Atlas of Genetics and Cytogenetics in Oncology and Haematology

Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA
Taking over the Atlas
Dear Colleagues,
The Atlas, once more, is in great danger, and I will have to proceed to a collective economic lay-off of all the team involved in the Atlas before the begining of April 2015 (a foundation having suddenly withdrawn its commitment to support the Atlas). I ask you herein if any Scientific Society (a Society of Cytogenetics, of Clinical Genetics, of Hematology, or a Cancer Society, or any other...), any University and/or Hospital, any Charity, or any database would be interested in taking over the Atlas, in whole or in part. If taking charge of the whole lot is too big, a consortium of various actors could be the solution (I am myself trying to find partners). Could you please spread the information, contact the relevant authorities, and find partners.
Survival of the Atlas will be critically dependant upon your ability to find solutions (and urgently!).
Kind regards.
Jean-Loup Huret
Donations are also welcome
If each casual visitor gives 3 Euros or Dollars, the Atlas is saved in a week !
If each professional gives 100 Euros or Dollars once a year (now), the Atlas is saved in 2 weeks !
Don't let the Atlas imminent demise
Note: we send fiscal receipts for donations equal or above 50 Euros or Dollars

Donate (in Euros)

Donate (in US Dollars)

PAX9 (Paired box gene 9)


Other namesPaired box homeotic gene 9
HGNC (Hugo) PAX9
LocusID (NCBI) 5083
Location 14q13.3
Location_base_pair Starts at 37126773 and ends at 37147011 bp from pter ( according to hg19-Feb_2009)  [Mapping]


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.

External links

HGNC (Hugo)PAX9   8623
Entrez_Gene (NCBI)PAX9  5083  paired box 9
GeneCards (Weizmann)PAX9
Ensembl hg19 (Hinxton)ENSG00000198807 [Gene_View]  chr14:37126773-37147011 [Contig_View]  PAX9 [Vega]
Ensembl hg38 (Hinxton)ENSG00000198807 [Gene_View]  chr14:37126773-37147011 [Contig_View]  PAX9 [Vega]
ICGC DataPortalENSG00000198807
AceView (NCBI)PAX9
Genatlas (Paris)PAX9
SOURCE (Princeton)PAX9
Genomic and cartography
GoldenPath hg19 (UCSC)PAX9  -     chr14:37126773-37147011 +  14q13.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)PAX9  -     14q13.3   [Description]    (hg38-Dec_2013)
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)AC_000146 NC_000014 NC_018925 NG_013357 NT_026437 NW_001838110 NW_004929393
Consensus coding sequences : CCDS (NCBI)PAX9
Cluster EST : UnigeneHs.609574 [ NCBI ]
CGAP (NCI)Hs.609574
Alternative Splicing : Fast-db (Paris)GSHG0008797
Alternative Splicing GalleryENSG00000198807
Gene ExpressionPAX9 [ NCBI-GEO ]     PAX9 [ SEEK ]   PAX9 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP55771 (Uniprot)
NextProtP55771  [Medical]
With graphics : InterProP55771
Splice isoforms : SwissVarP55771 (Swissvar)
Domaine pattern : Prosite (Expaxy)PAIRED_1 (PS00034)    PAIRED_2 (PS51057)   
Domains : Interpro (EBI)Homeodomain-like    Paired_dom    WHTH_DNA-bd_dom   
Related proteins : CluSTrP55771
Domain families : Pfam (Sanger)PAX (PF00292)   
Domain families : Pfam (NCBI)pfam00292   
Domain families : Smart (EMBL)PAX (SM00351)  
DMDM Disease mutations5083
Blocks (Seattle)P55771
Human Protein AtlasENSG00000198807
Peptide AtlasP55771
IPIIPI00413469   IPI01015854   IPI00383781   IPI01025900   
Protein Interaction databases
IntAct (EBI)P55771
Ontologies - Pathways
Ontology : AmiGODNA binding  protein binding  nucleus  transcription, DNA-templated  endoderm development  odontogenesis  regulation of odontogenesis  negative regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  face morphogenesis  cellular response to growth factor stimulus  
Ontology : EGO-EBIDNA binding  protein binding  nucleus  transcription, DNA-templated  endoderm development  odontogenesis  regulation of odontogenesis  negative regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  face morphogenesis  cellular response to growth factor stimulus  
Protein Interaction DatabasePAX9
DoCM (Curated mutations)PAX9
Wikipedia pathwaysPAX9
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerPAX9 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PAX9
Exome Variant ServerPAX9
SNP (GeneSNP Utah)PAX9
Genetic variants : HAPMAPPAX9
Genomic Variants (DGV)PAX9 [DGVbeta]
ICGC Data PortalENSG00000198807 
Somatic Mutations in Cancer : COSMICPAX9 
CONAN: Copy Number AnalysisPAX9 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
DECIPHER (Syndromes)14:37126773-37147011
Mutations and Diseases : HGMDPAX9
OMIM167416    604625   
NextProtP55771 [Medical]
Disease Genetic AssociationPAX9
Huge Navigator PAX9 [HugePedia]  PAX9 [HugeCancerGEM]
snp3D : Map Gene to Disease5083
DGIdb (Drug Gene Interaction db)PAX9
General knowledge
Homologs : HomoloGenePAX9
Homology/Alignments : Family Browser (UCSC)PAX9
Phylogenetic Trees/Animal Genes : TreeFamPAX9
Chemical/Protein Interactions : CTD5083
Chemical/Pharm GKB GenePA32963
Clinical trialPAX9
Cancer Resource (Charite)ENSG00000198807
Other databases
PubMed76 Pubmed reference(s) in Entrez


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
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
Pax9-deficient mice lack pharyngeal pouch derivatives and teeth and exhibit craniofacial and limb abnormalities.
Peters H, Neubˆšser 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
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
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, Hˆfler H, Balling R, Peters H
The Journal of pathology. 2002 ; 197 (3) : 293-297.
PMID 12115874
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
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
Pax1 and Pax9 activate Bapx1 to induce chondrogenic differentiation in the sclerotome.
Rodrigo I, Hill RE, Balling R, Mˆšnsterberg A, Imai K
Development (Cambridge, England). 2003 ; 130 (3) : 473-482.
PMID 12490554
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
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI


Written08-2005Ewan Robson, Jess Whall, Michael Eccles


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 ]

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Feb 17 20:13:13 CET 2015

Home   Genes   Leukemias   Solid Tumours   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us