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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)


Other aliasPaired box homeotic gene 9
LocusID (NCBI) 5083
Atlas_Id 41644
Location 14q13.3  [Link to chromosome band 14q13]
Location_base_pair Starts at and ends at bp from pter
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

Genomic and cartography
Gene and transcription
RefSeq transcript (Entrez)
RefSeq genomic (Entrez)
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
BioGPS (Tissue expression)5083
Protein : pattern, domain, 3D structure
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Protein Interaction databases
Ontologies - Pathways
Clinical trials, drugs, therapy
canSAR (ICR) (select the gene name)
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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