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Gene

OTX2

orthodenticle homeobox 2

Summary

Cytogenetic location
14q22.3
Coordinates
Chromosome 14: 56,799,905–56,810,479 (GRCh38)
Exons
5 exons across 10.6 kb
Protein
297 amino acids
MANE Select transcript
ENST00000672264.2NM_021728.4
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

  • Hypogonadotropic Hypogonadism

    • Abnormal ovarian or testicular function due to insufficient hormonal stimulation from the hypothalamic-pituitary axis.

      • 1 GenCC submitter rates it definitive or strong

  • Microphthalmia, Anophthalmia & Coloboma

    • Syndromic Microphthalmia

      Microphthalmia occurring with features outside the eye, caused by changes in genes such as SOX2, OTX2, BCOR, STRA6 and BMP4.

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

      A genetic diagnosis guides checks for associated features, such as pituitary hormone problems with SOX2 or OTX2, and informs recurrence risk.

  • Non-Acquired Combined Pituitary Hormone Deficiency

    • Combined pituitary hormone deficiency, genetic form

      Inherited deficiency of several pituitary hormones, including PROP1, POU1F1, HESX1 and related causes.

      • 1 GenCC submitter rates it definitive or strong

How OTX2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 14, with a bracket where OTX2 sits. OTX2 and 3 genes near it on chromosome 14, from 56,305,192 to 57,305,191.Chromosome 1414q22.3p13p12p11.2p11.1q11.1q11.2q12q13.1q13.2q13.3q21.1q21.2q21.3q22.1q22.2q22.3q23.1q23.2q23.3q24.1q24.2q24.3q31.1q31.2q31.3q32.11q32.12q32.13q32.2q32.31q32.32q32.3356.4 Mb56.6 Mb56.8 Mb57 Mb57.2 MbTMEM260: 56,488,354–56,650,606, forward strandTMEM260OTX2: 56,799,905–56,810,479, reverse strandOTX2EXOC5: 57,200,507–57,268,974, reverse strandEXOC5AP5M1: 57,268,446–57,298,742, forward strandAP5M1Diagram of OTX2: 5 exons on the reverse strand of chromosome 14Exon 5: 11 known disease-causing sitesExon 4: 1 known disease-causing siteExon 5: 56,799,905–56,802,355, 2,451 basesExon 4: 56,804,188–56,804,363, 176 basesExon 3: 56,805,360–56,805,575, 216 basesExon 2: 56,810,159–56,810,222, 64 basesExon 1: 56,810,376–56,810,479, 104 bases543215′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 kb of the gene's 10.6 kb; 894 of those bases code for the protein.

How a genome test reads OTX2

12

positions in OTX2 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 10.6 kb of OTX2, introns included, not only the 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.). OTX2 gene: orthodenticle homeobox 2. Retrieved 17 October 2026, from https://dantelabs.com/genes/otx2

Vancouver

Dante Labs. OTX2 gene: orthodenticle homeobox 2 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/otx2

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