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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PTPN3
protein tyrosine phosphatase non-receptor type 3
Chromosome 9 · 9q31.3
NCBI Gene: 5774Ensembl: ENSG00000070159.15HGNC: HGNC:9655UniProt: B7Z3V3
92PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
phosphotyrosine residue bindingprotein tyrosine phosphatase activityprotein bindingATPase bindingstomach diseasepremature birthLeft bundle branch blockneurodegenerative disease
✦AI Summary

PTPN3 (protein tyrosine phosphatase non-receptor type 3) is a multifunctional enzyme that plays complex roles in cancer biology and immune regulation. The protein contains both FERM and PDZ domains and exhibits tyrosine phosphatase activity 1. PTPN3 functions as a tumor suppressor in some contexts, suppressing lung cancer cell invasiveness by dephosphorylating DAAM1 and counteracting Src-mediated actin polymerization 1. However, activating mutations in PTPN3 promote cholangiocarcinoma cell proliferation and migration, with over 40% of intrahepatic cholangiocarcinomas containing somatic PTPN3 mutations 2. These gain-of-function mutations are associated with increased tumor recurrence rates 2. In breast cancer, PTPN3 is overexpressed and correlates with poor clinicopathological features 3. The protein also functions as an immune checkpoint in activated lymphocytes, with expression regulated by NFκB and TGFβ pathways 4. PTPN3's PDZ domain is targeted by high-risk human papillomavirus E6 proteins, contributing to viral oncogenesis 5. Pan-cancer analysis reveals PTPN3 as a prognostic biomarker associated with tumor immune microenvironment modulation and immunotherapy response prediction 6.

Sources cited
1
PTPN3 contains FERM and PDZ domains, exhibits tyrosine phosphatase activity, and suppresses lung cancer invasion by regulating Src-DAAM1 signaling
PMID: 31406243
2
Over 40% of intrahepatic cholangiocarcinomas contain PTPN3 mutations, with activating mutations promoting cell proliferation and associated with tumor recurrence
PMID: 24503127
3
PTPN3 is overexpressed in breast cancer and correlates with poor clinicopathological features
PMID: 40315635
4
PTPN3 functions as an immune checkpoint in activated lymphocytes with expression regulated by NFκB and TGFβ
PMID: 33137650
5
PTPN3's PDZ domain is targeted by high-risk HPV E6 proteins
PMID: 31092861
6
PTPN3 serves as a prognostic biomarker associated with tumor immune microenvironment and immunotherapy response
PMID: 38173048
Disease Associationsⓘ20
stomach diseaseOpen Targets
0.32Weak
premature birthOpen Targets
0.31Weak
Left bundle branch blockOpen Targets
0.31Weak
neurodegenerative diseaseOpen Targets
0.28Weak
ovarian neoplasmOpen Targets
0.26Weak
Abruptio PlacentaeOpen Targets
0.26Weak
placenta praeviaOpen Targets
0.26Weak
pancreatic adenocarcinomaOpen Targets
0.22Weak
pathological myopiaOpen Targets
0.19Weak
Familial prostate cancerOpen Targets
0.11Weak
prostate cancerOpen Targets
0.11Weak
breast cancerOpen Targets
0.10Suggestive
cancerOpen Targets
0.10Suggestive
neoplasmOpen Targets
0.09Suggestive
glioblastoma multiformeOpen Targets
0.08Suggestive
ovarian cancerOpen Targets
0.08Suggestive
small cell lung carcinomaOpen Targets
0.06Suggestive
Abnormality of the skeletal systemOpen Targets
0.05Suggestive
gastric cancerOpen Targets
0.04Suggestive
adrenal cortex carcinomaOpen Targets
0.04Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
MAPK12Protein interaction97%PTSProtein interaction86%SBK2Shared pathway20%RCE1Shared pathway20%MAP3K21Shared pathway17%MAP3K19Shared pathway17%
Tissue Expression6 tissues
Heart
100%
Liver
97%
Brain
16%
Lung
15%
Ovary
1%
Bone Marrow
0%
Gene Interaction Network
Click a node to explore
PTPN3MAPK12PTSSBK2RCE1MAP3K21MAP3K19
PROTEIN STRUCTURE
Preparing viewer…
PDB4RI5 · 1.26 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.87LoF Tolerant
pLIⓘ
0.00Tolerant
Observed/Expected LoF0.74 [0.62–0.87]
RankingsWhere PTPN3 stands among ~20K protein-coding genes
  • #5,213of 20,598
    Most Researched92
  • #7,708of 17,882
    Most Constrained (LOEUF)0.87
Genes detectedPTPN3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
NFκB and TGFβ contribute to the expression of PTPN3 in activated human lymphocytes.
PMID: 33137650
Cell Immunol · 2020
1.00
2
Structural and functional characterization of the PDZ domain of the human phosphatase PTPN3 and its interaction with the human papillomavirus E6 oncoprotein.
PMID: 31092861
Sci Rep · 2019
0.90
3
PTPN3 and PTPN4 tyrosine phosphatase expression in human gastric adenocarcinoma.
PMID: 16619586
Anticancer Res · 2006
0.80
4
Discovery of ALK-PTPN3 gene fusion from human non-small cell lung carcinoma cell line using next generation RNA sequencing.
PMID: 22334442
Genes Chromosomes Cancer · 2012
0.70
5
Identification and verification of PTPN3 as a novel biomarker in predicting cancer prognosis, immunity, and immunotherapeutic efficacy.
PMID: 38173048
Eur J Med Res · 2024
0.60