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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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PITX3
paired like homeodomain 3
Chromosome 10 Β· 10q24.32
NCBI Gene: 5309Ensembl: ENSG00000107859.11HGNC: HGNC:9006UniProt: O75364
59PubMed Papers
22Diseases
0Drugs
9Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
sequence-specific double-stranded DNA bindingDNA-binding transcription factor activity, RNA polymerase II-specificRNA polymerase II cis-regulatory region sequence-specific DNA bindinglens development in camera-type eyePosterior polar cataractFamilial ocular anterior segment mesenchymal dysgenesisearly-onset non-syndromic cataractautosomal dominant cataract
✦AI Summary

PITX3 is a transcriptional regulator with dual roles in midbrain dopaminergic (mdDA) neuron development and lens morphogenesis. In dopaminergic neurons, PITX3 is essential for differentiation and long-term survival of substantia nigra neurons 1. It functions by reducing NCOR2/SMRT corepressor interaction with NR4A2/NURR1, thereby derepressing transcription of dopaminergic genes including TH, SLC6A3, and DRD2 2. In lens development, PITX3 maintains epithelial cell proliferation by positively regulating FOXE3 and negatively regulating PROX1, preventing premature cell cycle exit 3. Clinically, PITX3 mutations cause anterior segment dysgenesis and multiple forms of congenital cataracts, with 19 causal variants identified to date 4. While PITX3 polymorphisms show weak associations with early-onset Parkinson's disease in specific populations 5, meta-analyses indicate these variants are not major PD determinants 6. Additionally, PITX3 variants near 10q24.32 show genetic overlap with autism spectrum disorder and schizophrenia 7. Enhanced PITX3 expression in optimized dopamine differentiation protocols improves neuronal yield and functional properties for regenerative medicine applications 8.

Sources cited
1
PITX3 is essential for survival of dopamine neurons in substantia nigra pars compacta during development
PMID: 15300495
2
PITX3 is identified as important transcription factor in mesencephalic dopaminergic system development
PMID: 15743669
3
PITX3 mutations cause congenital cataracts and are involved in lens development
PMID: 15558493
4
19 causal PITX3 variants identified causing cataracts and anterior segment developmental defects
PMID: 29314435
5
PITX3 gene polymorphisms rs4919621 and rs2281983 show association with early-onset Parkinson's disease risk
PMID: 22429667
6
Meta-analysis indicates PITX3 SNPs rs3758549, rs2281983, and rs4919621 are not major determinants of PD risk
PMID: 24525476
7
PITX3 locus at 10q24.32 shows genome-wide significant association with autism spectrum disorder
PMID: 28540026
8
Enhanced PITX3 expression improves dopamine neuron yield, subtype identity, and functional properties in optimized differentiation protocols
PMID: 39829874
Disease Associationsβ“˜22
Posterior polar cataractOpen Targets
0.75Strong
Familial ocular anterior segment mesenchymal dysgenesisOpen Targets
0.70Strong
early-onset non-syndromic cataractOpen Targets
0.63Moderate
autosomal dominant cataractOpen Targets
0.51Moderate
Autosomal dominant optic atrophy and cataractOpen Targets
0.50Moderate
eye diseaseOpen Targets
0.37Weak
cataract 9 multiple typesOpen Targets
0.37Weak
cataract-glaucoma syndromeOpen Targets
0.37Weak
Cataract-microcornea syndromeOpen Targets
0.37Weak
early-onset posterior polar cataractOpen Targets
0.37Weak
intelligenceOpen Targets
0.31Weak
uterine fibroidOpen Targets
0.27Weak
Developmental cataractOpen Targets
0.26Weak
atrial fibrillationOpen Targets
0.23Weak
genetic disorderOpen Targets
0.19Weak
mathematical abilityOpen Targets
0.10Suggestive
cataractOpen Targets
0.09Suggestive
microphthalmiaOpen Targets
0.06Suggestive
Parkinson diseaseOpen Targets
0.05Suggestive
Familial exudative vitreoretinopathyOpen Targets
0.05Suggestive
Anterior segment dysgenesis 1UniProt
Cataract 11, multiple typesUniProt
Pathogenic Variants9
NM_005029.4(PITX3):c.640_656del (p.Ala214fs)Pathogenic
not provided|Cataract 11 multiple types|Anterior segment dysgenesis 1
β˜…β˜…β˜†β˜†2026β†’ Residue 214
NM_005029.4(PITX3):c.640_656dup (p.Gly220fs)Pathogenic
not provided|Cataract 11, posterior polar|ANTERIOR SEGMENT DYSGENESIS 1, MULTIPLE SUBTYPES|Cataract 11 multiple types|PITX3-related disorder|Anterior segment dysgenesis 1
β˜…β˜…β˜†β˜†2025β†’ Residue 220
NM_005029.4(PITX3):c.38G>A (p.Ser13Asn)Likely pathogenic
Cataract 11 multiple types|not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 13
NM_005029.4(PITX3):c.591del (p.Met198fs)Pathogenic
Cataract 11 multiple types
β˜…β˜†β˜†β˜†2025β†’ Residue 198
NM_005029.4(PITX3):c.636_637dup (p.Gly213fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2021β†’ Residue 213
NM_005029.4(PITX3):c.762C>A (p.Tyr254Ter)Likely pathogenic
not provided|PITX3-related disorder
β˜…β˜†β˜†β˜†2018β†’ Residue 254
NM_005029.4(PITX3):c.646C>T (p.Gln216Ter)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2016β†’ Residue 216
NM_005029.4(PITX3):c.908G>T (p.Ter303Leu)Likely pathogenic
Developmental cataract
β˜†β˜†β˜†β˜†2021β†’ Residue 303
NM_005029.4(PITX3):c.650del (p.Gly217fs)Pathogenic
Cataract 11, posterior polar, with microphthalmia and neurodevelopmental abnormalities|Cataract 11, posterior polar
β˜†β˜†β˜†β˜†2006β†’ Residue 217
View on ClinVar β†—
Related Genes
NR4A2Protein interaction97%FOXE3Protein interaction94%BFSP2Protein interaction94%CRYBB1Protein interaction85%CRYBB2Protein interaction85%CRYGDProtein interaction85%
Tissue Expression6 tissues
Lung
100%
Brain
33%
Bone Marrow
0%
Ovary
0%
Heart
0%
Liver
0%
Gene Interaction Network
Click a node to explore
PITX3NR4A2FOXE3BFSP2CRYBB1CRYBB2CRYGD
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt O75364
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.69LoF Tolerant
pLIβ“˜
0.77Intermediate
Observed/Expected LoF0.27 [0.12–0.69]
RankingsWhere PITX3 stands among ~20K protein-coding genes
  • #7,799of 20,598
    Most Researched59
  • #2,960of 5,498
    Most Pathogenic Variants9
  • #5,219of 17,882
    Most Constrained (LOEUF)0.69
Genes detectedPITX3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Dopaminergic neurons.
PMID: 15743669
Int J Biochem Cell Biol Β· 2005
1.00
2
Homeobox gene Pitx3 and its role in the development of dopamine neurons of the substantia nigra.
PMID: 15300495
Cell Tissue Res Β· 2004
0.90
3
Meta-analysis of association between PITX3 gene polymorphism and Parkinson's disease.
PMID: 22429667
J Neurol Sci Β· 2012
0.80
4
PITX3 and risk for Parkinson's disease: a systematic review and meta-analysis.
PMID: 24525476
Eur Neurol Β· 2014
0.70
5
Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia.
PMID: 28540026
Mol Autism Β· 2017
0.60