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PAX9 (Paired box gene 9)

Written2005-08Ewan Robson, Jess Whall, Michael Eccles
Developmental Genetics Group, Department of Pathology, University of Otago, PO Box 913,Dunedin 9015, New Zealand

(Note : for Links provided by Atlas : click)


Alias_namespaired box gene 9
Other aliasPaired box homeotic gene 9
HGNC (Hugo) PAX9
LocusID (NCBI) 5083
Atlas_Id 41644
Location 14q13.3  [Link to chromosome band 14q13]
Location_base_pair Starts at 36657568 and ends at 36677806 bp from pter ( according to hg19-Feb_2009)  [Mapping PAX9.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)
PAX9 (14q13.3) / STXBP5L (3q13.33)


Description 4 exons
Transcription 3 alternative splicing isoforms
Pseudogene No


Description 341 amino acids; 36.3 kDa
Expression PAX9 is expressed in developing somites, specifically in the posterior ventrolateral region. These cells undergo an epithelial-mesenchymal transition, gaining increased motile capability as a consequence. Subsequent migration of this population generates the lateral sclerotome, which in turn gives rise to the ribs and neural arches. PAX9 contains a DNA binding paired domain, an octapeptide region and a carboxyl-terminal transactivation domain.
Localisation Nuclear.
Function PAX9 is a transcription factor that regulates the expression of genes involved in mediating cell proliferation, resistance to apoptosis, and cell migration. Mice homozygous for Pax9 mutations die shortly after birth, lacking the thymus, parathyroid glands and ultimobranchial bodies derived from the third and fourth pharangeal pouches, presenting aberrant head and visceral skeleton development and a complete absence of teeth.
Homology PAX9 shares homology through the conserved paired box domain with the other members of the nine strong PAX gene family.


Germinal PAX9 mutations are associated with oligodontia.

Implicated in

Entity Oligodontia
Disease Caused by missense and frameshift PAX9 mutations. Patients present normal primary dentition but lack most permanent molars.
Entity Jarcho-Levin syndrome
Disease In humans, a reduction in expression levels of Pax9, together with those of the related Pax1 gene, have been reported in vertebral column chondrocytes of autopsied foeti presenting Jarcho-Levin syndrome, a segmentation anomaly affecting thoracic and vertebral skeletal development. This syndrome shares similarities with the phenotype of the Pax9/Pax1 double mutant mouse.
Entity Oesophageal invasive carcinoma and epithelial dysplasia.
Disease PAX9 expression levels are significantly reduced in oesophageal invasive carcinoma and epithelial dysplasias compared to levels in normal tissue. There is a correlation between decreasing PAX9 expression and increased malignancy of the cancer.
Prognosis Elevated PAX9 expression may be a useful prognostic marker indicative of favourable outcome in patients presenting oesophageal invasive carcinoma.


Aberrant Pax1 and Pax9 expression in Jarcho-Levin syndrome: report of two Caucasian siblings and literature review.
Bannykh SI, Emery SC, Gerber JK, Jones KL, Benirschke K, Masliah E
American journal of medical genetics. Part A. 2003 ; 120 (2) : 241-246.
PMID 12833407
Pax genes and organogenesis.
Dahl E, Koseki H, Balling R
BioEssays : news and reviews in molecular, cellular and developmental biology. 1997 ; 19 (9) : 755-765.
PMID 9297966
Haploinsufficiency of PAX9 is associated with autosomal dominant hypodontia.
Das P, Stockton DW, Bauer C, Shaffer LG, D'Souza RN, Wright T, Patel PI
Human genetics. 2002 ; 110 (4) : 371-376.
PMID 11941488
Progressive loss of PAX9 expression correlates with increasing malignancy of dysplastic and cancerous epithelium of the human oesophagus.
Gerber JK, Richter T, Kremmer E, Adamski J, Höfler H, Balling R, Peters H
The Journal of pathology. 2002 ; 197 (3) : 293-297.
PMID 12115874
Novel mutation of the initiation codon of PAX9 causes oligodontia.
Klein ML, Nieminen P, Lammi L, Niebuhr E, Kreiborg S
Journal of dental research. 2005 ; 84 (1) : 43-47.
PMID 15615874
A missense mutation in PAX9 in a family with distinct phenotype of oligodontia.
Lammi L, Halonen K, Pirinen S, Thesleff I, Arte S, Nieminen P
European journal of human genetics : EJHG. 2003 ; 11 (11) : 866-871.
PMID 14571272
Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities.
Peters H, Neubüser A, Kratochwil K, Balling R
Genes & development. 1998 ; 12 (17) : 2735-2747.
PMID 9732271
Pax1 and Pax9 synergistically regulate vertebral column development.
Peters H, Wilm B, Sakai N, Imai K, Maas R, Balling R
Development (Cambridge, England). 1999 ; 126 (23) : 5399-5408.
PMID 10556064
Pax1 and Pax9 activate Bapx1 to induce chondrogenic differentiation in the sclerotome.
Rodrigo I, Hill RE, Balling R, Münsterberg A, Imai K
Development (Cambridge, England). 2003 ; 130 (3) : 473-482.
PMID 12490554
Mutation of PAX9 is associated with oligodontia.
Stockton DW, Das P, Goldenberg M, D'Souza RN, Patel PI
Nature genetics. 2000 ; 24 (1) : 18-19.
PMID 10615120
The paired box encodes a second DNA-binding domain in the paired homeo domain protein.
Treisman J, Harris E, Desplan C
Genes & development. 1991 ; 5 (4) : 594-604.
PMID 1672661


This paper should be referenced as such :
Robson, E ; Whall, J ; Eccles, M
PAX9 (paired box gene 9)
Atlas Genet Cytogenet Oncol Haematol. 2005;9(4):315-316.
Free journal version : [ pdf ]   [ DOI ]
On line version :

External links

HGNC (Hugo)PAX9   8623
Entrez_Gene (NCBI)PAX9  5083  paired box 9
GeneCards (Weizmann)PAX9
Ensembl hg19 (Hinxton)ENSG00000198807 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000198807 [Gene_View]  ENSG00000198807 [Sequence]  chr14:36657568-36677806 [Contig_View]  PAX9 [Vega]
ICGC DataPortalENSG00000198807
TCGA cBioPortalPAX9
AceView (NCBI)PAX9
Genatlas (Paris)PAX9
SOURCE (Princeton)PAX9
Genetics Home Reference (NIH)PAX9
Genomic and cartography
GoldenPath hg38 (UCSC)PAX9  -     chr14:36657568-36677806 +  14q13.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PAX9  -     14q13.3   [Description]    (hg19-Feb_2009)
EnsemblPAX9 - 14q13.3 [CytoView hg19]  PAX9 - 14q13.3 [CytoView hg38]
Mapping of homologs : NCBIPAX9 [Mapview hg19]  PAX9 [Mapview hg38]
OMIM167416   604625   
Gene and transcription
Genbank (Entrez)AB248958 AK310339 AK313627 AW293964 BC001159
RefSeq transcript (Entrez)NM_006194
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PAX9
Cluster EST : UnigeneHs.609574 [ NCBI ]
CGAP (NCI)Hs.609574
Alternative Splicing GalleryENSG00000198807
Gene ExpressionPAX9 [ NCBI-GEO ]   PAX9 [ EBI - ARRAY_EXPRESS ]   PAX9 [ SEEK ]   PAX9 [ MEM ]
Gene Expression Viewer (FireBrowse)PAX9 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5083
GTEX Portal (Tissue expression)PAX9
Human Protein AtlasENSG00000198807-PAX9 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP55771   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP55771  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP55771
Splice isoforms : SwissVarP55771
Domaine pattern : Prosite (Expaxy)PAIRED_1 (PS00034)    PAIRED_2 (PS51057)   
Domains : Interpro (EBI)Homeobox-like    Paired_dom    PAX9    WHTH_DNA-bd_dom   
Domain families : Pfam (Sanger)PAX (PF00292)   
Domain families : Pfam (NCBI)pfam00292   
Domain families : Smart (EMBL)PAX (SM00351)  
Conserved Domain (NCBI)PAX9
DMDM Disease mutations5083
Blocks (Seattle)PAX9
Human Protein Atlas [tissue]ENSG00000198807-PAX9 [tissue]
Peptide AtlasP55771
IPIIPI00413469   IPI01015854   IPI00383781   IPI01025900   
Protein Interaction databases
IntAct (EBI)P55771
Ontologies - Pathways
Ontology : AmiGORNA polymerase II regulatory region sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding  protein binding  nucleus  transcription by RNA polymerase II  endoderm development  odontogenesis  regulation of odontogenesis  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  face morphogenesis  cellular response to growth factor stimulus  
Ontology : EGO-EBIRNA polymerase II regulatory region sequence-specific DNA binding  transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding  protein binding  nucleus  transcription by RNA polymerase II  endoderm development  odontogenesis  regulation of odontogenesis  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  face morphogenesis  cellular response to growth factor stimulus  
NDEx NetworkPAX9
Atlas of Cancer Signalling NetworkPAX9
Wikipedia pathwaysPAX9
Orthology - Evolution
GeneTree (enSembl)ENSG00000198807
Phylogenetic Trees/Animal Genes : TreeFamPAX9
Homologs : HomoloGenePAX9
Homology/Alignments : Family Browser (UCSC)PAX9
Gene fusions - Rearrangements
Fusion : QuiverPAX9
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPAX9 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PAX9
Exome Variant ServerPAX9
ExAC (Exome Aggregation Consortium)ENSG00000198807
GNOMAD BrowserENSG00000198807
Genetic variants : HAPMAP5083
Genomic Variants (DGV)PAX9 [DGVbeta]
DECIPHERPAX9 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPAX9 
ICGC Data PortalPAX9 
TCGA Data PortalPAX9 
Broad Tumor PortalPAX9
OASIS PortalPAX9 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPAX9  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPAX9
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 PAX9
DgiDB (Drug Gene Interaction Database)PAX9
DoCM (Curated mutations)PAX9 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PAX9 (select a term)
NCG5 (London)PAX9
Cancer3DPAX9(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
OMIM167416    604625   
Genetic Testing Registry PAX9
NextProtP55771 [Medical]
Target ValidationPAX9
Huge Navigator PAX9 [HugePedia]
snp3D : Map Gene to Disease5083
BioCentury BCIQPAX9
ClinGenPAX9 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5083
Chemical/Pharm GKB GenePA32963
Clinical trialPAX9
canSAR (ICR)PAX9 (select the gene name)
PubMed88 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 : Fri Jun 22 17:15:35 CEST 2018

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