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Gene

PITX3

paired like homeodomain 3

Summary

Cytogenetic location
10q24.32
Coordinates
Chromosome 10: 102,230,189–102,241,512 (GRCh38)
Exons
4 exons across 11.3 kb
Protein
302 amino acids
Previous symbols
ASMD
MANE Select transcript
ENST00000370002.8NM_005029.4
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 reports relevant to this gene

  • Anterior Segment Dysgenesis, Axenfeld-Rieger Syndrome & Aniridia

    • 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.

  • Hereditary Congenital & Juvenile Cataract

    • Early-Onset Non-Syndromic Cataract

      Cataract that appears at birth or early in life without other features, caused by changes in lens genes such as the crystallins (CRYAA, CRYBB2, CRYGD and others), GJA3, GJA8 and MIP.

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

      Early detection and surgery in children help prevent permanent vision loss from amblyopia, and family members can be offered eye checks.

How PITX3 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 10, with a bracket where PITX3 sits. PITX3 and 22 genes near it on chromosome 10, from 101,735,851 to 102,735,850.Chromosome 1010q24.32p15.3p15.2p15.1p14p13p12.33p12.32p12.31p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.31q23.32q23.33q24.1q24.2q24.31q24.32q24.33q25.1q25.2q25.3q26.11q26.12q26.13q26.2q26.3101.8 Mb102 Mb102.2 Mb102.4 Mb102.6 MbFGF8: 101,769,817–101,780,371, reverse strandFGF8NPM3: 101,781,318–101,783,446, reverse strandNPM3OGA: 101,784,443–101,818,620, reverse strandOGAKCNIP2: 101,825,969–101,844,005, reverse strandKCNIP2ARMH3: 101,845,599–102,056,262, reverse strandARMH3HPS6: 102,065,349–102,068,036, forward strandHPS6LDB1: 102,106,489–102,120,451, reverse strandLDB1PPRC1: 102,132,994–102,150,333, forward strandPPRC1NOLC1: 102,152,170–102,163,875, forward strandNOLC1ELOVL3: 102,226,294–102,229,589, forward strandELOVL3PITX3: 102,230,189–102,241,512, reverse strandPITX3GBF1: 102,245,371–102,382,899, forward strandGBF1NFKB2: 102,394,110–102,402,529, forward strandNFKB2PSD: 102,402,614–102,421,539, reverse strandPSDFBXL15: 102,408,835–102,423,142, forward strandFBXL15CUEDC2: 102,423,239–102,432,718, reverse strandCUEDC2C10orf95: 102,449,619–102,451,548, reverse strandSLC68A1: 102,461,363–102,477,046, forward strandSLC68A1ACTR1A: 102,461,881–102,502,744, reverse strandACTR1ASUFU: 102,503,952–102,633,535, forward strandSUFUTRIM8: 102,642,394–102,662,789, forward strandTRIM8ARL3: 102,673,731–102,714,527, reverse strandARL3SFXN2: 102,714,476–102,743,492, forward strandSFXN2Diagram of PITX3: 4 exons on the reverse strand of chromosome 10Exon 4: 4 known disease-causing sitesExon 4: 102,230,189–102,231,101, 913 basesExon 3: 102,231,588–102,231,790, 203 basesExon 2: 102,231,963–102,232,092, 130 basesExon 1: 102,241,333–102,241,512, 180 bases43215′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 1.4 kb of the gene's 11.3 kb; 909 of those bases code for the protein.

How a genome test reads PITX3

4

positions in PITX3 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 11.3 kb of PITX3, introns included, not only the 1.4 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.). PITX3 gene: paired like homeodomain 3. Retrieved 16 October 2026, from https://dantelabs.com/genes/pitx3

Vancouver

Dante Labs. PITX3 gene: paired like homeodomain 3 [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/pitx3

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