PAX3 paired box 3 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 2q36.1

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (222199887..222298998, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (222684993..222784124, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (223064606..223163717, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Waardenburg syndrome type 1: a case report of a family with a intragenic PAX3 deletion with no hearing loss or heterochromia of iris.
Title: Waardenburg syndrome type 1: a case report of a family with a intragenic PAX3 deletion with no hearing loss or heterochromia of iris.
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.
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.
PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
Title: PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
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.
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.
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.
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.
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.
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.

Submit: New GeneRIF Correction See all GeneRIFs (174)

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	not available
Craniofacial-deafness-hand syndrome MedGen: C1852510 OMIM: 122880 GeneReviews: Not available	not available
Waardenburg syndrome type 1 MedGen: C1847800 OMIM: 193500 GeneReviews: Waardenburg Syndrome Type I	not available
Waardenburg syndrome type 3 MedGen: C0079661 OMIM: 148820 GeneReviews: Not available	not available

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 EBI GWAS CatalogPubMed
Genome-wide association study of three-dimensional facial morphology identifies a variant in PAX3 associated with nasion position. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of vitamin D levels in children: replication in the Western Australian Pregnancy Cohort (Raine) study. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PAX3_1834 (e-PCR)
- UniSTS:280887

D2S2599 (e-PCR)
- UniSTS:68410

NoName (e-PCR)
- UniSTS:484684

GDB:512330 (e-PCR)
- UniSTS:157527

RH92856 (e-PCR)
- UniSTS:91243

D3S4187 (e-PCR)
- UniSTS:6540

GDB:596326 (e-PCR)
- UniSTS:158094

GDB:187424 (e-PCR)
- UniSTS:155553

D2S2197 (e-PCR), detects polymorphism
- UniSTS:9390

AFMA288WG9 (e-PCR)
- UniSTS:22195

RH45698 (e-PCR)
- UniSTS:72129

D16Bir10 (e-PCR), detects polymorphism
- UniSTS:142034

GDB:603632 (e-PCR)
- UniSTS:158185

GDB:603639 (e-PCR)
- UniSTS:158186

RH123290 (e-PCR)
- UniSTS:135667

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 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	IBA Inferred from Biological aspect of Ancestor 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
located_in 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

NG_011632.1 RefSeqGene

Range

4984..104095

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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