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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PITX1
paired like homeodomain 1
Chromosome 5 Β· 5q31.1
NCBI Gene: 5307Ensembl: ENSG00000069011.16HGNC: HGNC:9004UniProt: P78337
112PubMed Papers
22Diseases
0Drugs
10Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
protein bindingRNA polymerase II-specific DNA-binding transcription factor bindingsequence-specific double-stranded DNA bindingnucleusclubfootbrachydactyly-elbow wrist dysplasia syndromeBrachydactyly - elbow wrist dysplasiaTalipes equinovarus
✦AI Summary

PITX1 is a sequence-specific transcription factor belonging to the paired-like homeodomain family that functions as a developmental regulator and tumor suppressor. As a transcriptional activator, PITX1 binds to gene promoters and regulates transcription through RNA polymerase II 1. PITX1 plays critical roles in anterior structure development, particularly in specifying hindlimb identity and morphogenesis 2. In developmental contexts, PITX1 expression is uniquely restricted to hindlimbs and plays essential roles in corneal epithelial differentiation, where it is activated by the transcription factor RORA to drive limbal stem/progenitor cell differentiation 3. Additionally, PITX1 regulates epithelial cell differentiation and wound healing in oral mucosa, conferring unique keratinocyte identity that enhances migration and repair 1. Pathologically, PITX1 functions as a tumor suppressor. Downregulation of PITX1 expression correlates with progression in cutaneous melanoma, with reduced expression linked to increased tumor thickness, metastasis frequency, and higher cell proliferation 4. Similarly, PITX1 is downregulated in lung cancer, where lower expression associates with higher tumor stages 5. In osteosarcoma, PITX1 suppresses cell proliferation and metastasis by antagonizing STAT3 transcriptional activity, which represses the oncogenic long non-coding RNA LINC00662 6. These findings suggest PITX1 loss promotes malignant progression across multiple cancer types, establishing its importance as a developmental regulator and cancer suppressor.

Sources cited
1
PITX1 is a transcriptional regulator expressed in oral keratinocytes; SOX2 and PITX1 transcriptional function promotes cell migration and wound resolution
PMID: 30045979
2
PITX1 and TBX4 form a key developmental pathway in clubfoot etiology; both genes are uniquely expressed in the hindlimb
PMID: 21817922
3
PITX1 expression is reduced in cutaneous melanoma; downregulation correlates with increased tumor thickness, metastasis frequency, and cell proliferation
PMID: 23816528
4
PITX1 is downregulated in lung cancer cell lines and primary tumors; lower PITX1 expression is significantly linked to higher tumor stages
PMID: 17157953
5
PITX1 suppresses osteosarcoma cell proliferation and migration by interacting with STAT3 to repress LINC00662 expression
PMID: 36334221
6
RORA activates PITX1 to drive corneal epithelial cell differentiation from limbal stem/progenitor cells through establishing CEC-specific enhancers and chromatin interactions
PMID: 38177186
7
PITX1 belongs to the PRD class of homeobox genes encoding developmental transcription factors; deletion of a PITX1 gene enhancer occurs in pelvic-reduced sticklebacks
PMID: 23799629
Disease Associationsβ“˜22
clubfootOpen Targets
0.75Strong
brachydactyly-elbow wrist dysplasia syndromeOpen Targets
0.69Moderate
Brachydactyly - elbow wrist dysplasiaOpen Targets
0.67Moderate
Talipes equinovarusOpen Targets
0.49Moderate
neurodegenerative diseaseOpen Targets
0.48Moderate
denturesOpen Targets
0.41Moderate
polydactylyOpen Targets
0.37Weak
familial clubfoot due to PITX1 point mutationOpen Targets
0.37Weak
colorectal cancerOpen Targets
0.34Weak
Barrett's esophagusOpen Targets
0.32Weak
prostate cancerOpen Targets
0.32Weak
Second degree atrioventricular blockOpen Targets
0.30Weak
benign colon neoplasmOpen Targets
0.29Weak
polyp of colonOpen Targets
0.29Weak
ulcerative colitisOpen Targets
0.27Weak
Hurler syndromeOpen Targets
0.27Weak
MicrognathiaOpen Targets
0.27Weak
dental cariesOpen Targets
0.26Weak
prostate carcinomaOpen Targets
0.26Weak
polyp of large intestineOpen Targets
0.23Weak
Clubfoot, congenital, with or without deficiency of long bones and/or mirror-image polydactylyUniProt
Liebenberg syndromeUniProt
Pathogenic Variants10
NM_002653.5(PITX1):c.186_187dup (p.Glu63fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 63
NM_002653.5(PITX1):c.388G>A (p.Glu130Lys)Pathogenic
Clubfoot|not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 130
NM_002653.5(PITX1):c.292del (p.Ser98fs)Likely pathogenic
Clubfoot
β˜…β˜†β˜†β˜†2023β†’ Residue 98
NM_002653.5(PITX1):c.738del (p.Asn246fs)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 246
NM_002653.5(PITX1):c.87del (p.Ala30fs)Likely pathogenic
Clubfoot
β˜…β˜†β˜†β˜†2021β†’ Residue 30
NM_002653.5(PITX1):c.412A>C (p.Lys138Gln)Likely pathogenic
Hurler syndrome
β˜…β˜†β˜†β˜†2020β†’ Residue 138
NM_002653.5(PITX1):c.414G>T (p.Lys138Asn)Likely pathogenic
Clubfoot
β˜…β˜†β˜†β˜†2018β†’ Residue 138
NM_002653.5(PITX1):c.170-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2016
NM_002653.5(PITX1):c.392dup (p.Arg132fs)Likely pathogenic
Clubfoot
β˜…β˜†β˜†β˜†β†’ Residue 132
NM_002653.5(PITX1):c.765_799del (p.Ala256fs)Pathogenic
Clubfoot
β˜†β˜†β˜†β˜†2012β†’ Residue 256
View on ClinVar β†—
Related Genes
TBX4Protein interaction92%TBX19Protein interaction89%EGR1Protein interaction86%POU1F1Protein interaction85%TBX5Protein interaction82%NR5A1Protein interaction78%
Tissue Expression6 tissues
Brain
100%
Ovary
31%
Lung
15%
Liver
13%
Bone Marrow
7%
Heart
0%
Gene Interaction Network
Click a node to explore
PITX1TBX4TBX19EGR1POU1F1TBX5NR5A1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P78337
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.57Moderately Constrained
pLIβ“˜
0.88Intermediate
Observed/Expected LoF0.32 [0.19–0.57]
RankingsWhere PITX1 stands among ~20K protein-coding genes
  • #4,239of 20,598
    Most Researched112 Β· top quartile
  • #2,842of 5,498
    Most Pathogenic Variants10
  • #3,807of 17,882
    Most Constrained (LOEUF)0.57 Β· top quartile
Genes detectedPITX1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Transcriptional signature primes human oral mucosa for rapid wound healing.
PMID: 30045979
Sci Transl Med Β· 2018
1.00
2
Genetics of clubfoot.
PMID: 21817922
J Pediatr Orthop B Β· 2012
0.90
3
Decreased PITX1 gene expression in human cutaneous malignant melanoma and its clinicopathological significance.
PMID: 23816528
Eur J Dermatol Β· 2013
0.80
4
Decreased PITX1 homeobox gene expression in human lung cancer.
PMID: 17157953
Lung Cancer Β· 2007
0.70
5
Eicosatrienoic acid inhibits estradiol synthesis through the CD36/FOXO1/CYP19A1 signaling pathway to improve PCOS in mice.
PMID: 39236935
Biochem Pharmacol Β· 2024
0.60