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Gene

PAX3

paired box 3

Summary

Cytogenetic location
2q36.1
Coordinates
Chromosome 2: 222,199,887–222,298,998 (GRCh38)
Exons
9 exons across 99.1 kb
Protein
484 amino acids
Also known as
HUP2, PAX-3
Previous symbols
WS1
MANE Select transcript
ENST00000392070.7NM_181458.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

  • Waardenburg Syndrome

    • A group of conditions (types 1 to 4) causing hearing loss and pigment changes of the hair, skin and eyes, caused by genes such as PAX3, MITF, SOX10, EDNRB and EDN3.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

How PAX3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 2, with a bracket where PAX3 sits. PAX3 and 4 genes near it on chromosome 2, from 221,749,443 to 222,749,442.Chromosome 22q36.1p25.3p25.2p25.1p24.3p24.2p24.1p23.3p23.2p23.1p22.3p22.2p22.1p21p16.3p16.2p16.1p15p14p13.3p13.2p13.1p12p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13q14.1q14.2q14.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.1q32.2q32.3q33.1q33.2q33.3q34q35q36.1q36.2q36.3q37.1q37.2q37.3221.8 Mb222 Mb222.2 Mb222.4 Mb222.6 MbPAX3: 222,199,887–222,298,998, reverse strandPAX3RNF228: 222,314,148–222,320,155, reverse strandRNF228SGPP2: 222,423,982–222,650,897, forward strandSGPP2FARSB: 222,566,899–222,656,313, reverse strandFARSBMOGAT1: 222,671,512–222,710,001, forward strandMOGAT1Diagram of PAX3: 9 exons on the reverse strand of chromosome 2Exon 9: 1 known disease-causing siteExon 8: 3 known disease-causing sitesExon 7: 7 known disease-causing sitesExon 6: 13 known disease-causing sitesExon 5: 19 known disease-causing sitesExon 4: 5 known disease-causing sitesExon 3: 9 known disease-causing sitesExon 2: 29 known disease-causing sitesExon 1: 2 known disease-causing sitesExon 9: 222,199,887–222,201,442, 1,556 basesExon 8: 222,201,944–222,202,190, 247 basesExon 7: 222,220,140–222,220,354, 215 basesExon 6: 222,221,222–222,221,387, 166 basesExon 5: 222,232,078–222,232,283, 206 basesExon 4: 222,294,167–222,294,301, 135 basesExon 3: 222,295,528–222,295,657, 130 basesExon 2: 222,296,978–222,297,213, 236 basesExon 1: 222,298,531–222,298,998, 468 bases9515′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 3.4 kb of the gene's 99.1 kb; 1,455 of those bases code for the protein.

How a genome test reads PAX3

101

positions in PAX3 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 99.1 kb of PAX3, introns included, not only the 3.4 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). PAX3 gene: paired box 3. Retrieved 17 October 2026, from https://dantelabs.com/genes/pax3

Vancouver

Dante Labs. PAX3 gene: paired box 3 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/pax3

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