OTX2

protein-coding

orthodenticle 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

NM_021728.4

Inheritance

AD

ClinVar variants

P:62U:149B:70

Top phenotype

Pituitary hormone deficiency, combined 6; Microphthalmia, syndromic 5; Retinal dystrophy, early-onset, and pituitary dysfunction

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr14:56,799,905-56,816,693

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~16.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

agnathia-otocephaly complexSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0008740

Submitter: PanelApp Australia

syndromic microphthalmia type 5SUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0012413

Submitter: Orphanet

syndromic microphthalmia type 5STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0012413

Submitter: Labcorp Genetics (formerly Invitae)

pituitary hormone deficiency, combined, 6STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0013518

Submitter: Labcorp Genetics (formerly Invitae)

isolated anophthalmia-microphthalmia syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016764

Submitter: Orphanet

patterned macular dystrophySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0020381

Submitter: Orphanet

combined pituitary hormone deficiencies, genetic formSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0013099

Submitter: Orphanet

septooptic dysplasiaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0008428

Submitter: Orphanet

syndromic microphthalmia type 5MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0012413

Submitter: Ambry Genetics

pituitary hormone deficiency, combined, 6MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0013518

Submitter: Ambry Genetics

syndromic microphthalmia type 5DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0012413

Submitter: G2P

Clinical Genomic Database (CGD)

Pituitary hormone deficiency, combined 6; Microphthalmia, syndromic 5; Retinal dystrophy, early-onset, and pituitary dysfunctionAD

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)

Refs: 15846561; 18628516; 18728160; 18781617; 19956411; 18854396; 19965921; 20396904; 20486942; 20494911; 21353197; 22198066; 24859618; 25293953; 25589041Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OTX2 variants in ClinVar

26 Conditions Cataloged
Anophthalmia-microphthalmia syndromeTotal: 180
not providedTotal: 66
Syndromic microphthalmia type 5Total: 39
Inborn genetic diseasesTotal: 36
Pituitary hormone deficiency, combined, 6Total: 20
not specifiedTotal: 18
OTX2-related disorderTotal: 10
Retinal dystrophyTotal: 3

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
59
clinvar
60
missense
4
clinvar
9
clinvar
142
clinvar
11
clinvar
166
nonsense
14
clinvar
3
clinvar
4
clinvar
21
start loss
0
frameshift
26
clinvar
5
clinvar
2
clinvar
33
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total4418149700281

Highest pathogenic variant AF is 0.00022798772

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_021728.4RefSeqNP_068374.13MANE Select
ENST00000672264.2EnsemblENSP00000500115.13MANE Select
NM_001270523.2RefSeqNP_001257452.13Standard
NM_001270524.2RefSeqNP_001257453.13Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
otx2bDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.051231600.7680.000007801908
Missense (PolyPhen)1954.2660.35013658
Synonymous-0.09996564.01.020.00000311616
Loss of Function3.03112.60.07926.56e-7140

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)00.0absent
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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