p15.2)
NUP98 (11p15.4)::HOXA9 (7p15.2)

Protein

Description 129 amino acids; DNA binding domain (homeobox) in C-term
Localisation nuclear
Function sequence specific transcription factor; role during embryonic development (patterning); HOX genes are also expressed in adult tissues, including blood cells; probable role in blood cell differenciation
Homology with class 1 homeodomain proteins

Implicated in

Note
  
Entity /AML --> NUP98- HOXA9
Disease M2-M4 AML mostly; occasionally: CML-like cases
Prognosis mean survival: 15 mths
Cytogenetics sole anomaly most often
Hybrid/Mutated Gene 5' NUP98 - 3' HOXA9
Abnormal Protein fuses the GLFG repeat domains of NUP98 to the HOXA9 homeobox
  

Breakpoints

 

Bibliography

The t(7;11)(p15;p15) translocation in acute myeloid leukaemia fuses the genes for nucleoporin NUP98 and class I homeoprotein HOXA9.
Borrow J, Shearman AM, Stanton VP Jr, Becher R, Collins T, Williams AJ, Dubé I, Katz F, Kwong YL, Morris C, Ohyashiki K, Toyama K, Rowley J, Housman DE
Nature genetics. 1996 ; 12 (2) : 159-167.
PMID 8563754
 
Mice bearing a targeted interruption of the homeobox gene HOXA9 have defects in myeloid, erythroid, and lymphoid hematopoiesis.
Lawrence HJ, Helgason CD, Sauvageau G, Fong S, Izon DJ, Humphries RK, Largman C
Blood. 1997 ; 89 (6) : 1922-1930.
PMID 9058712
 
Fusion of the nucleoporin gene NUP98 to HOXA9 by the chromosome translocation t(7;11)(p15;p15) in human myeloid leukaemia.
Nakamura T, Largaespada DA, Lee MP, Johnson LA, Ohyashiki K, Toyama K, Chen SJ, Willman CL, Chen IM, Feinberg AP, Jenkins NA, Copeland NG, Shaughnessy JD Jr
Nature genetics. 1996 ; 12 (2) : 154-158.
PMID 8563753
 

Citation

This paper should be referenced as such :
Jean-Loup Huret
HOXA9 (homeobox A9)
Atlas Genet Cytogenet Oncol Haematol. 1998;2(1):6-6.
Free journal version : [ pdf ]   [ DOI ]


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 25 ]
  inv(11)(p15q23) NUP98::KMT2A
Pediatric T-Cell Acute Lymphoblastic Leukemia
r(8)
t(1;11)(q24;p15) NUP98::PRRX1
t(2;11)(p21;q23) KMT2A::?
t(4;11)(q21;q23) KMT2A::AFF1
t(4;11)(q21;p15) NUP98::RAP1GDS1
t(6;11)(q27;q23) KMT2A::AFDN
t(6;11)(q13;q23) KMT2A::SMAP1
t(7;11)(p15;p15) NUP98::HOXA9
t(7;14)(p15;q11) TRD::HOXA10
t(7;17)(p15;q23) MSI2::HOXA9
t(X;11)(q28;p15) NUP98::HMGB3
t(10;11)(q22;q23) KMT2A::TET1
t(11;11)(q14;q23) KMT2A::PICALM::inv(11)(q14q23) KMT2A::PICALM
t(11;16)(q23;p13.3) KMT2A::CREBBP
t(11;17)(q23;q21) KMT2A::ACACA
t(11;19)(q23;p13) KMT2A::MYO1F
T-lineage acute lymphoblastic leukemia (T-ALL)
Therapy-Related Hematopoietic Neoplasia
t(3;7)(q21;p15) GATA2::HOXA9
t(5;7)(p13;p15) NIPBL::HOXA9
t(7;7)(p15;q34) TRB::HOXA9
t(7;8)(p15;q23) HOXA9::ANGPT1
t(X;7)(q13;p15) MED12::HOXA9


External links

 

Nomenclature
HGNC (Hugo)HOXA9   5109
Cards
AtlasHOXA9ID61
Entrez_Gene (NCBI)HOXA9    homeobox A9
AliasesABD-B; HOX1; HOX1.7; HOX1G
GeneCards (Weizmann)HOXA9
Ensembl hg19 (Hinxton)ENSG00000078399 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000078399 [Gene_View]  ENSG00000078399 [Sequence]  chr7:27162438-27165537 [Contig_View]  HOXA9 [Vega]
ICGC DataPortalENSG00000078399
TCGA cBioPortalHOXA9
AceView (NCBI)HOXA9
Genatlas (Paris)HOXA9
SOURCE (Princeton)HOXA9
Genetics Home Reference (NIH)HOXA9
Genomic and cartography
GoldenPath hg38 (UCSC)HOXA9  -     chr7:27162438-27165537 -  7p15.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HOXA9  -     7p15.2   [Description]    (hg19-Feb_2009)
GoldenPathHOXA9 - 7p15.2 [CytoView hg19]  HOXA9 - 7p15.2 [CytoView hg38]
ImmunoBaseENSG00000078399
Genome Data Viewer NCBIHOXA9 [Mapview hg19]  
OMIM142956   
Gene and transcription
Genbank (Entrez)AW612618 BC006537 BC010023 BG258601 BT006990
RefSeq transcript (Entrez)NM_152739
Consensus coding sequences : CCDS (NCBI)HOXA9
Gene ExpressionHOXA9 [ NCBI-GEO ]   HOXA9 [ EBI - ARRAY_EXPRESS ]   HOXA9 [ SEEK ]   HOXA9 [ MEM ]
Gene Expression Viewer (FireBrowse)HOXA9 [ Firebrowse - Broad ]
GenevisibleExpression of HOXA9 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3205
GTEX Portal (Tissue expression)HOXA9
Human Protein AtlasENSG00000078399-HOXA9 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP31269   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP31269  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP31269
PhosPhoSitePlusP31269
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Homeobox-like_sf    Homeobox_CS    Homeobox_dom    Homeobox_metazoa    Hox9_activation_N    HXA9/HXB9/HXC9   
Domain families : Pfam (Sanger)Homeodomain (PF00046)    Hox9_act (PF04617)   
Domain families : Pfam (NCBI)pfam00046    pfam04617   
Domain families : Smart (EMBL)HOX (SM00389)  
Conserved Domain (NCBI)HOXA9
SuperfamilyP31269
AlphaFold pdb e-kbP31269   
Human Protein Atlas [tissue]ENSG00000078399-HOXA9 [tissue]
HPRD00844
Protein Interaction databases
DIP (DOE-UCLA)P31269
IntAct (EBI)P31269
BioGRIDHOXA9
STRING (EMBL)HOXA9
ZODIACHOXA9
Ontologies - Pathways
QuickGOP31269
Ontology : AmiGOchromatin  RNA polymerase II cis-regulatory region sequence-specific DNA binding  DNA-binding transcription factor activity, RNA polymerase II-specific  DNA-binding transcription activator activity, RNA polymerase II-specific  DNA-binding transcription factor activity  protein binding  nucleus  nucleus  nucleoplasm  transcription regulator complex  transcription, DNA-templated  regulation of transcription by RNA polymerase II  multicellular organism development  spermatogenesis  single fertilization  male gonad development  anterior/posterior pattern specification  proximal/distal pattern formation  enzyme binding  mammary gland development  embryonic forelimb morphogenesis  endothelial cell activation  negative regulation of myeloid cell differentiation  positive regulation of transcription by RNA polymerase II  embryonic skeletal system morphogenesis  uterus development  definitive hemopoiesis  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 activator activity, RNA polymerase II-specific  DNA-binding transcription factor activity  protein binding  nucleus  nucleus  nucleoplasm  transcription regulator complex  transcription, DNA-templated  regulation of transcription by RNA polymerase II  multicellular organism development  spermatogenesis  single fertilization  male gonad development  anterior/posterior pattern specification  proximal/distal pattern formation  enzyme binding  mammary gland development  embryonic forelimb morphogenesis  endothelial cell activation  negative regulation of myeloid cell differentiation  positive regulation of transcription by RNA polymerase II  embryonic skeletal system morphogenesis  uterus development  definitive hemopoiesis  sequence-specific double-stranded DNA binding  
Pathways : KEGGTranscriptional misregulation in cancer   
NDEx NetworkHOXA9
Atlas of Cancer Signalling NetworkHOXA9
Wikipedia pathwaysHOXA9
Orthology - Evolution
OrthoDB3205
GeneTree (enSembl)ENSG00000078399
Phylogenetic Trees/Animal Genes : TreeFamHOXA9
Homologs : HomoloGeneHOXA9
Homology/Alignments : Family Browser (UCSC)HOXA9
Gene fusions - Rearrangements
Fusion : MitelmanGATA2::HOXA9 [3q21.3/7p15.2]  
Fusion : MitelmanMSI2::HOXA9 [17q22/7p15.2]  
Fusion : MitelmanNUP98::HOXA9 [11p15.4/7p15.2]  
Fusion : QuiverHOXA9
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHOXA9 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HOXA9
dbVarHOXA9
ClinVarHOXA9
MonarchHOXA9
1000_GenomesHOXA9 
Exome Variant ServerHOXA9
GNOMAD BrowserENSG00000078399
Varsome BrowserHOXA9
ACMGHOXA9 variants
VarityP31269
Genomic Variants (DGV)HOXA9 [DGVbeta]
DECIPHERHOXA9 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHOXA9 
Mutations
ICGC Data PortalHOXA9 
TCGA Data PortalHOXA9 
Broad Tumor PortalHOXA9
OASIS PortalHOXA9 [ Somatic mutations - Copy number]
Cancer Gene: CensusHOXA9 
Somatic Mutations in Cancer : COSMICHOXA9  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DHOXA9
Mutations and Diseases : HGMDHOXA9
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaHOXA9
DgiDB (Drug Gene Interaction Database)HOXA9
DoCM (Curated mutations)HOXA9
CIViC (Clinical Interpretations of Variants in Cancer)HOXA9
OncoKBHOXA9
NCG (London)HOXA9
Cancer3DHOXA9
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM142956   
Orphanet
DisGeNETHOXA9
MedgenHOXA9
Genetic Testing Registry HOXA9
NextProtP31269 [Medical]
GENETestsHOXA9
Target ValidationHOXA9
Huge Navigator HOXA9 [HugePedia]
ClinGenHOXA9
Clinical trials, drugs, therapy
MyCancerGenomeHOXA9
Protein Interactions : CTDHOXA9
Pharm GKB GenePA29386
PharosP31269
Clinical trialHOXA9
Miscellaneous
canSAR (ICR)HOXA9
HarmonizomeHOXA9
DataMed IndexHOXA9
Probes
Litterature
PubMed193 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXHOXA9
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 : Fri Oct 8 21:19:41 CEST 2021

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jlhuret@AtlasGeneticsOncology.org.