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PAX3 paired box 3 [ Homo sapiens (human) ]

Gene ID: 5077, updated on 5-Feb-2017
Official Symbol
PAX3provided by HGNC
Official Full Name
paired box 3provided by HGNC
Primary source
HGNC:HGNC:8617
See related
Ensembl:ENSG00000135903 MIM:606597; Vega:OTTHUMG00000133157
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
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]
Orthologs
Location:
2q36.1
Exon count:
10
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 2 NC_000002.12 (222199887..222298996, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223064606..223163715, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene heat shock protein family A (Hsp70) member 9 pseudogene 1 Neighboring gene ribosomal protein L23a pseudogene 28 Neighboring gene uncharacterized LOC107985991 Neighboring gene uncharacterized LOC105373901 Neighboring gene coiled-coil domain containing 140 Neighboring gene uncharacterized LOC440934 Neighboring gene sphingosine-1-phosphate phosphatase 2 Neighboring gene Nanog homeobox pseudogene 2

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Craniofacial deafness hand syndrome
MedGen: C1852510 OMIM: 122880 GeneReviews: Not available
Compare labs
Klein-Waardenberg's syndrome
MedGen: C0342680 OMIM: 148820 GeneReviews: Not available
Compare labs
Rhabdomyosarcoma alveolar
MedGen: C0206655 OMIM: 268220 GeneReviews: Not available
Compare labs
Waardenburg syndrome type 1
MedGen: C1847800 OMIM: 193500 GeneReviews: Waardenburg Syndrome Type I
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-11-02)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-11-02)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

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

Markers

Homology

Clone Names

  • MGC120381, MGC120382, MGC120383, MGC120384, MGC134778

Gene Ontology Provided by GOA

Function Evidence Code Pubs
HMG box domain binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription factor activity, sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
animal organ morphogenesis TAS
Traceable Author Statement
more info
PubMed 
apoptotic process TAS
Traceable Author Statement
more info
PubMed 
muscle organ development IEA
Inferred from Electronic Annotation
more info
 
nervous system development IEA
Inferred from Electronic Annotation
more info
 
neural crest formation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
sensory perception of sound TAS
Traceable Author Statement
more info
PubMed 
transcription from RNA polymerase II promoter TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
Preferred Names
paired box protein Pax-3
Names
paired box homeotic gene 3
paired domain gene 3
paired domain gene HuP2
transcriptional factor PAX3

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
    4986..102269
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000438.5NP_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, OTTHUMP00000202745, ENST00000409828, OTTHUMT00000328669
    Conserved Domains (1) summary
    pfam00292
    Location:34159
    PAX; 'Paired box' domain
  2. NM_001127366.2NP_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)
    AC012591, AI382779, BC101299, DA758804
    Consensus CDS
    CCDS46522.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000386750, OTTHUMP00000224703, ENST00000409551, OTTHUMT00000375096
    Conserved Domains (3) summary
    pfam00046
    Location:221274
    Homeobox; Homeobox domain
    pfam00292
    Location:34158
    PAX; 'Paired box' domain
    pfam12360
    Location:346390
    Pax7; Paired box protein 7
  3. NM_013942.4NP_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)
    BC063547, BC101299, DA758804, S69370
    Consensus CDS
    CCDS2451.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000258387, OTTHUMP00000164209, ENST00000258387, OTTHUMT00000256859
    Conserved Domains (1) summary
    pfam00292
    Location:34159
    PAX; 'Paired box' domain
  4. NM_181457.3NP_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)
    AC012591, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS42826.1
    UniProtKB/Swiss-Prot
    P23760
    UniProtKB/TrEMBL
    A0A024R470
    Related
    ENSP00000343052, OTTHUMP00000202746, ENST00000350526, OTTHUMT00000328670
    Conserved Domains (3) summary
    pfam00046
    Location:222275
    Homeobox; Homeobox domain
    pfam00292
    Location:34159
    PAX; 'Paired box' domain
    pfam12360
    Location:347391
    Pax7; Paired box protein 7
  5. NM_181458.3NP_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)
    AC012591, AI382779, AK291278, BC101299, BC101301
    Consensus CDS
    CCDS42825.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000375922, OTTHUMP00000202744, ENST00000392070, OTTHUMT00000328668
    Conserved Domains (3) summary
    pfam00046
    Location:222275
    Homeobox; Homeobox domain
    pfam00292
    Location:34159
    PAX; 'Paired box' domain
    pfam12360
    Location:347391
    Pax7; Paired box protein 7
  6. NM_181459.3NP_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)
    AC012591, AI382779, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS2448.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000375921, OTTHUMP00000205137, ENST00000392069, OTTHUMT00000334035
    Conserved Domains (3) summary
    pfam00046
    Location:222275
    Homeobox; Homeobox domain
    pfam00292
    Location:34159
    PAX; 'Paired box' domain
    pfam12360
    Location:347391
    Pax7; Paired box protein 7
  7. NM_181460.3NP_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)
    AC012591, AI382779, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS2449.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000338767, OTTHUMP00000164208, ENST00000336840, OTTHUMT00000256858
    Conserved Domains (3) summary
    pfam00046
    Location:222275
    Homeobox; Homeobox domain
    pfam00292
    Location:34159
    PAX; 'Paired box' domain
    pfam12360
    Location:347391
    Pax7; Paired box protein 7
  8. NM_181461.3NP_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)
    AC012591, AI382779, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS2450.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000342092, OTTHUMP00000164207, ENST00000344493, OTTHUMT00000256857
    Conserved Domains (3) summary
    pfam00046
    Location:222275
    Homeobox; Homeobox domain
    pfam00292
    Location:34159
    PAX; 'Paired box' domain
    pfam12360
    Location:347391
    Pax7; Paired box protein 7

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p7 Primary Assembly

    Range
    222199887..222298996 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 Alternate CHM1_1.1

    Range
    223071095..223170215 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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