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Gene

PITX2

paired like homeodomain 2

Summary

Cytogenetic location
4q25
Coordinates
Chromosome 4: 110,617,423–110,623,077 (GRCh38)
Exons
3 exons across 5.7 kb
Protein
324 amino acids
Inheritance
Autosomal dominant
Also known as
IGDS, RS, Brx1, Otlx2, ARP1
Previous symbols
IRID2, IHG2, RIEG, RIEG1, RGS
MANE Select transcript
ENST00000644743.1NM_000325.6
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

  • Anterior Segment Dysgenesis, Axenfeld-Rieger Syndrome & Aniridia

    • Axenfeld-Rieger SyndromeAutosomal dominant

      A dominant condition caused by changes in PITX2 or FOXC1, affecting the iris and drainage angle and sometimes the teeth, face and navel.

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

      Lifelong glaucoma surveillance is recommended, as about half of affected people develop glaucoma.

    • 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.

      • ClinGen rates the link definitive
      • 3 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.

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 PITX2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 4, with a bracket where PITX2 sits. PITX2 and 2 genes near it on chromosome 4, from 110,120,250 to 111,120,249.Chromosome 44q25p16.3p16.2p16.1p15.33p15.32p15.31p15.2p15.1p14p13p12p11q11q12q13.1q13.2q13.3q21.1q21.21q21.22q21.23q21.3q22.1q22.2q22.3q23q24q25q26q27q28.1q28.2q28.3q31.1q31.21q31.22q31.23q31.3q32.1q32.2q32.3q33q34.1q34.2q34.3q35.1q35.2110.2 Mb110.4 Mb110.6 Mb110.8 Mb111 MbELOVL6: 110,045,846–110,199,205, reverse strandELOVL6ENPEP: 110,365,733–110,565,286, forward strandENPEPPITX2: 110,617,423–110,623,077, reverse strandPITX2Diagram of PITX2: 3 exons on the reverse strand of chromosome 4Exon 3: 25 known disease-causing sitesExon 2: 22 known disease-causing sitesExon 3: 110,617,423–110,618,688, 1,266 basesExon 2: 110,621,164–110,621,369, 206 basesExon 1: 110,622,256–110,623,077, 822 bases3215′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 2.3 kb of the gene's 5.7 kb; 975 of those bases code for the protein.

How a genome test reads PITX2

52

positions in PITX2 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 5.7 kb of PITX2, introns included, not only the 2.3 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.). PITX2 gene: paired like homeodomain 2. Retrieved 16 October 2026, from https://dantelabs.com/genes/pitx2

Vancouver

Dante Labs. PITX2 gene: paired like homeodomain 2 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pitx2

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