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Aliases for PAX3 Gene

Aliases for PAX3 Gene

  • Paired Box 3 2 3 5
  • HUP2 3 4
  • Paired Box Gene 3 (Waardenburg Syndrome 1) 2
  • Transcriptional Factor PAX3 3
  • Paired Box Homeotic Gene 3 3
  • Paired Box Protein Pax-3 3
  • Paired Domain Gene HuP2 3
  • Waardenburg Syndrome 1 2
  • Paired Domain Gene 3 3
  • CDHS 3
  • WS3 3
  • WS1 3

External Ids for PAX3 Gene

Previous HGNC Symbols for PAX3 Gene

  • WS1

Previous GeneCards Identifiers for PAX3 Gene

  • GC02M221089
  • GC02M221788
  • GC02M223029
  • GC02M223267
  • GC02M222890
  • GC02M222772
  • GC02M214918
  • GC02M223064

Summaries for PAX3 Gene

Entrez Gene Summary for PAX3 Gene

  • This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. Mutations in paired box gene 3 are associated with Waardenburg syndrome, craniofacial-deafness-hand syndrome, and alveolar rhabdomyosarcoma. The translocation t(2;13)(q35;q14), which represents a fusion between PAX3 and the forkhead gene, is a frequent finding in alveolar rhabdomyosarcoma. Alternative splicing results in transcripts encoding isoforms with different C-termini. [provided by RefSeq, Jul 2008]

GeneCards Summary for PAX3 Gene

PAX3 (Paired Box 3) is a Protein Coding gene. Diseases associated with PAX3 include Craniofacial-Deafness-Hand Syndrome and Waardenburg Syndrome, Type 1. Among its related pathways are Ectoderm Differentiation and Neural Crest Differentiation. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and chromatin binding. An important paralog of this gene is PAX7.

UniProtKB/Swiss-Prot for PAX3 Gene

  • Transcription factor that may regulate cell proliferation, migration and apoptosis. Involved in neural development and myogenesis. Transcriptional activator of MITF, acting synergistically with SOX10 (PubMed:21965087).

Gene Wiki entry for PAX3 Gene

Additional gene information for PAX3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PAX3 Gene

Genomics for PAX3 Gene

GeneHancer (GH) Regulatory Elements for PAX3 Gene

Promoters and enhancers for PAX3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02I222319 Promoter/Enhancer 1.3 Ensembl ENCODE 550.8 +0.9 928 2.3 PKNOX1 RB1 ZNF2 ZNF335 GLIS2 ZNF143 ATF7 BCLAF1 RUNX3 SMARCA5 ENSG00000267034 PAX3 LOC440934
GH02I222293 Promoter/Enhancer 1.3 EPDnew ENCODE 550.3 +24.3 24317 5.9 ZSCAN4 ZNF76 ZNF48 ZNF335 GLIS2 ZNF366 SCRT2 SP3 ZBTB11 ZNF398 CCDC140 PAX3 GC02P222238
GH02I222289 Enhancer 0.9 FANTOM5 ENCODE 11.8 +30.2 30237 3.4 CTCF USF1 ZNF189 SUZ12 SIN3A OSR2 SP1 CBX8 POLR2A CTBP2 PAX3 CCDC140 GC02P222238
GH02I222318 Promoter/Enhancer 1.3 Ensembl ENCODE 0.8 +2.9 2907 0.7 HDGF PKNOX1 RB1 SIN3A DMAP1 ZNF48 RAD21 ZNF335 ZNF366 SCRT2 ENSG00000267034 ENSG00000261428 LOC440934 PAX3
GH02I222363 Enhancer 1 FANTOM5 Ensembl ENCODE 0.3 -43.2 -43219 1.1 JUN BACH1 NFE2 NFE2L2 SGPP2 GC02P222405 PAX3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PAX3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PAX3 gene promoter:

Genomic Locations for PAX3 Gene

Genomic Locations for PAX3 Gene
121,377 bases
Minus strand

Genomic View for PAX3 Gene

Genes around PAX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PAX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PAX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PAX3 Gene

Proteins for PAX3 Gene

  • Protein details for PAX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Paired box protein Pax-3
    Protein Accession:
    Secondary Accessions:
    • G5E9C1
    • Q16448
    • Q494Z3
    • Q494Z4
    • Q53T90
    • Q6GSJ9
    • Q86UQ2
    • Q86UQ3

    Protein attributes for PAX3 Gene

    479 amino acids
    Molecular mass:
    52968 Da
    Quaternary structure:
    • Can bind to DNA as a homodimer or a heterodimer with PAX7. Interacts with PAXBP1; the interaction links PAX3 to a WDR5-containing histone methyltransferase complex. Interacts with DAXX. Interacts with TBX18. Interacts with SOX10 (PubMed:21965087).

    Three dimensional structures from OCA and Proteopedia for PAX3 Gene

    Alternative splice isoforms for PAX3 Gene

neXtProt entry for PAX3 Gene

Post-translational modifications for PAX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PAX3 Gene

Domains & Families for PAX3 Gene

Gene Families for PAX3 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the paired homeobox family.
  • Belongs to the paired homeobox family.
genes like me logo Genes that share domains with PAX3: view

Function for PAX3 Gene

Molecular function for PAX3 Gene

GENATLAS Biochemistry:
paired box (DNA binding) containing protein 3 (HuP2),with an homeo domain,mouse Pax3,splotch homolog,involved in neurogenesis and in melanogenesis through MITF transactivation ? and other processes (see BARMS2,WS1,WS2,WS3),interacting with HIRA,activating MYOD1 gene
UniProtKB/Swiss-Prot Function:
Transcription factor that may regulate cell proliferation, migration and apoptosis. Involved in neural development and myogenesis. Transcriptional activator of MITF, acting synergistically with SOX10 (PubMed:21965087).

Phenotypes From GWAS Catalog for PAX3 Gene

Gene Ontology (GO) - Molecular Function for PAX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 DNA binding transcription factor activity TAS 9500554
GO:0005515 protein binding IPI 11029584
GO:0043565 sequence-specific DNA binding IDA 11863357
GO:0071837 HMG box domain binding IEA --
genes like me logo Genes that share ontologies with PAX3: view
genes like me logo Genes that share phenotypes with PAX3: view

Human Phenotype Ontology for PAX3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PAX3 Gene

MGI Knock Outs for PAX3:

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PAX3 Gene

Localization for PAX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PAX3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PAX3 gene
Compartment Confidence
nucleus 5
extracellular 2
cytoskeleton 2
plasma membrane 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PAX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with PAX3: view

Pathways & Interactions for PAX3 Gene

genes like me logo Genes that share pathways with PAX3: view

Pathways by source for PAX3 Gene

1 Qiagen pathway for PAX3 Gene
1 Cell Signaling Technology pathway for PAX3 Gene

SIGNOR curated interactions for PAX3 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for PAX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II TAS 9500554
GO:0006915 apoptotic process TAS 10871843
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with PAX3: view

Drugs & Compounds for PAX3 Gene

(4) Drugs for PAX3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for PAX3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PAX3: view

Transcripts for PAX3 Gene

Unigene Clusters for PAX3 Gene

Paired box 3:
Representative Sequences:

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PAX3 Gene

No ASD Table

Relevant External Links for PAX3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PAX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PAX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PAX3 Gene

This gene is overexpressed in Minor Salivary Gland (x12.3), Brain - Cerebellum (x6.8), and Muscle - Skeletal (x4.0).

Protein differential expression in normal tissues from HIPED for PAX3 Gene

This gene is overexpressed in Placenta (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PAX3 Gene

Protein tissue co-expression partners for PAX3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PAX3 Gene:


SOURCE GeneReport for Unigene cluster for PAX3 Gene:


Evidence on tissue expression from TISSUES for PAX3 Gene

  • Skin(4.6)
  • Muscle(2.9)
  • Nervous system(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PAX3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cheek
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • inner ear
  • jaw
  • lacrimal apparatus
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • skull
  • tooth
  • chest wall
  • lung
  • rib
  • rib cage
  • scapula
  • intestine
  • large intestine
  • vagina
  • ankle
  • arm
  • digit
  • elbow
  • finger
  • foot
  • forearm
  • hand
  • hip
  • knee
  • lower limb
  • nail
  • shoulder
  • toe
  • ulna
  • upper limb
  • wrist
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with PAX3: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for PAX3 Gene

Orthologs for PAX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PAX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PAX3 34 33
  • 99.59 (n)
(Monodelphis domestica)
Mammalia PAX3 34
  • 98 (a)
(Ornithorhynchus anatinus)
Mammalia PAX3 34
  • 97 (a)
(Bos Taurus)
Mammalia PAX3 33 34
  • 93.72 (n)
(Mus musculus)
Mammalia Pax3 33 16 34
  • 91.79 (n)
(Rattus norvegicus)
Mammalia Pax3 33
  • 90.75 (n)
(Canis familiaris)
Mammalia PAX3 33 34
  • 90.64 (n)
(Gallus gallus)
Aves PAX3 33 34
  • 85.51 (n)
(Anolis carolinensis)
Reptilia PAX3 34
  • 98 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pax3 33
  • 81.34 (n)
(Danio rerio)
Actinopterygii pax3a 33 34
  • 71.33 (n)
pax3b 34
  • 68 (a)
fruit fly
(Drosophila melanogaster)
Insecta Poxn 35
  • 67 (a)
gsb 34
  • 44 (a)
gsb-n 34
  • 43 (a)
prd 34
  • 34 (a)
(Caenorhabditis elegans)
Secernentea K06B9.5 35
  • 69 (a)
K07C11.1 35
  • 61 (a)
egl-38 35
  • 59 (a)
pax-3 34
  • 45 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 36 (a)
Species where no ortholog for PAX3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PAX3 Gene

Gene Tree for PAX3 (if available)
Gene Tree for PAX3 (if available)

Paralogs for PAX3 Gene

Paralogs for PAX3 Gene

(10) SIMAP similar genes for PAX3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PAX3: view

Variants for PAX3 Gene

Sequence variations from dbSNP and Humsavar for PAX3 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1020175890 syndrome 1 (WS1) [MIM:193500] 222,221,362(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant
rs104893650 pathogenic, Waardenburg syndrome type 1, Waardenburg syndrome 1 (WS1) [MIM:193500] 222,297,150(-) G/A coding_sequence_variant, missense_variant
rs104893651 pathogenic, Klein-Waardenberg's syndrome, Waardenburg syndrome type 1, Waardenburg syndrome 3 (WS3) [MIM:148820] 222,297,048(-) G/A coding_sequence_variant, missense_variant
rs104893652 pathogenic, Craniofacial deafness hand syndrome, Craniofacial-deafness-hand syndrome (CDHS) [MIM:122880] 222,297,158(-) G/C coding_sequence_variant, missense_variant
rs104893653 pathogenic, Klein-Waardenberg's syndrome, Waardenburg syndrome 3 (WS3) [MIM:148820] 222,297,160(-) T/G coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for PAX3 Gene

Variant ID Type Subtype PubMed ID
esv3584357 CNV loss 25503493
nsv516764 CNV loss 19592680
nsv834549 CNV gain 17160897
nsv834550 CNV gain 17160897

Variation tolerance for PAX3 Gene

Residual Variation Intolerance Score: 59.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.12; 51.28% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PAX3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PAX3 Gene

Disorders for PAX3 Gene

MalaCards: The human disease database

(38) MalaCards diseases for PAX3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PAX3 in MalaCards View complete list of genes associated with diseases


  • Craniofacial-deafness-hand syndrome (CDHS) [MIM:122880]: Thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness. {ECO:0000269 PubMed:8664898}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children. {ECO:0000269 PubMed:15313887}.
  • Rhabdomyosarcoma 2 (RMS2) [MIM:268220]: A form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchymal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. {ECO:0000269 PubMed:8275086}. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator. {ECO:0000269 PubMed:8275086}.
  • Waardenburg syndrome 1 (WS1) [MIM:193500]: WS1 is an autosomal dominant disorder characterized by non-progressive sensorineural deafness, pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma, and wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum). WS1 shows variable clinical expression and some affected individuals do not manifest hearing impairment or iris pigmentation disturbances. Dystopia canthorum is the most consistent sign and is found in 98% of the patients. {ECO:0000269 PubMed:10779847, ECO:0000269 PubMed:12949970, ECO:0000269 PubMed:1303193, ECO:0000269 PubMed:1347148, ECO:0000269 PubMed:1347149, ECO:0000269 PubMed:16971891, ECO:0000269 PubMed:20478267, ECO:0000269 PubMed:21965087, ECO:0000269 PubMed:7825605, ECO:0000269 PubMed:7833953, ECO:0000269 PubMed:7981674, ECO:0000269 PubMed:8447316, ECO:0000269 PubMed:8490648, ECO:0000269 PubMed:8533800, ECO:0000269 PubMed:8589691, ECO:0000269 PubMed:8845842, ECO:0000269 PubMed:9067759, ECO:0000269 PubMed:9452070, ECO:0000269 PubMed:9541113, ECO:0000269 Ref.35}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Waardenburg syndrome 3 (WS3) [MIM:148820]: WS3 is an autosomal dominant disorder characterized by sensorineural deafness, pigmentary disturbances, dystopia canthorum and limb anomalies such as hypoplasia of the musculoskeletal system, flexion contractures, fusion of the carpal bones, syndactylies. {ECO:0000269 PubMed:12949970, ECO:0000269 PubMed:7726174, ECO:0000269 PubMed:8447316, ECO:0000269 Ref.36}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PAX3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PAX3: view

No data available for Genatlas for PAX3 Gene

Publications for PAX3 Gene

  1. Structural basis for DNA recognition by the human PAX3 homeodomain. (PMID: 19199574) Birrane G … Ladias JA (Biochemistry 2009) 3 4 22 58
  2. A novel mutation of PAX3 in a Chinese family with Waardenburg syndrome. (PMID: 16971891) Qin W … He L (Molecular vision 2006) 3 4 22 58
  3. Homozygous and heterozygous inheritance of PAX3 mutations causes different types of Waardenburg syndrome. (PMID: 12949970) Wollnik B … Yuksel-Apak M (American journal of medical genetics. Part A 2003) 3 4 22 58
  4. The Pax3-FKHR oncoprotein is unresponsive to the Pax3-associated repressor hDaxx. (PMID: 10393185) Hollenbach AD … Grosveld G (The EMBO journal 1999) 3 4 22 58
  5. Septo-optic dysplasia and WS1 in the proband of a WS1 family segregating for a novel mutation in PAX3 exon 7. (PMID: 9541113) Carey ML … Innis JW (Journal of medical genetics 1998) 3 4 22 58

Products for PAX3 Gene

Sources for PAX3 Gene

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