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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
OTX2
orthodenticle homeobox 2
Chromosome 14 Β· 14q22.3
NCBI Gene: 5015Ensembl: ENSG00000165588.19HGNC: HGNC:8522UniProt: F1T0C9
123PubMed Papers
23Diseases
0Drugs
61Pathogenic Variants
FUNCTIONAL ROLE
Highly Constrained
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein-containing complex assemblypositive regulation of transcription by RNA polymerase IIRNA polymerase II cis-regulatory region sequence-specific DNA bindingprotein-containing complexsyndromic microphthalmia type 5pituitary hormone deficiency, combined, 6Combined pituitary hormone deficiencies, genetic formsanophthalmia-microphthalmia syndrome
✦AI Summary

OTX2 is a transcription factor that functions as a critical regulator of early mammalian development and embryonic genome activation. In humans, OTX2 is maternally provided and acts as a PRD-like homeobox transcription factor essential for proper embryonic genome activation (EGA) beginning at the four-cell stage 1. OTX2 directly binds promoters and enhancers of key EGA genes including TPRX1 and TPRX2, promoting chr14 accessibility and activation of early developmental genes 1. The gene is also enriched at sites of 5-hydroxymethylcytosine modification and regulates early lineage gene expression during preimplantation development 2. Beyond EGA, OTX2 functions in formative pluripotency transitions, where it serves as a critical dependency factor for stem cell maintenance and lineage competency 3. OTX2 participates in establishing the anterior-posterior axis during post-implantation development and guides epiblast patterning through DKK1/OTX2 interactions 4. Clinically, OTX2 mutations cause combined pituitary hormone deficiency and syndromic microphthalmia 5. OTX2 also functions in the mouth gene program conserved across animal evolution 6. Aberrant OTX2 function appears linked to Group 4 medulloblastoma, where OTX2 knockdown relieves differentiation blockade in cerebellar progenitors 7.

Sources cited
1
OTX2 is a maternally provided PRD-like homeobox TF required for human EGA, directly binds EGA gene promoters and enhancers, and promotes chromatin accessibility
PMID: 41145868
2
OTX2 is enriched at 5hmC sites and regulates early lineage gene expression; knockdown compromises embryonic gene activation
PMID: 39080410
3
OTX2 is a critical transcription factor dependency in formative pluripotent stem cells
PMID: 33271069
4
OTX2 functions in anterior-posterior axis patterning and epiblast development through DKK1/OTX2 interactions in bilaminoid structures
PMID: 38052228
5
OTX2 mutations cause combined pituitary hormone deficiency
PMID: 28476222
6
OTX2 is part of conserved mouth gene program across animal evolution
PMID: 28514120
7
OTX2 mutations affect Group 4 medulloblastoma development; knockdown relieves differentiation blockade in cerebellar progenitors
PMID: 36131014
8
OTX2 expression in epiblast is suppressed by persistent Wnt signaling during peri-implantation development
PMID: 40441968
Disease Associationsβ“˜23
syndromic microphthalmia type 5Open Targets
0.82Strong
pituitary hormone deficiency, combined, 6Open Targets
0.69Moderate
Combined pituitary hormone deficiencies, genetic formsOpen Targets
0.62Moderate
anophthalmia-microphthalmia syndromeOpen Targets
0.55Moderate
AnophthalmiaOpen Targets
0.47Moderate
agnathia-otocephaly complexOpen Targets
0.46Moderate
major depressive disorderOpen Targets
0.44Moderate
Retinal dystrophyOpen Targets
0.42Moderate
mathematical abilityOpen Targets
0.41Moderate
genetic disorderOpen Targets
0.41Moderate
smoking initiationOpen Targets
0.40Weak
microphthalmiaOpen Targets
0.39Weak
nanophthalmiaOpen Targets
0.39Weak
microphthalmia, isolated, with colobomaOpen Targets
0.38Weak
syndromic microphthalmiaOpen Targets
0.37Weak
eye diseaseOpen Targets
0.37Weak
neurodegenerative diseaseOpen Targets
0.37Weak
Agnathia - holoprosencephaly - situs inversusOpen Targets
0.37Weak
Butterfly-shaped pigment dystrophyOpen Targets
0.37Weak
combined pituitary hormone deficiencies, genetic formOpen Targets
0.37Weak
Microphthalmia, syndromic, 5UniProt
Pituitary hormone deficiency, combined, 6UniProt
Retinal dystrophy, early-onset, with or without pituitary dysfunctionUniProt
Pathogenic Variants61
NM_021728.4(OTX2):c.226C>T (p.Arg76Ter)Pathogenic
not provided|Inborn genetic diseases|Anophthalmia-microphthalmia syndrome
β˜…β˜…β˜†β˜†2025β†’ Residue 76
NM_021728.4(OTX2):c.130del (p.Arg44fs)Pathogenic
Anophthalmia-microphthalmia syndrome|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 44
NM_021728.4(OTX2):c.591T>G (p.Tyr197Ter)Pathogenic
Syndromic microphthalmia type 5|OTX2-related disorder|not provided
β˜…β˜…β˜†β˜†2024β†’ Residue 197
NM_172337.2(OTX2):c.402dup (p.Ser135Leufs)Pathogenic
Syndromic microphthalmia type 5|not provided|Anophthalmia-microphthalmia syndrome
β˜…β˜…β˜†β˜†2023β†’ Residue 135
NM_021728.4(OTX2):c.274-1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2025
NM_021728.4(OTX2):c.290G>C (p.Arg97Pro)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 97
NM_021728.4(OTX2):c.322C>T (p.Gln108Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 108
NM_021728.4(OTX2):c.259G>A (p.Glu87Lys)Likely pathogenic
Syndromic microphthalmia type 5|not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 87
NM_021728.4(OTX2):c.591del (p.Gly196_Tyr197insTer)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 196
NM_021728.4(OTX2):c.761C>G (p.Ser254Ter)Likely pathogenic
Syndromic microphthalmia type 5
β˜…β˜†β˜†β˜†2024β†’ Residue 254
NM_021728.4(OTX2):c.273G>C (p.Gln91His)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 91
NM_021728.4(OTX2):c.471_474dup (p.Ile159fs)Pathogenic
OTX2-related disorder
β˜…β˜†β˜†β˜†2023β†’ Residue 159
NM_021728.4(OTX2):c.632C>A (p.Ser211Ter)Pathogenic
Anophthalmia-microphthalmia syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 211
NM_021728.4(OTX2):c.130dup (p.Arg44fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 44
NM_021728.4(OTX2):c.190_191del (p.Leu64fs)Pathogenic
Anophthalmia-microphthalmia syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 64
NM_021728.4(OTX2):c.130_131dup (p.Lys45fs)Likely pathogenic
OTX2-related disorder
β˜…β˜†β˜†β˜†2023β†’ Residue 45
NM_021728.4(OTX2):c.658_659delinsG (p.Leu220fs)Pathogenic
Anophthalmia-microphthalmia syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 220
NM_021728.4(OTX2):c.516del (p.Leu172fs)Pathogenic
Anophthalmia-microphthalmia syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 172
NM_021728.4(OTX2):c.363del (p.Lys122fs)Pathogenic
Anophthalmia-microphthalmia syndrome
β˜…β˜†β˜†β˜†2023β†’ Residue 122
NM_021728.4(OTX2):c.655C>T (p.Gln219Ter)Pathogenic
Anophthalmia-microphthalmia syndrome
β˜…β˜†β˜†β˜†2022β†’ Residue 219
View on ClinVar β†—
Related Genes
POU5F1Protein interaction100%SOX2Protein interaction100%SIX6Protein interaction89%SIX3Protein interaction88%PAX2Protein interaction83%RCVRNProtein interaction81%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
2%
Liver
0%
Lung
0%
Heart
0%
Ovary
0%
Gene Interaction Network
Click a node to explore
OTX2POU5F1SOX2SIX6SIX3PAX2RCVRN
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P32243
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.32Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.14 [0.07–0.32]
RankingsWhere OTX2 stands among ~20K protein-coding genes
  • #3,833of 20,598
    Most Researched123 Β· top quartile
  • #1,153of 5,498
    Most Pathogenic Variants61 Β· top quartile
  • #1,325of 17,882
    Most Constrained (LOEUF)0.32 Β· top 10%
Genes detectedOTX2
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Failure of human rhombic lip differentiation underlies medulloblastoma formation.
PMID: 36131014
Nature Β· 2022
1.00
2
Capture of Mouse and Human Stem Cells with Features of Formative Pluripotency.
PMID: 33271069
Cell Stem Cell Β· 2021
0.90
3
Hypoblast from human pluripotent stem cells regulates epiblast development.
PMID: 38052228
Nature Β· 2024
0.80
4
Pituitary Hypoplasia.
PMID: 28476222
Endocrinol Metab Clin North Am Β· 2017
0.70
5
Mouth development.
PMID: 28514120
Wiley Interdiscip Rev Dev Biol Β· 2017
0.60