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Gene

PAX9

paired box 9

Summary

Cytogenetic location
14q13.3
Coordinates
Chromosome 14: 36,661,860–36,679,362 (GRCh38)
Exons
4 exons across 17.5 kb
Protein
341 amino acids
MANE Select transcript
ENST00000361487.7NM_001372076.1
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

  • Hypodontia and Anodontia

    • Tooth Agenesis (Hypodontia)
      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

How PAX9 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 14, with a bracket where PAX9 sits. PAX9 and 5 genes near it on chromosome 14, from 36,170,611 to 37,170,610.Chromosome 1414q13.3p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.11q32.12q32.13q32.2q32.31q32.32q32.3336.2 Mb36.4 Mb36.6 Mb36.8 Mb37 MbMBIP: 36,298,231–36,320,680, reverse strandMBIPSFTA3: 36,473,207–36,521,149, reverse strandSFTA3NKX2-1: 36,516,392–36,521,149, reverse strandNKX2-1NKX2-8: 36,580,004–36,582,614, reverse strandNKX2-8PAX9: 36,661,860–36,679,362, forward strandPAX9SLC25A21: 36,677,921–37,172,743, reverse strandSLC25A21Diagram of PAX9: 4 exons on the forward strand of chromosome 14Exon 1: 2 known disease-causing sitesExon 2: 28 known disease-causing sitesExon 3: 2 known disease-causing sitesExon 1: 36,661,860–36,662,093, 234 basesExon 2: 36,662,897–36,663,523, 627 basesExon 3: 36,666,462–36,666,601, 140 basesExon 4: 36,676,198–36,679,362, 3,165 bases12345′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 4.2 kb of the gene's 17.5 kb; 1,026 of those bases code for the protein.

How a genome test reads PAX9

33

positions in PAX9 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 17.5 kb of PAX9, introns included, not only the 4.2 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.). PAX9 gene: paired box 9. Retrieved 16 October 2026, from https://dantelabs.com/genes/pax9

Vancouver

Dante Labs. PAX9 gene: paired box 9 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pax9

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