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PAX3 (paired box gene 3 (Waardenburg syndrome 1))

Written2006-07Eun Hyun Ahn, Frederic G. Barr
University of Pennsylvania, School of Medicine,Dept of Pathology, Laboratory Medicine, 506 Stellar-chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104, USA

(Note : for Links provided by Atlas : click)

Identity

Alias_namesWS1
Waardenburg syndrome 1
paired box gene 3 (Waardenburg syndrome 1)
Alias_symbol (synonym)HUP2
Other aliasCDHS
MGC120381
MGC120382
MGC120383
MGC120384
MGC134778
WS3
HGNC8617
HGNC (Hugo) PAX3
LocusID (NCBI) 5077
Atlas_Id 70
Location 2q36.1  [Link to chromosome band 2q36]
Location_base_pair Starts at 222293630 and ends at 222298996 bp from pter ( according to hg19-Feb_2009)  [Mapping PAX3.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)
FOXO1 (13q14.11) / PAX3 (2q36.1)NCOA1 (2p23.3) / PAX3 (2q36.1)PAX3 (2q36.1) / FOXO1 (13q14.11)
PAX3 (2q36.1) / FOXO4 (Xq13.1)PAX3 (2q36.1) / MAML3 (4q31.1)PAX3 (2q36.1) / MMP16 (8q21.3)
PAX3 (2q36.1) / NCOA1 (2p23.3)PAX3 (2q36.1) / NCOA2 (8q13.3)PAX3 (2q36.1) / PAX3 (2q36.1)
PPHLN1 (12q12) / PAX3 (2q36.1)

DNA/RNA

Description The PAX3 gene extends approximately 100 kb and consists of 10 exons.
Transcription In human tissues and tumors, seven alternatively spliced transcripts have been described. The abundant transcripts, which have been studied in neural-related tumor specimens and cell lines, appear to consist of the first eight or nine exons (PAX3c and PAX3d). In addition, there is also frequent alternative splicing at the 5' end of exon 3 in human tissues and tumors that results in inclusion or exclusion of a single codon encoding a glutamine residue.

Protein

Description 479 amino acids, 53.0 kDa (8 exon form, PAX3c) or 484 amino acids, 53.5 kDa (9 exon form, PAX3d). The isoform containing the variable glutamine residue at the exon 3/4 junction is referred to as Q+, while the isoform lacking the Q is designated as Q-.
Expression Based on experiments in the mouse, Pax3 is expressed in the spinal cord and selected regions of the brain. Pax3 is expressed in the neural crest and is involved in development of neural crest derivatives including spinal ganglia, melanocytes and Schwann cells. Pax3 expression is also detected in somite compartments that give rise to embryonic skeletal muscle progenitors, and in cells that give rise to skeletal muscle compartments of the developing limb buds. In addition, Pax3 (as well as Pax7 ) is also expressed in a proliferating population without skeletal muscle specific markers that reside within limb and trunk muscles throughout later development; and a subset of adult muscles subsequently contain Pax3-expressing satellite cells.
Localisation Nucleus.
Function PAX3 is a transcription factor characterized by three highly converved motifs in the N-terminal region: a paired box DNA binding domain, an intervening octapeptide of unclear function, and a homeobox DNA binding domain. The C-terminal region contains a proline-, serine- and threonine-rich transactivation domain.
Based on the studies of the mutant Pax3 alleles in the mouse (Splotch phenotype) as well as studies of patients with mutant PAX3 genes (see below), Pax3 is postulated to have a crucial role in the development of the early neural structures, derivatives of the neural crest, and skeletal musculature. In these developmental processes, there is evidence that the transcriptional function of Pax3 impacts at four biological activities:
1. proliferation
2. apoptosis
3. differentiation
4. motility
Homology PAX3 shares homology through the conserved paired box with eight other members of the PAX gene family. In particular, within the PAX gene family, PAX3 and PAX7 constitute a subfamily characterized by a paired box, intervening octapeptide and complete homeobox as well as homology between the C-terminal transcriptional activation domains.

Mutations

Germinal Germ-line sequence changes involving the PAX3 gene are found in Waardenburg syndrome type I and type III, a non-neoplastic autosomal dominant disorder characterized by hearing loss and pigmentary abnormalities. The majority of these alterations are nucleotide substitutions resulting in missense mutations, usually in the regions encoding the paired box or homeobox. A smaller number of base substitutions at splicing sites and small deletions and insertions, which usually alter the reading frame, have also been reported. Finally, there have also been several cases of large deletions and other rearrangements of chromosome 2.
Somatic The PAX3 gene is rearranged by the characteristic and recurrent acquired chromosomal translocation - t(2;13)(q35;q14) - in the myogenic soft tissue cancer alveolar rhabdomyosarcoma. As a result of this 2;13 translocation, portions of the PAX3 gene are juxtaposed with portions of the FKHR (also called FOXO1A) gene on chromosome 13. In particular, the 5' region of PAX3 including the first seven exons is joined to the 3' region of FKHR including its last two exons. Though the reciprocal chimeric gene is also generated, this PAX3-FKHR chimeric gene is more consistent and highly expressed, and results in expression of a fusion protein consisting of the intact PAX3 N-terminal DNA binding domain fused in-framed to the intact FKHR C-terminal transcriptional activation domain. This fusion protein functions as an aberrant transcription factor. In rare cases of alveolar rhabdomyosarcoma, PAX3 is fused to alternative C-terminal partners - MLLT7 (AFX, FOXO4) and

Implicated in

Note
  
Entity Alveolar Rhabdomyosarcoma (ARMS)
Disease ARMS is one subtype of a family of pediatric soft tissue tumors that is related to the skeletal muscle lineage. In contrast to the embryonal rhabdomyosarcoma (ERMS), the other major subtype in this family, ARMS often occurs in adolescents and young adults, with primary tumors located in the vicinity of skeletal muscle, such as in the extremities and trunk.
Prognosis In contrast to the favorable outcome in most cases of ERMS, ARMS is associated with an unfavorable prognosis. In the IRS-IV clinical trial, the three year failure-free survival rate was 66% for patients presenting without metastatic disease and 16% for patients presenting with metastatic disease (compared to 83% and 37% for non-metastatic and metastatic ERMS, respectively). This unfavorable prognosis in ARMS is related to the propensity for early and wide dissemination, often involving bone marrow, and to poor response to chemotherapy.
Cytogenetics Chromosomal studies identified nonrandom chromosomal translocations that distinguish the majority of ARMS tumors from ERMS and other pediatric solid tumors. The t(2;13)(q35;q14) translocation is the most prevalent and the t(1;13)(p36;q14) is identified in a smaller subset of cases.
Hybrid/Mutated Gene The 2;13 or 1;13 chromosome translocation juxtapose the PAX3 gene on chromosome 2 or the PAX7 gene on chromosome 1 with the FKHR (FOXO1A) gene on chromosome 13 to generate two chimeric genes. These chimeric genes are transcribed to generate chimeric transcripts, of which the PAX3-FKHR and PAX7-FKHR transcripts are the most highly and consistently expressed of the pair of potential products. Based on RT-PCR assays for these chimeric transcripts, approximately 60% of ARMS cases express PAX3-FKHR and thus contain the t(2;13), 20% express PAX7-FKHR and thus contain the t(1;13), and 20% are fusion-negative.
 
a) Diagram of t(2;13)(q35;q14) and t(1;13)(p36;q14) chromosomal translocations generating PAX3-FKHR and PAX7-FKHR fusions

b) Generation of chimeric genes by the t(2;13)(q35;q14) translocation in ARMS. The exons of the wild-type and fusion genes are shown as boxes above each map and the translocation breakpoint distributions are shown as line segments below the map of the wild-type genes.

c) Comparison of wild-type and fusion products associated with the 2;13 and 1;13 translocations. The paired box, octapeptide, homeobox and fork head domain are indicated as open boxes, and transcriptional domains (DNA binding domain, DBD; transcriptional activiation domain, TAD; transcriptional inhibitory domain, TID) are shown as solid bars. The sites phosphorylated by Akt are indicated by stars, and the alternative splice in the paired box is shown by an arrowhead. The vertical dash line indicates the translocation fusion point. {Reproduced from: Barr (2001) Oncogene 20: 5736- 5746}

Oncogenesis The PAX3-FKHR and PAX7-FKHR chimeric genes encode fusion proteins that contain the intact DNA binding domain of PAX3 or PAX7 in the N-terminal region fused in frame with a C-terminal FKHR (FOXO1A) segment containing the transactivation domain. The chromosomal changes in ARMS result in high level expression, potent transcriptional activity, and constitutive nuclear localization of the PAX3-FKHR or PAX7-FKHR fusion products. The end result is exaggerated activity at multiple biological levels that converges to inappropriate activation of PAX3/PAX7 target genes and ultimately contributes to tumourigenic behavior.
  
  
Entity Waardenburg syndrome (type I et III)
Disease Waardenburg syndrome (WS) is an inherited autosomal-dominant disorder characterized by sensorineural hearing loss (of varying severity), dystopia canthorum (lateral displacement of inner corners of eye), and pigmentary disturbances of the eye, skin and hair. It is a common cause of inherited deafness in infants. Depending on additional symptoms, WS is classified into four types, WS1, WS2, WS3, and WS4, with only WS1 and WS3 being associated with PAX3 mutations. Deletions, insertion, base pair substitution, or dominant point mutations of PAX3 cause WS1 and WS3. WS3 (Klein-Waardenburg syndrome) is similar to WS1 but WS3 is also characterized by musculoskeletal abnormalities, usually involving the upper limbs. It should be noted that WS3 is often associated with deletions of the long arm of chromosome 2 involving multiples genes including PAX3 whereas WS1 is generally is associated with mutations within the PAX3 gene. WS2 is heterogenous, being caused by mutations in the MITF gene in some but not all affected families. WS4 is caused by mutations in the EDN3, EDNRB, or SOX10 ID genes.
  
  
Entity Craniofacial-deafness-hand syndrome (CDHS)
Disease Craniofacial-deafness-hand syndrome is inherited as an autosomal dominant mutation. CDHS shows clinical characteristics of the absence or hypoplasia of the nasal bones, profound sensorineural deafness, a small and short nose with slitlike nares, hypertelorism, short palpebral fissures, and limited movement at the wrist and ulnar deviations of the fingers. A missense mutation (Asn47Lys) in the paired domain (exon 2) of PAX3 was detected in a family of three (a mother and two children) first reported with this syndrome.
  

Breakpoints

 

Bibliography

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Predominant expression of alternative PAX3 and PAX7 forms in myogenic and neural tumor cell lines.
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Rearrangement of the PAX3 paired box gene in the paediatric solid tumour alveolar rhabdomyosarcoma.
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Genetic heterogeneity in the alveolar rhabdomyosarcoma subset without typical gene fusions.
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The oncogenic potential of the Pax3-FKHR fusion protein requires the Pax3 homeodomain recognition helix but not the Pax3 paired-box DNA binding domain.
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PMID 9858583
 
Pax3 functions at a nodal point in melanocyte stem cell differentiation.
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Citation

This paper should be referenced as such :
Ahn, EH ; Barr, FG
PAX3 (paired box gene 3 (Waardenburg syndrome 1))
Atlas Genet Cytogenet Oncol Haematol. 2006;10(4):253-256.
Free journal version : [ pdf ]   [ DOI ]
On line version : http://AtlasGeneticsOncology.org/Genes/PAX3ID70ch2q35.html

Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  t(1;9)(p13;p12) PAX5/HIPK1
t(X;9)(q21;p13) PAX5/DACH2

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 6 ]
  Soft Tissues: Alveolar rhabdomyosarcoma
Soft Tissues: Rhabdomyosarcoma
Soft tissue tumors: an overview
Soft Tissues: Rhabdomyosarcomas with t(11;22)(q24;q12) EWSR1/FLI1
Soft Tissues: Alveolar rhabdomyosarcoma with t(2;13)(q35;q14) PAX3/FOXO1
Soft Tissues: Alveolar rhabdomyosarcoma with t(2;2)(p23;q35) PAX3/NCOA1

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

External links

Nomenclature
HGNC (Hugo)PAX3   8617
Cards
AtlasPAX3ID70ch2q35
Entrez_Gene (NCBI)PAX3  5077  paired box 3
AliasesCDHS; HUP2; WS1; WS3
GeneCards (Weizmann)PAX3
Ensembl hg19 (Hinxton)ENSG00000135903 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000135903 [Gene_View]  chr2:222293630-222298996 [Contig_View]  PAX3 [Vega]
ICGC DataPortalENSG00000135903
TCGA cBioPortalPAX3
AceView (NCBI)PAX3
Genatlas (Paris)PAX3
WikiGenes5077
SOURCE (Princeton)PAX3
Genetics Home Reference (NIH)PAX3
Genomic and cartography
GoldenPath hg38 (UCSC)PAX3  -     chr2:222293630-222298996 -  2q36.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PAX3  -     2q36.1   [Description]    (hg19-Feb_2009)
EnsemblPAX3 - 2q36.1 [CytoView hg19]  PAX3 - 2q36.1 [CytoView hg38]
Mapping of homologs : NCBIPAX3 [Mapview hg19]  PAX3 [Mapview hg38]
OMIM122880   148820   193500   268220   606597   
Gene and transcription
Genbank (Entrez)AI382779 AI399816 AK291278 AY251279 AY251280
RefSeq transcript (Entrez)NM_000438 NM_001127366 NM_013942 NM_181457 NM_181458 NM_181459 NM_181460 NM_181461
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PAX3
Cluster EST : UnigeneHs.42146 [ NCBI ]
CGAP (NCI)Hs.42146
Alternative Splicing GalleryENSG00000135903
Gene ExpressionPAX3 [ NCBI-GEO ]   PAX3 [ EBI - ARRAY_EXPRESS ]   PAX3 [ SEEK ]   PAX3 [ MEM ]
Gene Expression Viewer (FireBrowse)PAX3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5077
GTEX Portal (Tissue expression)PAX3
Human Protein AtlasENSG00000135903-PAX3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP23760   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP23760  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP23760
Splice isoforms : SwissVarP23760
PhosPhoSitePlusP23760
Domaine pattern : Prosite (Expaxy)HOMEOBOX_1 (PS00027)    HOMEOBOX_2 (PS50071)    PAIRED_1 (PS00034)    PAIRED_2 (PS51057)   
Domains : Interpro (EBI)Homeobox-like    Homeobox_CS    Homeobox_dom    Paired_dom    Pax3    Pax7_C    WHTH_DNA-bd_dom   
Domain families : Pfam (Sanger)Homeobox (PF00046)    PAX (PF00292)    Pax7 (PF12360)   
Domain families : Pfam (NCBI)pfam00046    pfam00292    pfam12360   
Domain families : Smart (EMBL)HOX (SM00389)  PAX (SM00351)  
Conserved Domain (NCBI)PAX3
DMDM Disease mutations5077
Blocks (Seattle)PAX3
PDB (SRS)3CMY   
PDB (PDBSum)3CMY   
PDB (IMB)3CMY   
PDB (RSDB)3CMY   
Structural Biology KnowledgeBase3CMY   
SCOP (Structural Classification of Proteins)3CMY   
CATH (Classification of proteins structures)3CMY   
SuperfamilyP23760
Human Protein Atlas [tissue]ENSG00000135903-PAX3 [tissue]
Peptide AtlasP23760
HPRD09421
IPIIPI00012896   IPI00219092   IPI00219093   IPI01025818   IPI01025463   IPI00328761   IPI00328760   IPI00375387   IPI00375388   IPI00895878   
Protein Interaction databases
DIP (DOE-UCLA)P23760
IntAct (EBI)P23760
FunCoupENSG00000135903
BioGRIDPAX3
STRING (EMBL)PAX3
ZODIACPAX3
Ontologies - Pathways
QuickGOP23760
Ontology : AmiGOtranscription factor activity, sequence-specific DNA binding  protein binding  nucleoplasm  nucleoplasm  transcription from RNA polymerase II promoter  apoptotic process  nervous system development  muscle organ development  sensory perception of sound  animal organ morphogenesis  neural crest formation  sequence-specific DNA binding  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  HMG box domain binding  
Ontology : EGO-EBItranscription factor activity, sequence-specific DNA binding  protein binding  nucleoplasm  nucleoplasm  transcription from RNA polymerase II promoter  apoptotic process  nervous system development  muscle organ development  sensory perception of sound  animal organ morphogenesis  neural crest formation  sequence-specific DNA binding  positive regulation of transcription, DNA-templated  positive regulation of transcription from RNA polymerase II promoter  HMG box domain binding  
Pathways : BIOCARTARegulation of transcriptional activity by PML [Genes]   
Pathways : KEGGTranscriptional misregulation in cancer   
REACTOMEP23760 [protein]
REACTOME PathwaysR-HSA-3214847 [pathway]   
NDEx NetworkPAX3
Atlas of Cancer Signalling NetworkPAX3
Wikipedia pathwaysPAX3
Orthology - Evolution
OrthoDB5077
GeneTree (enSembl)ENSG00000135903
Phylogenetic Trees/Animal Genes : TreeFamPAX3
HOVERGENP23760
HOGENOMP23760
Homologs : HomoloGenePAX3
Homology/Alignments : Family Browser (UCSC)PAX3
Gene fusions - Rearrangements
Fusion : MitelmanPAX3/FOXO1 [2q36.1/13q14.11]  
Fusion : MitelmanPAX3/FOXO4 [2q36.1/Xq13.1]  [t(X;2)(q13;q36)]  
Fusion : MitelmanPAX3/MAML3 [2q36.1/4q31.1]  [t(2;4)(q36;q31)]  
Fusion : MitelmanPAX3/NCOA1 [2q36.1/2p23.3]  [t(2;2)(p23;q36)]  
Fusion : MitelmanPAX3/NCOA2 [2q36.1/8q13.3]  [t(2;8)(q36;q13)]  
Fusion : COSMICFOXO1 [13q14.11]  -  PAX3 [2q36.1]  [fusion_387]  [fusion_906]  
Fusion : COSMICPAX3 [2q36.1]  -  FOXO1 [13q14.11]  [fusion_247]  [fusion_248]  [fusion_343]  
Fusion : COSMICPAX3 [2q36.1]  -  NCOA1 [2p23.3]  [fusion_1042]  [fusion_1043]  YfusinnW289]  [fusion_290]  
Fusion : COSMICPAX3 [2q36.1]  -  NCOA2 [8q13.3]  [fusion_1040]  [fusion_1041]  
Fusion : TICdbFOXO1 [13q14.11]  -  PAX3 [2q36.1]
Fusion : TICdbPAX3 [2q36.1]  -  NCOA1 [2p23.3]
Fusion : TICdbPAX3 [2q36.1]  -  NCOA2 [8q13.3]
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPAX3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PAX3
dbVarPAX3
ClinVarPAX3
1000_GenomesPAX3 
Exome Variant ServerPAX3
ExAC (Exome Aggregation Consortium)ENSG00000135903
GNOMAD BrowserENSG00000135903
Genetic variants : HAPMAP5077
Genomic Variants (DGV)PAX3 [DGVbeta]
DECIPHERPAX3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPAX3 
Mutations
ICGC Data PortalPAX3 
TCGA Data PortalPAX3 
Broad Tumor PortalPAX3
OASIS PortalPAX3 [ Somatic mutations - Copy number]
Cancer Gene: CensusPAX3 
Somatic Mutations in Cancer : COSMICPAX3  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPAX3
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
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
BioMutasearch PAX3
DgiDB (Drug Gene Interaction Database)PAX3
DoCM (Curated mutations)PAX3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PAX3 (select a term)
intoGenPAX3
NCG5 (London)PAX3
Cancer3DPAX3(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM122880    148820    193500    268220    606597   
Orphanet221    219    1695    14329   
MedgenPAX3
Genetic Testing Registry PAX3
NextProtP23760 [Medical]
TSGene5077
GENETestsPAX3
Target ValidationPAX3
Huge Navigator PAX3 [HugePedia]
snp3D : Map Gene to Disease5077
BioCentury BCIQPAX3
ClinGenPAX3 (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5077
Chemical/Pharm GKB GenePA32957
Clinical trialPAX3
Miscellaneous
canSAR (ICR)PAX3 (select the gene name)
Probes
Litterature
PubMed195 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePAX3
EVEXPAX3
GoPubMedPAX3
iHOPPAX3
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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