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MNX1 (homeo box HB9)

Written2003-12Anne RM von Bergh, H Berna Beverloo
Afdeling Klinische Genetica, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands

(Note : for Links provided by Atlas : click)


Alias (NCBI)HLXB9 (homeo box HB9)
HGNC (Hugo) MNX1
HGNC Alias symbHB9
HGNC Previous nameHLXB9
HGNC Previous namehomeo box HB9
 homeobox HB9
LocusID (NCBI) 3110
Atlas_Id 393
Location 7q36.3  [Link to chromosome band 7q36]
Location_base_pair Starts at 157004854 and ends at 157010663 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping MNX1.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)
ETV6 (12p13.2)::MNX1 (7q36.3)MNX1 (7q36.3)::ETV6 (12p13.2)MNX1 (7q36.3)::MYB (6q23.3)
MNX1 (7q36.3)::TRPM3 (9q21.12)MYB (6q23.3)::MNX1 (7q36.3)
Note telomeric to c7orf3 and SHH


Description 3 exons stretched over an area of 5-6 kb.
Transcription In a telomere to centromere direction; 2061 bp mRNA, 1206 bp open reading frame.


Description The homeobox gene HLXB9 encodes the nuclear protein HB9. The protein contains a polyalanine repeat region and a homeobox domain.
Expression Expressed in lymphoid and pancreatic tissues. Highly expressed in CD34+ bone marrow cells, down regulated upon differentiation.
Localisation Nuclear
Function Putative transcription factor.
Homology Related to Mnr2.


Note Mutations in HLXB9 cause an autosomal dominant form of sacral agenesis, known as Currarino syndrome.

Implicated in

Entity - associated infant acute myeloid leukemia (AML)
Prognosis Prognosis probably poor: median survival is 13 months.
Cytogenetics t(7;12)(q36;p13), but not always visible by chromosome banding; may also be misdiagnosed as .
Hybrid/Mutated Gene 5' HLXB9 _ 3' ETV6
Fig. 3. Schematic representation of the HLXB9 and ETV6 proteins and the putative HLXB9-ETV6 chimeric protein resulting from the t(7;12)(q36;p13). Arrow, the observed breakpoints. nt numbers (cDNA level) are given above each protein, and amino acid numbers are given in bold type below each protein.
Abnormal Protein N-term HLXB9, including its polyalanine repeat, is fused to a large C-term part of the ETV6 protein including its HLH domain and ETS domain; the homeobox domain of HLXB9 is not retained in the fusion protein; the reciprocal transcript is not expressed.

To be noted

The t(7;12) is heterogeneous at the molecular level. The formation of a fusion gene has only been described in 2 cases and may not be the only mechanism by which HLXB9 is involved in t(7;12)-associated leukaemias. Additional 7q36 genes may also be involved.


Fusion of the homeobox gene HLXB9 and the ETV6 gene in infant acute myeloid leukemias with the t(7;12)(q36;p13).
Beverloo HB, Panagopoulos I, Isaksson M, van Wering E, van Drunen E, de Klein A, Johansson B, Slater R
Cancer research. 2001 ; 61 (14) : 5374-5377.
PMID 11454678
A novel human homeobox gene distantly related to proboscipedia is expressed in lymphoid and pancreatic tissues.
Harrison KA, Druey KM, Deguchi Y, Tuscano JM, Kehrl JH
The Journal of biological chemistry. 1994 ; 269 (31) : 19968-19975.
PMID 7914194
A homeobox gene, HLXB9, is the major locus for dominantly inherited sacral agenesis.
Ross AJ, Ruiz-Perez V, Wang Y, Hagan DM, Scherer S, Lynch SA, Lindsay S, Custard E, Belloni E, Wilson DI, Wadey R, Goodman F, Orstavik KH, Monclair T, Robson S, Reardon W, Burn J, Scambler P, Strachan T
Nature genetics. 1998 ; 20 (4) : 358-361.
PMID 9843207


This paper should be referenced as such :
von Bergh, ARM ; Beverloo, HB
HLXB9 (homeo box HB9)
Atlas Genet Cytogenet Oncol Haematol. 2004;8(1):12-13.
Free journal version : [ pdf ]   [ DOI ]

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
  t(7;12)(q36;p13) MNX1::ETV6
t(7;12)(q34;p13) TRB::CCND2::t(12;14)(p13;q11) TRA or TRD::CCND2
t(6;7)(q23;q36) MYB::MNX1

Other Cancer prone implicated (Data extracted from papers in the Atlas) [ 1 ]
  Currarino syndrome

External links


HGNC (Hugo)MNX1   4979
Atlas Explorer : (Salamanque)MNX1
Entrez_Gene (NCBI)MNX1    motor neuron and pancreas homeobox 1
AliasesHB9; HLXB9; HOXHB9; SCRA1
GeneCards (Weizmann)MNX1
Ensembl hg19 (Hinxton)ENSG00000130675 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000130675 [Gene_View]  ENSG00000130675 [Sequence]  chr7:157004854-157010663 [Contig_View]  MNX1 [Vega]
ICGC DataPortalENSG00000130675
TCGA cBioPortalMNX1
AceView (NCBI)MNX1
Genatlas (Paris)MNX1
SOURCE (Princeton)MNX1
Genetics Home Reference (NIH)MNX1
Genomic and cartography
GoldenPath hg38 (UCSC)MNX1  -     chr7:157004854-157010663 -  7q36.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)MNX1  -     7q36.3   [Description]    (hg19-Feb_2009)
GoldenPathMNX1 - 7q36.3 [CytoView hg19]  MNX1 - 7q36.3 [CytoView hg38]
Genome Data Viewer NCBIMNX1 [Mapview hg19]  
OMIM142994   176450   
Gene and transcription
Genbank (Entrez)AF107457 AY927457 AY927459 AY927460 AY927461
RefSeq transcript (Entrez)NM_001165255 NM_005515
Consensus coding sequences : CCDS (NCBI)MNX1
Gene ExpressionMNX1 [ NCBI-GEO ]   MNX1 [ EBI - ARRAY_EXPRESS ]   MNX1 [ SEEK ]   MNX1 [ MEM ]
Gene Expression Viewer (FireBrowse)MNX1 [ Firebrowse - Broad ]
GenevisibleExpression of MNX1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3110
GTEX Portal (Tissue expression)MNX1
Human Protein AtlasENSG00000130675-MNX1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP50219   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP50219  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP50219
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)   
Domains : Interpro (EBI)Homeobox-like_sf    Homeobox_CS    Homeobox_dom    Homeobox_metazoa    MNX1/Ceh-12   
Domain families : Pfam (Sanger)Homeodomain (PF00046)   
Domain families : Pfam (NCBI)pfam00046   
Domain families : Smart (EMBL)HOX (SM00389)  
Conserved Domain (NCBI)MNX1
AlphaFold pdb e-kbP50219   
Human Protein Atlas [tissue]ENSG00000130675-MNX1 [tissue]
Protein Interaction databases
IntAct (EBI)P50219
Ontologies - Pathways
Ontology : AmiGOchromatin  DNA-binding transcription factor activity, RNA polymerase II-specific  nucleus  nucleoplasm  nucleolus  cytosol  regulation of transcription by RNA polymerase II  central nervous system development  spinal cord motor neuron cell fate specification  endocrine pancreas development  neuron projection morphogenesis  sequence-specific double-stranded DNA binding  sequence-specific double-stranded DNA binding  
Ontology : EGO-EBIchromatin  DNA-binding transcription factor activity, RNA polymerase II-specific  nucleus  nucleoplasm  nucleolus  cytosol  regulation of transcription by RNA polymerase II  central nervous system development  spinal cord motor neuron cell fate specification  endocrine pancreas development  neuron projection morphogenesis  sequence-specific double-stranded DNA binding  sequence-specific double-stranded DNA binding  
NDEx NetworkMNX1
Atlas of Cancer Signalling NetworkMNX1
Wikipedia pathwaysMNX1
Orthology - Evolution
GeneTree (enSembl)ENSG00000130675
Phylogenetic Trees/Animal Genes : TreeFamMNX1
Homologs : HomoloGeneMNX1
Homology/Alignments : Family Browser (UCSC)MNX1
Gene fusions - Rearrangements
Fusion : MitelmanMNX1::ETV6 [7q36.3/12p13.2]  
Fusion : MitelmanMYB::MNX1 [6q23.3/7q36.3]  
Fusion : FusionHubETV6--MNX1    MLL3--MNX1    MNX1--ETV6    MNX1--MYB   
Fusion : QuiverMNX1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerMNX1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)MNX1
Exome Variant ServerMNX1
GNOMAD BrowserENSG00000130675
Varsome BrowserMNX1
ACMGMNX1 variants
Genomic Variants (DGV)MNX1 [DGVbeta]
DECIPHERMNX1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisMNX1 
ICGC Data PortalMNX1 
TCGA Data PortalMNX1 
Broad Tumor PortalMNX1
OASIS PortalMNX1 [ Somatic mutations - Copy number]
Cancer Gene: CensusMNX1 
Somatic Mutations in Cancer : COSMICMNX1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DMNX1
Mutations and Diseases : HGMDMNX1
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
DgiDB (Drug Gene Interaction Database)MNX1
DoCM (Curated mutations)MNX1
CIViC (Clinical Interpretations of Variants in Cancer)MNX1
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
OMIM142994    176450   
Genetic Testing Registry MNX1
NextProtP50219 [Medical]
Target ValidationMNX1
Huge Navigator MNX1 [HugePedia]
ClinGenMNX1 (curated)
Clinical trials, drugs, therapy
Protein Interactions : CTDMNX1
Pharm GKB GenePA162396041
Clinical trialMNX1
DataMed IndexMNX1
PubMed59 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 : Thu Jan 20 14:08:56 CET 2022

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