OTX2
protein-codingorthodenticle homeobox 2, the group of PRD class homeoboxes and pseudogenes
Gene summary
This gene encodes a member of the bicoid subfamily of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and plays a role in brain, craniofacial, and sensory organ development. The encoded protein also influences the proliferation and differentiation of dopaminergic neuronal progenitor cells during mitosis. Mutations in this gene cause syndromic microphthalmia 5 (MCOPS5) and combined pituitary hormone deficiency 6 (CPHD6). This gene is also suspected of having an oncogenic role in medulloblastoma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Pseudogenes of this gene are known to exist on chromosomes two and nine. [provided by RefSeq, Jul 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0008740
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0012413
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0012413
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0013518
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0016764
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0020381
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0013099
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0008428
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0012413
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0013518
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0012413
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Endocrine; Genitourinary; Neurologic; Ophthalmologic
Intervention: Endocrine; Genitourinary
Rationale: Hormone replacement therapy can be effective, as individuals may have multiple pituitary insufficiency (eg, manifesting with hypothyroidism, growth hormone, gonadotropin, and cortisol deficiency)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to OTX2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021728.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 59 | 60 | |||
| missense | 4 | 9 | 142 | 11 | 166 | |
| nonsense | 14 | 3 | 4 | 21 | ||
| start loss | 0 | |||||
| frameshift | 26 | 5 | 2 | 33 | ||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 44 | 18 | 149 | 70 | 0 | 281 |
Highest pathogenic variant AF is 0.00022798772
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_068374.1 | 3 | MANE Select | |
| Ensembl | ENSP00000500115.1 | 3 | MANE Select | |
| RefSeq | NP_001257452.1 | 3 | Standard | |
| RefSeq | NP_001257453.1 | 3 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| otx2b | Danio rerio | Structure: ceratobranchial cartilage Quality: shortened abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- TP53 Network
- Endoderm Differentiation
- Dopaminergic Neurogenesis
Biological Process
- axon guidance
- regulation of smoothened signaling pathway
- forebrain development
- midbrain development
- positive regulation of embryonic development
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription activator activity, RNA polymerase II-specific
- protein binding
- eukaryotic initiation factor 4E binding
Cellular Component
- nucleus
- growth cone
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000339475
- Coding exons
- 3
- Length
- 9773
- Individuals with no LoFs
- 124669
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 124672
- p
- 0.0000120
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.05 | 123 | 160 | 0.768 | 0.00000780 | 1908 |
| Missense (PolyPhen) | 19 | 54.266 | 0.35013 | 658 | ||
| Synonymous | -0.0999 | 65 | 64.0 | 1.02 | 0.00000311 | 616 |
| Loss of Function | 3.03 | 1 | 12.6 | 0.0792 | 6.56e-7 | 140 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcription factor probably involved in the development of the brain and the sense organs. Can bind to the bicoid/BCD target sequence (BTS): 5'-TCTAATCCC-3'. {ECO:0000269|PubMed:22715480}.;
- Disease
- DISEASE: Microphthalmia, syndromic, 5 (MCOPS5) [MIM:610125]: Patients manifest unilateral or bilateral microphthalmia/clinical anophthalmia and variable additional features including pituitary dysfunction, coloboma, microcornea, cataract, retinal dystrophy, hypoplasia or agenesis of the optic nerve, agenesis of the corpus callosum, developmental delay, joint laxity, hypotonia, and seizures. Microphthalmia is a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities. {ECO:0000269|PubMed:15846561, ECO:0000269|PubMed:20396904, ECO:0000269|PubMed:22577225, ECO:0000269|PubMed:24167467}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Pituitary hormone deficiency, combined, 6 (CPHD6) [MIM:613986]: Combined pituitary hormone deficiency is defined as the impaired production of growth hormone and one or more of the other five anterior pituitary hormones. CPHD6 patients manifest neonatal hypoglycemia, and deficiencies of growth hormone, thyroid-stimulating hormone, luteinizing hormone, follicle stimulating hormone and adrenocorticotropic hormone. {ECO:0000269|PubMed:18728160, ECO:0000269|PubMed:22715480}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Retinal dystrophy, early-onset, with or without pituitary dysfunction (RDEOP) [MIM:610125]: An autosomal dominant ocular disease characterized by pattern dystrophy of the retinal pigment epithelium, and photoreceptor degeneration. Mild developmental anomalies include optic nerve head dysplasia, microcornea, and Rathke's cleft cyst. Some patients manifest pituary dysfunction. {ECO:0000269|PubMed:19956411, ECO:0000269|PubMed:25293953}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.344
Intolerance Scores
- LoFtool
- 0.0813
- RVIS EVS
- -0.38
- RVIS percentile EVS
- 27.42
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.796
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |