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GeneE
26 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PAX3
paired box 3
Chromosome 2 Β· 2q36.1
NCBI Gene: 5077Ensembl: ENSG00000135903.20HGNC: HGNC:8617UniProt: P23760
258PubMed Papers
24Diseases
0Drugs
190Pathogenic Variants
FUNCTIONAL ROLE
OncogeneTranscription Factor
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingsequence-specific DNA bindingsequence-specific double-stranded DNA bindingpositive regulation of transcription by RNA polymerase IIWaardenburg syndrome type 1Waardenburg syndrome type 3craniofacial-deafness-hand syndromeWaardenburg syndrome
✦AI Summary

PAX3 (paired box 3) is a transcription factor containing a highly conserved paired box motif and homeodomain that plays critical roles in development and disease 1. The protein consists of an N-terminal DNA-binding domain and a C-terminal transcriptional activation domain, functioning primarily as a transcriptional activator through two separate DNA-binding domains: the Paired Domain (PD) and Homeodomain (HD) 12. PAX3 is essential during embryonic development of skeletal muscle, central nervous system, and neural crest derivatives, regulating target genes that control proliferation, survival, differentiation, and cell motility 1. Loss-of-function mutations cause developmental defects including Waardenburg syndrome in humans, occurring through haploinsufficiency mechanisms 34. In cancer, PAX3 contributes to pathogenesis through chr2 rearrangements, particularly the PAX3-FOXO1 fusion in fusion-positive rhabdomyosarcoma (FP-RMS), an aggressive pediatric sarcoma 15. This fusion oncoprotein can reprogram non-myogenic cells like endothelial progenitors into malignant myogenic cells 5. PAX3-FOXO1 drives metabolic vulnerabilities in RMS cells, including increased dependence on pyrimidine synthesis enzymes like DHFR, making these tumors sensitive to methotrexate treatment 6. Wild-type PAX3 is also overexpressed in various cancers including melanoma and neuroblastoma, where it promotes oncogenic cellular behaviors 17.

Sources cited
1
PAX genes encode transcription factors with paired domains, and loss-of-function mutations cause developmental defects through haploinsufficiency
PMID: 7919921
2
PAX3 has two DNA-binding domains (Paired Domain and Homeodomain) that bind different DNA motifs and predominantly act on active genomic sites
PMID: 40428399
3
PAX3-FOXO1 fusion can reprogram endothelial progenitors to rhabdomyosarcoma and functional myogenic stem cells
PMID: 37968277
4
PAX3 structure, developmental roles, disease associations including Waardenburg syndrome and rhabdomyosarcoma
PMID: 29730428
5
PAX3-FOXO1 drives fusion-positive rhabdomyosarcoma and can be targeted through KDM inhibitors
PMID: 38402212
6
PAX3 regulates growth, migration, differentiation and survival during development and is overexpressed in multiple cancers
PMID: 41897383
7
Homozygous PAX3 mutations cause more severe phenotypes than heterozygous mutations in Waardenburg syndrome
PMID: 9021013
8
PAX3-FOXO1 drives metabolic vulnerabilities including pyrimidine dependence and DHFR sensitivity to methotrexate
PMID: 40911784
Disease Associationsβ“˜24
Waardenburg syndrome type 1Open Targets
0.85Strong
Waardenburg syndrome type 3Open Targets
0.77Strong
craniofacial-deafness-hand syndromeOpen Targets
0.76Strong
Waardenburg syndromeOpen Targets
0.68Moderate
alveolar rhabdomyosarcomaOpen Targets
0.64Moderate
rhabdomyosarcomaOpen Targets
0.58Moderate
Rare genetic deafnessOpen Targets
0.49Moderate
androgenetic alopeciaOpen Targets
0.48Moderate
hair colorOpen Targets
0.48Moderate
neurodegenerative diseaseOpen Targets
0.46Moderate
genetic disorderOpen Targets
0.41Moderate
skin agingOpen Targets
0.41Moderate
carcinoma of liver and intrahepatic biliary tractOpen Targets
0.37Weak
embryonal rhabdomyosarcomaOpen Targets
0.37Weak
spindle cell rhabdomyosarcomaOpen Targets
0.37Weak
desmoplastic small round cell tumorOpen Targets
0.37Weak
Ewing sarcoma/peripheral primitive neuroectodermal tumor of boneOpen Targets
0.37Weak
lymphoid neoplasmOpen Targets
0.37Weak
malignant soft tissue neoplasmOpen Targets
0.37Weak
Sinonasal Undifferentiated CarcinomaOpen Targets
0.37Weak
Craniofacial-deafness-hand syndromeUniProt
Rhabdomyosarcoma 2UniProt
Waardenburg syndrome 1UniProt
Waardenburg syndrome 3UniProt
Pathogenic Variants190
NM_181458.4(PAX3):c.808C>T (p.Arg270Cys)Pathogenic
Waardenburg syndrome type 1|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 270
NM_181458.4(PAX3):c.1277C>A (p.Ser426Ter)Pathogenic
Waardenburg syndrome type 1|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 426
NM_181458.4(PAX3):c.811C>T (p.Arg271Cys)Pathogenic
Waardenburg syndrome type 1|not provided|Waardenburg syndrome|Inborn genetic diseases
β˜…β˜…β˜†β˜†2025β†’ Residue 271
NM_181458.4(PAX3):c.86-2A>CPathogenic
Waardenburg syndrome type 1|not provided
β˜…β˜…β˜†β˜†2025
NM_181458.4(PAX3):c.452-1G>APathogenic
Craniofacial-deafness-hand syndrome;Waardenburg syndrome type 3;Alveolar rhabdomyosarcoma;Waardenburg syndrome type 1|Waardenburg syndrome type 1|Monogenic hearing loss
β˜…β˜…β˜†β˜†2025
NM_181458.4(PAX3):c.793-1G>APathogenic
Waardenburg syndrome type 1|not provided
β˜…β˜…β˜†β˜†2025
NM_181458.4(PAX3):c.873dup (p.Gly292fs)Pathogenic
Rare genetic deafness|See cases|not provided|Waardenburg syndrome type 1
β˜…β˜…β˜†β˜†2025β†’ Residue 292
NM_181458.4(PAX3):c.812G>A (p.Arg271His)Pathogenic
not provided|Waardenburg syndrome type 1|Craniofacial-deafness-hand syndrome;Alveolar rhabdomyosarcoma;Waardenburg syndrome type 3;Waardenburg syndrome type 1|Craniofacial-deafness-hand syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 271
NM_181458.4(PAX3):c.879del (p.Phe294fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 294
NM_181458.4(PAX3):c.583C>T (p.Arg195Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 195
NM_181458.4(PAX3):c.667C>T (p.Arg223Ter)Pathogenic
not provided|Waardenburg syndrome type 1|Waardenburg syndrome type 3
β˜…β˜…β˜†β˜†2025β†’ Residue 223
NM_181458.4(PAX3):c.142G>C (p.Gly48Arg)Pathogenic
Waardenburg syndrome type 1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 48
NM_181458.4(PAX3):c.784C>T (p.Arg262Ter)Pathogenic
not provided|Waardenburg syndrome type 1
β˜…β˜…β˜†β˜†2025β†’ Residue 262
NM_181458.4(PAX3):c.142G>T (p.Gly48Cys)Likely pathogenic
Waardenburg syndrome type 1|Waardenburg syndrome type 3
β˜…β˜…β˜†β˜†2024β†’ Residue 48
NM_181458.4(PAX3):c.218C>T (p.Ser73Leu)Pathogenic
Waardenburg syndrome type 1|Waardenburg syndrome
β˜…β˜…β˜†β˜†2024β†’ Residue 73
NM_181458.4(PAX3):c.241G>C (p.Gly81Arg)Pathogenic
Waardenburg syndrome type 1|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 81
NM_181458.4(PAX3):c.136dup (p.Ile46fs)Pathogenic
Waardenburg syndrome type 1|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 46
NM_181458.4(PAX3):c.210C>A (p.Cys70Ter)Pathogenic
Waardenburg syndrome type 1|not provided|PAX3-related disorder
β˜…β˜…β˜†β˜†2024β†’ Residue 70
NM_181458.4(PAX3):c.668G>A (p.Arg223Gln)Pathogenic
Rare genetic deafness;Waardenburg syndrome|not provided|Waardenburg syndrome type 1
β˜…β˜…β˜†β˜†2024β†’ Residue 223
NM_181458.4(PAX3):c.178G>A (p.Val60Met)Likely pathogenic
not provided|Waardenburg syndrome type 1
β˜…β˜…β˜†β˜†2024β†’ Residue 60
View on ClinVar β†—
Related Genes
DACH1Protein interaction96%EYA2Protein interaction95%FOXO1Protein interaction94%NCOA1Protein interaction94%MYF5Protein interaction90%MYF6Protein interaction90%
Tissue Expression6 tissues
Brain
100%
Lung
13%
Ovary
6%
Bone Marrow
0%
Heart
0%
Liver
0%
Gene Interaction Network
Click a node to explore
PAX3DACH1EYA2FOXO1NCOA1MYF5MYF6
PROTEIN STRUCTURE
Preparing viewer…
PDB3CMY Β· 1.95 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.41Moderately Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.26 [0.17–0.41]
RankingsWhere PAX3 stands among ~20K protein-coding genes
  • #1,484of 20,598
    Most Researched258 Β· top 10%
  • #367of 5,498
    Most Pathogenic Variants190 Β· top 10%
  • #2,090of 17,882
    Most Constrained (LOEUF)0.41 Β· top quartile
Genes detectedPAX3
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
PAX genes.
PMID: 7919921
Curr Opin Genet Dev Β· 1994
1.00
2
PAX3 Regulatory Signatures and Gene Targets in Melanoma Cells.
PMID: 40428399
Genes (Basel) Β· 2025
0.90
3
PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
PMID: 37968277
Nat Commun Β· 2023
0.80
4
Normal and rearranged PAX3 expression in human rhabdomyosarcoma.
PMID: 9546061
Cancer Genet Cytogenet Β· 1998
0.72
5
The expression and function of PAX3 in development and disease.
PMID: 29730428
Gene Β· 2018
0.70