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Gene

PAX6

paired box 6

Summary

Cytogenetic location
11p13
Coordinates
Chromosome 11: 31,789,026–31,811,322 (GRCh38)
Exons
14 exons across 22.3 kb
Protein
436 amino acids
Inheritance
Autosomal dominant
Also known as
D11S812E, AN, WAGR
Previous symbols
AN1, AN2
MANE Select transcript
ENST00000640368.2NM_001368894.2
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 reports relevant to this gene

  • Anterior Segment Dysgenesis, Axenfeld-Rieger Syndrome & Aniridia

    • AniridiaAutosomal dominant

      A dominant condition, usually caused by changes in or deletions of PAX6, in which the iris is partly or completely absent, often with reduced vision and nystagmus.

      • 3 GenCC submitters rate it definitive or strong
      What knowing changes

      Regular monitoring for glaucoma, cataract and corneal changes is recommended; when a deletion also includes the nearby WT1 gene, children need screening for Wilms tumour.

    • Anterior Segment Dysgenesis

      A group of developmental conditions of the front of the eye, including Peters anomaly, caused by changes in genes such as FOXC1, PITX3, FOXE3, CYP1B1 and CPAMD8.

      • 2 GenCC submitters rate it definitive or strong
      What knowing changes

      There is a high lifetime risk of glaucoma, so regular eye-pressure monitoring is recommended.

  • Diabetes Mellitus

    • A metabolic disorder characterized by abnormally high blood sugar levels due to diminished production of insulin or insulin resistance/desensitization.

      • 1 GenCC submitter rates it definitive or strong
      What knowing changes

      Teplizumab (Tzield) for stage 2 presymptomatic T1D (FDA approved 2022); insulin replacement at clinical T1D onset; TrialNet autoantibody screening for high-risk relatives; closed-loop insulin delivery systems

  • Kidney Cancer

    • Primary or metastatic malignant neoplasm involving the kidney.

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

  • Urinary and Renal System Tumour

    • Urinary System Neoplasm

      A benign or malignant, primary or metastatic neoplasm involving the urinary system.

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

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How PAX6 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 11, with a bracket where PAX6 sits. PAX6 and 6 genes near it on chromosome 11, from 31,300,174 to 32,300,173.Chromosome 1111p13p15.5p15.4p15.3p15.2p15.1p14.3p14.2p14.1p13p12p11.2p11.12p11.11q11q12.1q12.2q12.3q13.1q13.2q13.3q13.4q13.5q14.1q14.2q14.3q21q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q2531.4 Mb31.6 Mb31.8 Mb32 Mb32.2 MbDCDC1: 30,830,369–31,369,810, reverse strandDCDC1DNAJC24: 31,369,799–31,432,835, forward strandDNAJC24IMMP1L: 31,432,399–31,509,656, reverse strandIMMP1LELP4: 31,509,745–31,790,324, forward strandELP4PAX6: 31,789,026–31,811,322, reverse strandPAX6: 31,812,391–32,104,665, forward strandRCN1: 32,090,968–32,107,639, forward strandRCN1Diagram of PAX6: 14 exons on the reverse strand of chromosome 11Exon 14: 5 known disease-causing sitesExon 13: 12 known disease-causing sitesExon 12: 10 known disease-causing sitesExon 11: 14 known disease-causing sitesExon 10: 5 known disease-causing sitesExon 9: 15 known disease-causing sitesExon 8: 27 known disease-causing sitesExon 7: 29 known disease-causing sitesExon 5: 39 known disease-causing sitesExon 4: 5 known disease-causing sitesExon 3: 1 known disease-causing siteExon 14: 31,789,026–31,790,019, 994 basesExon 13: 31,790,710–31,790,860, 151 basesExon 12: 31,793,438–31,793,553, 116 basesExon 11: 31,793,652–31,793,802, 151 basesExon 10: 31,794,032–31,794,114, 83 basesExon 9: 31,794,630–31,794,788, 159 basesExon 8: 31,800,691–31,800,856, 166 basesExon 7: 31,801,561–31,801,776, 216 basesExon 6: 31,801,871–31,801,912, 42 basesExon 5: 31,802,704–31,802,834, 131 basesExon 4: 31,806,402–31,806,462, 61 basesExon 3: 31,806,849–31,806,925, 77 basesExon 2: 31,810,828–31,811,015, 188 basesExon 1: 31,811,115–31,811,322, 208 bases1410515′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 2.7 kb of the gene's 22.3 kb; 1,311 of those bases code for the protein.

How a genome test reads PAX6

201

positions in PAX6 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 22.3 kb of PAX6, introns included, not only the 2.7 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.). PAX6 gene: paired box 6. Retrieved 16 October 2026, from https://dantelabs.com/genes/pax6

Vancouver

Dante Labs. PAX6 gene: paired box 6 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pax6

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