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PAX3 paired box 3 [ Homo sapiens (human) ]

Gene ID: 5077, updated on 10-Mar-2024

Summary

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Official Symbol
PAX3provided by HGNC
Official Full Name
paired box 3provided by HGNC
Primary source
HGNC:HGNC:8617
See related
Ensembl:ENSG00000135903 MIM:606597; AllianceGenome:HGNC:8617
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
WS1; WS3; CDHS; HUP2; PAX-3
Summary
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]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
2q36.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (222199887..222298998, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (222684993..222784124, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223064606..223163717, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:222849491-222850043 Neighboring gene heat shock protein family A (Hsp70) member 9 pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:222889616-222890602 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:222890603-222891589 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:222917569-222918330 Neighboring gene ribosomal protein L23a pseudogene 28 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:223072996-223073618 Neighboring gene uncharacterized LOC107985991 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:223084735-223085934 Neighboring gene NANOG hESC enhancer GRCh37_chr2:223137199-223137802 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:223154577-223155490 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:223155491-223156404 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:223158467-223159003 Neighboring gene PAX3 promoter region Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171419-223171954 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223171955-223172489 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:223182883-223183478 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12367 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12368 Neighboring gene CCDC140 long non-coding RNA Neighboring gene ring finger protein 228 Neighboring gene cancer/testis associated transcript 75 Neighboring gene NANOG hESC enhancer GRCh37_chr2:223258471-223259068 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12369 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17164 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17165 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17166 Neighboring gene sphingosine-1-phosphate phosphatase 2 Neighboring gene Nanog homeobox pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Restoration of functional PAX3 transcriptional factor enhanced neuronal differentiation in PAX3b isoform-depleted neuroblastoma cells. Muralidharan N, et al. Cell Tissue Res, 2023 Jan. PMID 36378335
  2. A Novel Variant in Paired Box 3 Gene-related with Waardenburg Syndrome Type-1 in an Afghan Family. Dogan M, et al. J Coll Physicians Surg Pak, 2022 Aug. PMID 36210664
  3. Downregulation of the paired box gene 3 inhibits the progression of skin cutaneous melanoma by inhibiting c-MET tyrosine kinase : PAX3 downregulation inhibits melanoma progression. Zhang K, et al. Mol Biol Rep, 2022 Oct. PMID 36057879
  4. A Novel PAX3 Variant in a Chinese Pedigree with Nonsyndromic Cleft Lip With or Without Palate. Liang W, et al. Genet Test Mol Biomarkers, 2021 Dec. PMID 34918979
  5. [Genotype and phenotype analysis of a family with Waardenburg syndrome type â… caused by a novel mutation in PAX3 gene]. Li X, et al. Lin Chuang Er Bi Yan Hou Tou Jing Wai Ke Za Zhi, 2021 Jul. PMID 34304492, Free PMC Article

See all (254) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PAX3 mutation suppress otic progenitors proliferation and induce apoptosis by inhibiting WNT1/beta-catenin signaling pathway in WS1 patient iPSC-derived inner ear organoids.
    Title: PAX3 mutation suppress otic progenitors proliferation and induce apoptosis by inhibiting WNT1/β-catenin signaling pathway in WS1 patient iPSC-derived inner ear organoids.
  2. Comparative study on the expression of Pax3, Rad51 and VEGF-C in esophageal gastric junction adenocarcinoma and distal gastric adenocarcinoma.
    Title: Comparative study on the expression of Pax3, Rad51 and VEGF-C in esophageal gastric junction adenocarcinoma and distal gastric adenocarcinoma.
  3. PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
    Title: PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
  4. Identification of two variants in PAX3 and FBN1 in a Chinese family with Waardenburg and Marfan syndrome via whole exome sequencing.
    Title: Identification of two variants in PAX3 and FBN1 in a Chinese family with Waardenburg and Marfan syndrome via whole exome sequencing.
  5. Restoration of functional PAX3 transcriptional factor enhanced neuronal differentiation in PAX3b isoform-depleted neuroblastoma cells.
    Title: Restoration of functional PAX3 transcriptional factor enhanced neuronal differentiation in PAX3b isoform-depleted neuroblastoma cells.
  6. A Novel Variant in Paired Box 3 Gene-related with Waardenburg Syndrome Type-1 in an Afghan Family.
    Title: A Novel Variant in Paired Box 3 Gene-related with Waardenburg Syndrome Type-1 in an Afghan Family.
  7. Identification of nine novel variants across PAX3, SOX10, EDNRB, and MITF genes in Waardenburg syndrome with next-generation sequencing.
    Title: Identification of nine novel variants across PAX3, SOX10, EDNRB, and MITF genes in Waardenburg syndrome with next-generation sequencing.
  8. Downregulation of the paired box gene 3 inhibits the progression of skin cutaneous melanoma by inhibiting c-MET tyrosine kinase : PAX3 downregulation inhibits melanoma progression.
    Title: Downregulation of the paired box gene 3 inhibits the progression of skin cutaneous melanoma by inhibiting c-MET tyrosine kinase : PAX3 downregulation inhibits melanoma progression.
  9. Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs.
    Title: Divergent transcriptional and transforming properties of PAX3-FOXO1 and PAX7-FOXO1 paralogs.
  10. [Alveolar rhabdomyosarcoma: Two fusion-negative cases lacking PAX3-FOXO1 and PAX7-FOXO1].", trans "Rabdomiosarcoma alveolar. Dos casos negativos para la fusion PAX3-FOXO1 y PAX7-FOXO1.
    Title: [Alveolar rhabdomyosarcoma: Two fusion-negative cases lacking PAX3-FOXO1 and PAX7-FOXO1].
Submit: New GeneRIF Correction See all GeneRIFs (173)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Alveolar rhabdomyosarcoma
MedGen: C0206655 OMIM: 268220 GeneReviews: Not available
Compare labs
Craniofacial-deafness-hand syndrome
MedGen: C1852510 OMIM: 122880 GeneReviews: Not available
Compare labs
Waardenburg syndrome type 1
MedGen: C1847800 OMIM: 193500 GeneReviews: Waardenburg Syndrome Type I
Compare labs
Waardenburg syndrome type 3
MedGen: C0079661 OMIM: 148820 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-05-27)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-05-27)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
EBI GWAS Catalog
Genome-wide association study of three-dimensional facial morphology identifies a variant in PAX3 associated with nasion position.
EBI GWAS Catalog
Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC120381, MGC120382, MGC120383, MGC120384, MGC134778

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables HMG box domain binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in animal organ morphogenesis TAS
Traceable Author Statement
more info
 PubMed 
involved_in apoptotic process TAS
Traceable Author Statement
more info
 PubMed 
involved_in muscle organ development IEA
Inferred from Electronic Annotation
more info
  
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sensory perception of sound TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
paired box protein Pax-3
Names
paired box homeotic gene 3
paired domain gene 3
paired domain gene HuP2
transcriptional factor PAX3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011632.1 RefSeqGene

    Range
    4984..104095
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000438.6 → NP_000429.2  paired box protein Pax-3 isoform PAX3a

    See identical proteins and their annotated locations for NP_000429.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3A) differs in the 3' UTR, includes an alternate segment in the coding region, which causes a frameshift, and lacks several segments in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3a) has a shorter and distinct C-terminus, compared to isoform PAX3. Isoform PAX3a lacks the paired-type homeodomain.
    Source sequence(s)
    AC010980, BC101299, DA758804, S69369
    Consensus CDS
    CCDS46523.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000386817.3, ENST00000409828.7
    Conserved Domains (1) summary
    pfam00292
    Location:34 → 159
    PAX; 'Paired box' domain

  2. NM_001127366.3 → NP_001120838.1  paired box protein Pax-3 isoform PAX3i

    See identical proteins and their annotated locations for NP_001120838.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3I) differs in the 3' UTR, uses an alternate in-frame splice site in the 5' coding region, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3i, also known as isoform PAX3dQ-) is longer and has a distinct C-terminus, compared to isoform PAX3.
    Source sequence(s)
    AC010980, AC012591, AI382779, BC101299, DA758804
    Consensus CDS
    CCDS46522.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000386750.3, ENST00000409551.7
    Conserved Domains (3) summary
    smart00351
    Location:34 → 158
    PAX; Paired Box domain
    pfam00046
    Location:221 → 275
    Homeobox; Homeobox domain
    pfam12360
    Location:346 → 390
    Pax7; Paired box protein 7

  3. NM_013942.5 → NP_039230.1  paired box protein Pax-3 isoform PAX3b

    See identical proteins and their annotated locations for NP_039230.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3B) differs in the 3' UTR, includes an alternate segment in the coding region, which causes a frameshift, and lacks several segments in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3a) has a shorter and distinct C-terminus, compared to isoform PAX3. Isoform PAX3b lacks the paired-type homeodomain.
    Source sequence(s)
    AC010980, BC063547, BC101299, DA758804
    Consensus CDS
    CCDS2451.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000258387.5, ENST00000258387.6
    Conserved Domains (1) summary
    pfam00292
    Location:34 → 159
    PAX; 'Paired box' domain

  4. NM_181457.4 → NP_852122.1  paired box protein Pax-3 isoform PAX3

    See identical proteins and their annotated locations for NP_852122.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3) encodes isoform PAX3 (also known as isoform PAX3c).
    Source sequence(s)
    AC010980, AC012591, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS42826.1
    UniProtKB/Swiss-Prot
    G5E9C1, P23760, Q16448, Q494Z3, Q494Z4, Q53T90, Q6GSJ9, Q86UQ2, Q86UQ3
    Related
    ENSP00000343052.4, ENST00000350526.9
    Conserved Domains (4) summary
    pfam12360
    Location:347 → 391
    Pax7; Paired box protein 7
    pfam00046
    Location:222 → 275
    Homeobox; Homeobox domain
    pfam00292
    Location:34 → 159
    PAX; 'Paired box' domain
    pfam06991
    Location:163 → 286
    MFAP1; Microfibril-associated/Pre-mRNA processing

  5. NM_181458.4 → NP_852123.1  paired box protein Pax-3 isoform PAX3d

    See identical proteins and their annotated locations for NP_852123.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3D) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3d) is longer and has a distinct C-terminus, compared to isoform PAX3.
    Source sequence(s)
    AC010980, AC012591, AI382779, AK291278, BC101299, BC101301
    Consensus CDS
    CCDS42825.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000375922.3, ENST00000392070.7
    Conserved Domains (3) summary
    smart00351
    Location:34 → 159
    PAX; Paired Box domain
    pfam00046
    Location:222 → 276
    Homeobox; Homeobox domain
    pfam12360
    Location:347 → 391
    Pax7; Paired box protein 7

  6. NM_181459.4 → NP_852124.1  paired box protein Pax-3 isoform PAX3e

    See identical proteins and their annotated locations for NP_852124.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3E) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3e) is longer and has a distinct C-terminus, compared to isoform PAX3.
    Source sequence(s)
    AC010980, AC012591, AI382779, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS2448.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000375921.2, ENST00000392069.6
    Conserved Domains (3) summary
    smart00351
    Location:34 → 159
    PAX; Paired Box domain
    pfam00046
    Location:222 → 276
    Homeobox; Homeobox domain
    pfam12360
    Location:347 → 391
    Pax7; Paired box protein 7

  7. NM_181460.4 → NP_852125.1  paired box protein Pax-3 isoform PAX3h

    See identical proteins and their annotated locations for NP_852125.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3H) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3h) is shorter and has a distinct C-terminus, compared to variant PAX3.
    Source sequence(s)
    AC010980, AC012591, AI382779, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS2449.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000338767.5, ENST00000336840.11
    Conserved Domains (4) summary
    pfam12360
    Location:347 → 391
    Pax7; Paired box protein 7
    pfam00046
    Location:222 → 275
    Homeobox; Homeobox domain
    pfam00292
    Location:34 → 159
    PAX; 'Paired box' domain
    pfam06991
    Location:163 → 286
    MFAP1; Microfibril-associated/Pre-mRNA processing

  8. NM_181461.4 → NP_852126.1  paired box protein Pax-3 isoform PAX3g

    See identical proteins and their annotated locations for NP_852126.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3G) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3g) is shorter and has a distinct C-terminus, compared to variant PAX3.
    Source sequence(s)
    AC010980, AC012591, AI382779, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS2450.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000342092.4, ENST00000344493.9
    Conserved Domains (3) summary
    pfam00046
    Location:222 → 275
    Homeobox; Homeobox domain
    pfam00292
    Location:34 → 159
    PAX; 'Paired box' domain
    pfam12360
    Location:347 → 391
    Pax7; Paired box protein 7

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    222199887..222298998 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    222684993..222784124 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P23760.2 GenPept UniProtKB/Swiss-Prot:P23760

Gene LinkOut

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