PTPN3

gene
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Also known as PTPH1

Summary

PTPN3 (protein tyrosine phosphatase non-receptor type 3, HGNC:9655) is a protein-coding gene on chromosome 9q31.3, encoding Tyrosine-protein phosphatase non-receptor type 3 (P26045). May act at junctions between the membrane and the cytoskeleton.

The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This protein contains a C-terminal PTP domain and an N-terminal domain homologous to the band 4.1 superfamily of cytoskeletal-associated proteins. P97, a cell cycle regulator involved in a variety of membrane related functions, has been shown to be a substrate of this PTP. This PTP was also found to interact with, and be regulated by adaptor protein 14-3-3 beta. Several alternatively spliced transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 5774 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): schizophrenia (No Known Disease Relationship, GenCC)
  • GWAS associations: 36
  • Clinical variants (ClinVar): 175 total
  • Phenotypes (HPO): 8
  • Druggable target: yes
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 1 cancer types
  • MANE Select transcript: NM_002829

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9655
Approved symbolPTPN3
Nameprotein tyrosine phosphatase non-receptor type 3
Location9q31.3
Locus typegene with protein product
StatusApproved
AliasesPTPH1
Ensembl geneENSG00000070159
Ensembl biotypeprotein_coding
OMIM176877
Entrez5774

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000262539, ENST00000374541, ENST00000412145, ENST00000446349, ENST00000447271, ENST00000497739, ENST00000865410, ENST00000865411, ENST00000865412, ENST00000865413, ENST00000865414, ENST00000865415, ENST00000865416, ENST00000865417

RefSeq mRNA: 6 — MANE Select: NM_002829 NM_001145368, NM_001145369, NM_001145370, NM_001145371, NM_001145372, NM_002829

CCDS: CCDS48000, CCDS48001, CCDS6776

Canonical transcript exons

ENST00000374541 — 26 exons

ExonStartEnd
ENSE00000806055109420424109420600
ENSE00000806056109422718109422852
ENSE00000983477109428621109428684
ENSE00000983478109426950109427122
ENSE00001090538109389233109389379
ENSE00001090539109406462109406618
ENSE00001090542109383423109383551
ENSE00001090545109404448109404608
ENSE00001463784109375700109379633
ENSE00001463801109498219109498307
ENSE00001606103109438114109438234
ENSE00001625396109445240109445292
ENSE00001689765109454496109454574
ENSE00001747223109436883109436970
ENSE00001750132109433073109433161
ENSE00001788195109448811109448855
ENSE00003497921109410229109410415
ENSE00003516468109408321109408377
ENSE00003528171109409999109410076
ENSE00003580705109391138109391199
ENSE00003604086109391471109391561
ENSE00003716139109382302109382447
ENSE00003720438109457173109457215
ENSE00003730229109381652109381787
ENSE00003737404109463297109463451
ENSE00003748211109457292109457399

Expression profiles

Bgee: expression breadth ubiquitous, 264 present calls, max score 96.95.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.4441 / max 178.5957, expressed in 1024 samples.

FANTOM5 promoters (16 alternative TSS)

Promoter IDTPM avgSamples expressed
1019045.4412994
1019020.2672144
1019050.2025116
1018980.139416
1018960.083812
1019030.073521
1018970.06627
1018950.03748
1019000.029712
1019060.027611

Top tissues by expression

293 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
oocyteCL:000002396.95gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451196.24gold quality
secondary oocyteCL:000065596.20gold quality
triceps brachiiUBERON:000150995.58gold quality
gluteal muscleUBERON:000200095.32gold quality
lower esophagus mucosaUBERON:003583495.26gold quality
hindlimb stylopod muscleUBERON:000425295.15gold quality
diaphragmUBERON:000110395.04gold quality
lateral nuclear group of thalamusUBERON:000273694.77gold quality
gastrocnemiusUBERON:000138893.91gold quality
biceps brachiiUBERON:000150793.82gold quality
apex of heartUBERON:000209893.77gold quality
skeletal muscle tissueUBERON:000113493.38gold quality
vastus lateralisUBERON:000137993.30gold quality
muscle organUBERON:000163092.99gold quality
skeletal muscle organUBERON:001489292.98gold quality
muscle of legUBERON:000138392.90gold quality
right lobe of liverUBERON:000111492.81gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450292.80gold quality
quadriceps femorisUBERON:000137792.72gold quality
metanephros cortexUBERON:001053392.34gold quality
amniotic fluidUBERON:000017392.17gold quality
nasal cavity epitheliumUBERON:000538491.75gold quality
corpus epididymisUBERON:000435991.70gold quality
upper arm skinUBERON:000426391.32gold quality
adult mammalian kidneyUBERON:000008291.07gold quality
islet of LangerhansUBERON:000000691.05gold quality
deltoidUBERON:000147691.02silver quality
heart left ventricleUBERON:000208490.10gold quality
skin of legUBERON:000151189.91gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes13.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

233 targeting PTPN3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-8485100.0077.574731
HSA-MIR-5692A100.0074.406850
HSA-MIR-5193100.0067.261744
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-6856-5P100.0065.471298
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-9-5P100.0072.282361
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-50799.9770.111915
HSA-MIR-314899.9775.066478
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-3605-5P99.9667.12932
HSA-MIR-55799.9670.011640
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-9-3P99.9670.882068
HSA-MIR-971899.9468.91918
HSA-MIR-335-3P99.9373.364958
HSA-MIR-497-5P99.9271.832674
HSA-MIR-515-5P99.9269.822343
HSA-MIR-519E-5P99.9269.622358
HSA-MIR-145-5P99.9271.131836

Literature-anchored findings (GeneRIF, showing 30)

  • regulates TACE (tnf-alpha convertase} (PMID:12207026)
  • first reported demonstration that protein tyrosine phosphatase H1(PTPH1) is capable of interacting with and dephosphorylating T cell receptor zeta subunit (PMID:14672952)
  • PTPH1 binds to the PDZ-domain binding motif of the cardiac voltage-gated sodium channel Na(v)1 and regulates the activity of Na(v)1. (PMID:16930557)
  • Degradation of PTPN3 by HPV-16 E6 requires E6AP, the proteasome, and an interaction between the carboxy terminus of E6 and the PDZ domain of PTPN3. (PMID:17166906)
  • phosphatase activity and FERM domain of PTPN3 are essential for its suppression of HBV gene expression. (PMID:17588219)
  • PTP-H1 has a role in modulating GHR signaling and systemic growth through insulin-like growth factor 1 secretion (PMID:17921143)
  • Data suggest that reducing the level of PTPH1 may contribute to the oncogenic activity of high-risk genital E6 proteins. (PMID:17947517)
  • PTPH1 plays a role in Ras-dependent malignant growth by a mechanism depending on its p38gamma-binding activity. Ras increases p38gamma and PTPH1 expression and there is a coupling of increased p38gamma and PTPH1 protein expression in colon cancer. (PMID:20332238)
  • PTPH1 stimulated breast cancer growth through regulating vitamin D receptor expression. PTPH1 was overexpressed in primary breast cancer and levels of its protein expression positively correlated with clinical metastasis. (PMID:21119599)
  • The fusion transcript of ALK and PTPN3 identified resulted from translocation of a part of ALK gene into the third intron of PTPN3. Analysis of the transcript sequence indicates that no protein with any enzymatic activity is produced. (PMID:22334442)
  • p38gamma Mitogen-activated protein kinase signals through phosphorylating its phosphatase PTPH1 in regulating ras protein oncogenesis and stress response. (PMID:22730326)
  • These studies thus identified PTPH1 as a novel ER phosphatase and further demonstrate a therapeutic potential of enhancing breast cancer sensitivity to antiestrogens through dephosphorylating ER by PTPH1. (PMID:24227889)
  • Activating mutations in and high expression levels of PTPN3 were associated with tumor recurrence in cholangiocarcinoma. (PMID:24503127)
  • Results indicate that protein tyrosine phosphatase non-receptor type 3 (PTPN3) may act as a tumor suppressor in lung cancer through its modulation of epidermal growth factor receptor (EGFR) signaling. (PMID:25263444)
  • analysis of how allosteric regulation of p38gamma and PTPN3 involves a PDZ domain-modulated complex formation (PMID:25314968)
  • PTPN3 promotes tumorigenicity, stemness and drug resistance in ovarian cancer. (PMID:27833130)
  • PTPH1 is upregulated in breast cancer from Indian population; its expression is correlative with ER, and PR status. The 2 kb region upstream of PTPH1 gene harbored CpG sites within, and was ubiquitously methylated in breast cancer. (PMID:30189107)
  • High expression of PTPN3 was significantly associated with unfavorable prognosis of GBM. Moreover, in GBM cell lines, PTPN3 promoted cell proliferation and invasion, and the PTP common inhibitor pervanadate suppressed GBM proliferation and invasion. (PMID:30348936)
  • E6 oncoprotein of the betaHPV type 8-mediated targeting of PTPH1 might result in higher level of EGFR and enhanced keratinocyte proliferation. (PMID:30875834)
  • Structural and functional characterization of the PDZ domain of the human phosphatase PTPN3 and its interaction with the human papillomavirus E6 oncoprotein. (PMID:31092861)
  • Study reports that PTPN3 suppresses liver cancer progression through positively regulating TGF-b signaling. Furthermore, the recurrent L232R mutation in liver cancer disables its role in enhancing TGF-beta signaling and abolishes its tumor-suppressive function. (PMID:31304624)
  • findings reveal a novel mechanism by which reversible tyrosine phosphorylation of DAAM1 by Src and PTPN3 regulates actin dynamics and lung cancer invasivenes (PMID:31406243)
  • PTPN3 suppressed the proliferation of perihilar cholangiocarcinoma by inhibiting AKT phosphorylation and arresting cell cycle. (PMID:31706106)
  • Low PTPN3 expression is associated with gastric cancer angiogenesis. (PMID:31972307)
  • PTPN3 Inhibits the Growth and Metastasis of Clear Cell Renal Cell Carcinoma via Inhibition of PI3K/AKT Signaling. (PMID:32169891)
  • NFkappaB and TGFbeta contribute to the expression of PTPN3 in activated human lymphocytes. (PMID:33137650)
  • Molecular basis of the interaction of the human tyrosine phosphatase PTPN3 with the hepatitis B virus core protein. (PMID:33441627)
  • PTPN3 Could Betae a Therapeutic Target of Pancreatic Cancer. (PMID:35641270)
  • Identification and verification of PTPN3 as a novel biomarker in predicting cancer prognosis, immunity, and immunotherapeutic efficacy. (PMID:38173048)
  • Inhibition of PTPN3 Expressed in Activated Lymphocytes Enhances the Antitumor Effects of Anti-PD-1 Therapy in Head and Neck Cancer, Especially in Hypoxic Environments. (PMID:38297883)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioptpn3ENSDARG00000055784
mus_musculusPtpn3ENSMUSG00000038764
rattus_norvegicusPtpn3ENSRNOG00000011425

Paralogs (35): PTPRN (ENSG00000054356), PTPRU (ENSG00000060656), PTPN21 (ENSG00000070778), PTPN18 (ENSG00000072135), PTPN23 (ENSG00000076201), PTPRH (ENSG00000080031), PTPRC (ENSG00000081237), PTPN4 (ENSG00000088179), PTPRS (ENSG00000105426), PTPRZ1 (ENSG00000106278), PTPN5 (ENSG00000110786), PTPN6 (ENSG00000111679), PTPRB (ENSG00000127329), PTPN12 (ENSG00000127947), PTPRE (ENSG00000132334), PTPRA (ENSG00000132670), PTPN22 (ENSG00000134242), PTPRF (ENSG00000142949), PTPN7 (ENSG00000143851), PTPRG (ENSG00000144724), PTPRJ (ENSG00000149177), PTPRO (ENSG00000151490), PTPN14 (ENSG00000152104), PTPRK (ENSG00000152894), PTPRR (ENSG00000153233), PTPRD (ENSG00000153707), PTPRN2 (ENSG00000155093), PTPN13 (ENSG00000163629), PTPN9 (ENSG00000169410), PTPRM (ENSG00000173482), PTPN2 (ENSG00000175354), PTPN11 (ENSG00000179295), PTPRT (ENSG00000196090), PTPN1 (ENSG00000196396), PTPN20 (ENSG00000204179)

Protein

Protein identifiers

Tyrosine-protein phosphatase non-receptor type 3P26045 (reviewed: P26045)

Alternative names: Protein-tyrosine phosphatase H1

All UniProt accessions (2): P26045, J3KN34

UniProt curated annotations — full annotation on UniProt →

Function. May act at junctions between the membrane and the cytoskeleton. Possesses tyrosine phosphatase activity.

Subcellular location. Cell membrane. Cytoplasm. Cytoskeleton.

Similarity. Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily.

Isoforms (3)

UniProt IDNamesCanonical?
P26045-11yes
P26045-22
P26045-33

RefSeq proteins (6): NP_001138840, NP_001138841, NP_001138842, NP_001138843, NP_001138844, NP_002820* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000242PTP_catDomain
IPR000299FERM_domainDomain
IPR000387Tyr_Pase_domDomain
IPR001478PDZDomain
IPR003595Tyr_Pase_catDomain
IPR011993PH-like_dom_sfHomologous_superfamily
IPR012151Tyr_Pase_non-rcpt_typ-3/4Family
IPR014352FERM/acyl-CoA-bd_prot_sfHomologous_superfamily
IPR016130Tyr_Pase_ASActive_site
IPR018979FERM_NDomain
IPR018980FERM_PH-like_CDomain
IPR019747FERM_CSConserved_site
IPR019748FERM_centralDomain
IPR019749Band_41_domainDomain
IPR029021Prot-tyrosine_phosphatase-likeHomologous_superfamily
IPR029071Ubiquitin-like_domsfHomologous_superfamily
IPR035963FERM_2Homologous_superfamily
IPR036034PDZ_sfHomologous_superfamily
IPR041783PTPN3/4_FERM_CDomain

Pfam: PF00102, PF00373, PF00595, PF09379, PF09380

Enzyme classification (BRENDA):

  • EC 3.1.3.48 — protein-tyrosine-phosphatase (BRENDA: 59 organisms, 501 substrates, 1326 inhibitors, 270 Km, 165 kcat entries)

Substrate kinetics (BRENDA)

70 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
4-NITROPHENYL PHOSPHATE0.0008–14884
6,8-DIFLUORO-4-METHYLUMBELLIFERYL PHOSPHATE0.0039–0.86227
P-NITROPHENYL PHOSPHATE0.0024–1020
DADEPYLIPQQG0.0003–0.112
PHOSPHOTYROSINE0.012–3011
LYSOZYME0.0003–0.0125
MYELIN BASIC PROTEIN0.0001–0.0225
ACETYL-DADEPY-NH20.0228–0.2194
ACETYL-DADEPYL-NH21.1–97.54
4,6,8-TRIMETHYL-2-OXO-2H-CHROMEN-7-YL DIHYDROGEN0.02–0.1563
SASASPYSASA0.53–2.33
1-NAPHTHYL PHOSPHATE1.19–1.882
3,6-FLUORESCEIN DIPHOSPHATE15–192
4-METHYLUMBELLIFERYL PHOSPHATE0.953–2.412
BOVINE SERUM ALBUMIN0.0001–0.00032

Catalyzed reactions (Rhea), 1 shown:

  • O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate (RHEA:10684)

UniProt features (65 total): strand 22, helix 13, modified residue 6, sequence variant 5, domain 3, binding site 3, turn 3, compositionally biased region 3, splice variant 2, region of interest 2, chain 1, sequence conflict 1, active site 1

Structure

Experimental structures (PDB)

13 structures.

PDBMethodResolution (Å)
4RI5X-RAY DIFFRACTION1.26
2B49X-RAY DIFFRACTION1.54
4RHGX-RAY DIFFRACTION1.58
4RI4X-RAY DIFFRACTION1.6
4RH9X-RAY DIFFRACTION1.6
4RH5X-RAY DIFFRACTION1.6
8CQYX-RAY DIFFRACTION1.7
4S0GX-RAY DIFFRACTION1.72
4QUNX-RAY DIFFRACTION1.86
6T36X-RAY DIFFRACTION1.86
8OEPX-RAY DIFFRACTION1.87
6HKSX-RAY DIFFRACTION2.19
4QUMX-RAY DIFFRACTION2.52

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P26045-F173.850.42

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 842 (phosphocysteine intermediate)

Ligand- & substrate-binding residues (3): 811; 842–848; 886

Post-translational modifications (6): 357, 359, 367, 376, 381, 425

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-182971EGFR downregulation
R-HSA-5675221Negative regulation of MAPK pathway

MSigDB gene sets: 279 (showing top): GOBP_MEMBRANE_DEPOLARIZATION, GOBP_NEGATIVE_REGULATION_OF_PROTEOLYSIS, GOBP_REGULATION_OF_ERBB_SIGNALING_PATHWAY, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_SODIUM_ION_TRANSMEMBRANE_TRANSPORT, GOBP_NEGATIVE_REGULATION_OF_ERBB_SIGNALING_PATHWAY, GOBP_MEMBRANE_DEPOLARIZATION_DURING_ACTION_POTENTIAL, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, GOBP_REGULATION_OF_MEMBRANE_DEPOLARIZATION, BONCI_TARGETS_OF_MIR15A_AND_MIR16_1, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_MONOATOMIC_CATION_TRANSPORT, HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_UP, ATGTTAA_MIR302C, GOBP_REGULATION_OF_SODIUM_ION_TRANSPORT

GO Biological Process (8): MAPK cascade (GO:0000165), negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059), negative regulation of mitotic cell cycle (GO:0045930), negative regulation of membrane protein ectodomain proteolysis (GO:0051045), regulation of membrane depolarization during action potential (GO:0098902), regulation of sodium ion transmembrane transport (GO:1902305), protein dephosphorylation (GO:0006470), dephosphorylation (GO:0016311)

GO Molecular Function (8): phosphotyrosine residue binding (GO:0001784), protein tyrosine phosphatase activity (GO:0004725), cytoskeletal protein binding (GO:0008092), sodium channel regulator activity (GO:0017080), ATPase binding (GO:0051117), phosphoprotein phosphatase activity (GO:0004721), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (6): cytoplasm (GO:0005737), cytosol (GO:0005829), cytoskeleton (GO:0005856), plasma membrane (GO:0005886), cytoplasmic side of plasma membrane (GO:0009898), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Signaling by EGFR1
RAF/MAP kinase cascade1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
intracellular signaling cassette1
epidermal growth factor receptor signaling pathway1
regulation of epidermal growth factor receptor signaling pathway1
negative regulation of ERBB signaling pathway1
mitotic cell cycle1
regulation of mitotic cell cycle1
negative regulation of cell cycle1
membrane protein ectodomain proteolysis1
negative regulation of protein catabolic process1
negative regulation of proteolysis1
regulation of membrane protein ectodomain proteolysis1
regulation of membrane depolarization1
membrane depolarization during action potential1
regulation of sodium ion transport1
sodium ion transmembrane transport1
regulation of monoatomic cation transmembrane transport1
dephosphorylation1
protein modification process1
phosphate-containing compound metabolic process1
protein phosphorylated amino acid binding1
phosphoprotein phosphatase activity1
protein binding1
sodium channel activity1
ion channel regulator activity1
enzyme binding1
phosphatase activity1
catalytic activity, acting on a protein1
binding1
catalytic activity1
intracellular anatomical structure1
cytoplasm1
intracellular membraneless organelle1
membrane1
cell periphery1
plasma membrane1
cytoplasmic side of membrane1

Protein interactions and networks

STRING

1094 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PTPN3PTSQ03393852
PTPN3DLG1Q12959656
PTPN3VCPP55072574
PTPN3UBE3AP78355554
PTPN3BET1LQ9NYM9545
PTPN3VCPIP1Q96JH7524
PTPN3NPLOC4Q8TAT6523
PTPN3IGDCC3Q8IVU1522
PTPN3MPDZO75970504
PTPN3NHERF2Q15599502
PTPN3TP53P04637490
PTPN3DTNBO60941485
PTPN3ALKQ9UM73483
PTPN3SCN5AQ14524482
PTPN3DMDP11532464

IntAct

503 interactions, top by confidence:

ABTypeScore
PTPN3YWHAQpsi-mi:“MI:2364”(proximity)0.850
PTPN3VANGL1psi-mi:“MI:0915”(physical association)0.750
VANGL1PTPN3psi-mi:“MI:0407”(direct interaction)0.750
PTPN3LMO1psi-mi:“MI:0915”(physical association)0.720
PTPN3AKR1C1psi-mi:“MI:0915”(physical association)0.720
WDR6PTPN3psi-mi:“MI:0915”(physical association)0.720
AKR1C1PTPN3psi-mi:“MI:0915”(physical association)0.720
LMO1PTPN3psi-mi:“MI:0915”(physical association)0.720
PTPN3WDR6psi-mi:“MI:0915”(physical association)0.720
SCN5APTPN3psi-mi:“MI:0407”(direct interaction)0.670
PTPN3MCCpsi-mi:“MI:0914”(association)0.660
PTPN3MCCpsi-mi:“MI:0915”(physical association)0.660
MCCPTPN3psi-mi:“MI:0407”(direct interaction)0.660
PTPN3GHRpsi-mi:“MI:0407”(direct interaction)0.650
PTPN3GHRpsi-mi:“MI:0203”(dephosphorylation reaction)0.650
PTPN3GHRpsi-mi:“MI:0915”(physical association)0.650
EPS15PTPN3psi-mi:“MI:0407”(direct interaction)0.650
PTPN3EPS15psi-mi:“MI:0915”(physical association)0.650
PTPN3EPS15psi-mi:“MI:0407”(direct interaction)0.650
PTPN3EPS15psi-mi:“MI:0203”(dephosphorylation reaction)0.650
PTPN3MAPK12psi-mi:“MI:0203”(dephosphorylation reaction)0.620
MAPK12PTPN3psi-mi:“MI:0407”(direct interaction)0.620
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610

BioGRID (208): PTPN3 (Two-hybrid), PTPN3 (Two-hybrid), WDR6 (Two-hybrid), DIP2A (Two-hybrid), ZCCHC10 (Two-hybrid), NXT2 (Two-hybrid), PTPN3 (Two-hybrid), PTPN3 (Two-hybrid), ACOT8 (Affinity Capture-MS), KCTD3 (Affinity Capture-MS), SHKBP1 (Affinity Capture-MS), SLC1A5 (Affinity Capture-MS), SRRM2 (Affinity Capture-MS), VANGL1 (Affinity Capture-MS), YWHAB (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2JXT6, A0JMF6, A0JMK5, A2ALK8, A2BGG1, A6QLT4, A7MB43, G5ED68, O13819, O14830, P26045, P33402, P51432, Q09M05, Q13496, Q13613, Q15111, Q3USB7, Q4KWH5, Q4R6N0, Q4U2V3, Q52KU6, Q5EB32, Q5F452, Q5R6F6, Q5R9S3, Q5U581, Q62688, Q6AXQ4, Q6NU08, Q6TEL0, Q6XPS3, Q7TPM9, Q7ZXF1, Q8K394, Q8NCE2, Q8VE11, Q8VEL2, Q96EF0, Q96MI9

Diamond homologs: A0A6I8TCE0, A1L1L3, A2ALK8, A4IFW2, B0V2N1, B0X4T2, B1AUH1, B2GV87, B2RU80, B3DK56, B9EKR1, E9Q0N2, E9Q612, F1NWE3, G5EC24, G5EGJ9, H2KZM6, O02695, O08617, O13016, O35239, O55082, P06800, P16620, P17706, P18031, P18052, P18433, P20417, P23467, P23468, P23469, P23470, P23471, P26045, P28191, P29074, P29350, P29351, P29352

SIGNOR signaling

5 interactions.

AEffectBMechanism
PTPN3“down-regulates activity”VCPdephosphorylation
PTPN3“up-regulates activity”ESR1dephosphorylation
MAP3K7unknownPTPN3phosphorylation
PTPN3“down-regulates activity”GHRdephosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 136 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Activation of BAD and translocation to mitochondria649.6×3e-07
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex643.8×3e-07
SARS-CoV-1 targets host intracellular signalling and regulatory pathways643.8×3e-07
Activation of BH3-only proteins632.4×2e-06
RHO GTPases activate PKNs620.7×3e-05
Intrinsic Pathway for Apoptosis619.1×4e-05
RND2 GTPase cycle616.9×6e-05
RND1 GTPase cycle514.4×6e-04

GO biological processes:

GO termPartnersFoldFDR
protein targeting514.3×8e-03
transport across blood-brain barrier79.8×7e-03
intracellular protein localization86.5×8e-03

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 1 cancer types — PAAD.

Clinical variants and AI predictions

ClinVar

175 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance138
Likely benign6
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

4499 predictions. Top by Δscore:

VariantEffectΔscore
9:109379559:A:Cdonor_gain1.0000
9:109381646:ACT:Adonor_loss1.0000
9:109381647:CTC:Cdonor_loss1.0000
9:109381647:CTCA:Cdonor_gain1.0000
9:109381648:TCACT:Tdonor_loss1.0000
9:109381649:CACTG:Cdonor_loss1.0000
9:109381650:A:ACdonor_gain1.0000
9:109381651:C:CGdonor_gain1.0000
9:109381651:CTG:Cdonor_gain1.0000
9:109381651:CTGA:Cdonor_gain1.0000
9:109381651:CTGAT:Cdonor_gain1.0000
9:109381783:CAGCA:Cacceptor_gain1.0000
9:109381785:GCA:Gacceptor_gain1.0000
9:109381786:CA:Cacceptor_gain1.0000
9:109381786:CAC:Cacceptor_gain1.0000
9:109381788:C:CCacceptor_gain1.0000
9:109381789:T:Cacceptor_loss1.0000
9:109382296:CCATA:Cdonor_loss1.0000
9:109382297:CATAC:Cdonor_loss1.0000
9:109382298:ATACC:Adonor_loss1.0000
9:109382299:TACCT:Tdonor_loss1.0000
9:109382300:A:Cdonor_loss1.0000
9:109382301:C:CAdonor_loss1.0000
9:109382443:CCGGT:Cacceptor_gain1.0000
9:109382444:CGGT:Cacceptor_gain1.0000
9:109382444:CGGTC:Cacceptor_gain1.0000
9:109382446:GTC:Gacceptor_loss1.0000
9:109382447:TC:Tacceptor_loss1.0000
9:109383417:GCTCA:Gdonor_loss1.0000
9:109383418:CTCAC:Cdonor_loss1.0000

AlphaMissense

6018 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:109382403:C:AW809C1.000
9:109382403:C:GW809C1.000
9:109382405:A:GW809R1.000
9:109382405:A:TW809R1.000
9:109383546:T:AK753N1.000
9:109383546:T:GK753N1.000
9:109383547:T:AK753I1.000
9:109406479:A:GL592P1.000
9:109406485:A:GL590P1.000
9:109408377:C:GG527R1.000
9:109408377:C:TG527R1.000
9:109410009:A:GF523S1.000
9:109410012:C:TG522E1.000
9:109379609:C:GA897P0.999
9:109379619:A:CF893L0.999
9:109379619:A:TF893L0.999
9:109379621:A:GF893L0.999
9:109379627:A:CY891D0.999
9:109381675:G:TR881S0.999
9:109381683:C:GR878P0.999
9:109381767:C:TG850D0.999
9:109381768:C:GG850R0.999
9:109381774:G:CR848G0.999
9:109381776:C:TG847D0.999
9:109381777:C:GG847R0.999
9:109381782:C:TG845E0.999
9:109381783:C:GG845R0.999
9:109381783:C:TG845R0.999
9:109381785:G:TA844D0.999
9:109382304:G:CC842W0.999

dbSNP variants (sampled 300 via entrez): RS1000067520 (9:109399262 A>G,T), RS1000070057 (9:109424100 G>A,T), RS1000125312 (9:109428555 G>A), RS1000126508 (9:109467796 G>A), RS1000127083 (9:109438909 T>C), RS1000141272 (9:109479010 T>A,G), RS1000152166 (9:109434166 C>G,T), RS1000185234 (9:109434448 C>G), RS1000209887 (9:109514046 G>C), RS1000236433 (9:109473543 C>A,G,T), RS1000251839 (9:109451790 C>G), RS1000261713 (9:109432846 T>A), RS1000262387 (9:109514319 G>A,T), RS1000300708 (9:109462596 G>A), RS1000303494 (9:109520768 G>A)

Disease associations

OMIM: gene MIM:176877 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
schizophreniaNo Known Disease RelationshipUnknown

Mondo (2): prostate cancer (MONDO:0008315), schizophrenia (MONDO:0005090)

Orphanet (1): Familial prostate cancer (Orphanet:1331)

HPO phenotypes

8 total (8 of 8 shown, HPO-id order):

HPOTerm
HP:0000952Jaundice
HP:0000989Pruritus
HP:0001945Fever
HP:0002027Abdominal pain
HP:0002039Anorexia
HP:0011985Acholic stools
HP:0012378Fatigue
HP:0100574Biliary tract neoplasm

GWAS associations

36 associations (top):

StudyTraitp-value
GCST003182_3Staphylococcus aureus nasal carriage (persistent)8.000000e-07
GCST004379_3Red blood cell density in sickle cell anemia1.000000e-06
GCST004409_1HIV-associated neurocognitive disorder1.000000e-07
GCST004410_2HIV-associated neurocognitive disorder (asymptomatic neurocogntive impairment)5.000000e-06
GCST004411_1HIV-associated neurocognitive disorder (mild neurocognitive disorder or asymptomatic neurocognitive impairment)2.000000e-07
GCST005173_78Coronary artery calcified atherosclerotic plaque (130 HU threshold) in type 2 diabetes9.000000e-06
GCST005175_19Coronary artery calcified atherosclerotic plaque (90 or 130 HU threshold) in type 2 diabetes7.000000e-06
GCST005988_9Serum albumin levels2.000000e-09
GCST007740_22Iris color (a* coordinate)9.000000e-06
GCST007741_42Iris color (b* coordinate)9.000000e-07
GCST007876_110Estimated glomerular filtration rate1.000000e-08
GCST010244_206Triglyceride levels1.000000e-08
GCST010796_151Electrocardiogram morphology (amplitude at temporal datapoints)6.000000e-09
GCST010796_152Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-09
GCST010796_153Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-08
GCST010796_154Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-09
GCST010796_155Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-10
GCST010796_156Electrocardiogram morphology (amplitude at temporal datapoints)6.000000e-10
GCST010796_157Electrocardiogram morphology (amplitude at temporal datapoints)1.000000e-09
GCST010796_158Electrocardiogram morphology (amplitude at temporal datapoints)8.000000e-10
GCST010796_159Electrocardiogram morphology (amplitude at temporal datapoints)1.000000e-09
GCST010796_160Electrocardiogram morphology (amplitude at temporal datapoints)7.000000e-09
GCST010796_161Electrocardiogram morphology (amplitude at temporal datapoints)1.000000e-08
GCST010796_162Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-08
GCST010796_163Electrocardiogram morphology (amplitude at temporal datapoints)3.000000e-08
GCST010796_164Electrocardiogram morphology (amplitude at temporal datapoints)4.000000e-08
GCST010796_165Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-08
GCST010796_167Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-08
GCST010796_168Electrocardiogram morphology (amplitude at temporal datapoints)2.000000e-08
GCST010796_169Electrocardiogram morphology (amplitude at temporal datapoints)3.000000e-08

EFO canonical traits (8, from GWAS)

EFO IDTrait name
EFO:0007757persistent Staphylococcus aureus carrier status
EFO:0007948HIV-associated neurocognitive disorder
EFO:0007983asymptomatic neurocognitive impairment
EFO:0007982mild neurocognitive disorder
EFO:0004723coronary artery calcification
EFO:0009764eye colour measurement
EFO:0004530triglyceride measurement
EFO:0004327electrocardiography

MeSH disease descriptors (1)

DescriptorNameTree numbers
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL2396509 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

Binding affinities (BindingDB)

1 measured of 2 human assays (2 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValuePatent
6-hydroxy-3-iodo-1-methyl-2-[3-[[2-oxo-2-(4-thiophen-3-ylanilino)acetyl]amino]phenyl]indole-5-carboxylic acidIC502900 nMUS-9522881: Hydroxyindole carboxylic acid based inhibitors for oncogenic Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2)

ChEMBL bioactivities

3 potent at pChembl≥5 of 5 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.97IC501070nMCHEMBL3319356
5.80IC501600nMCHEMBL2396718

PubChem BioAssay actives

2 with measured affinity, of 8 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
6-hydroxy-3-iodo-1-methyl-2-[3-[[2-oxo-2-(4-thiophen-3-ylanilino)acetyl]amino]phenyl]indole-5-carboxylic acid1182543: Inhibition of PTPH1 (unknown origin)ic501.0700uM
3-[2-(3-chlorophenyl)ethynyl]-6-hydroxy-2-[4-[2-oxo-2-(propylamino)ethoxy]phenyl]-1-benzofuran-5-carboxylic acid755772: Inhibition of recombinant PTPH1 (unknown origin) using pNPP as substrate by spectrophotometric analysisic501.6000uM

CTD chemical–gene interactions

56 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, decreases methylation8
Tretinoinaffects expression, decreases expression, increases expression4
Acetaminophendecreases expression, increases expression3
Benzo(a)pyreneaffects methylation, increases expression2
Calcitrioldecreases expression, increases expression2
Cyclosporineincreases expression, increases methylation2
aristolochic acid Idecreases expression1
FR900359affects phosphorylation1
N(6)-(delta(2)-isopentenyl)adeninedecreases expression1
methylmercuric chlorideincreases expression1
bisphenol Adecreases methylation1
2-butenaldecreases expression1
hydroxyhydroquinonedecreases expression, decreases reaction1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arsenitedecreases expression1
butyraldehydedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
coumarindecreases phosphorylation1
4-aminobenzhydrazidedecreases reaction, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
tamibaroteneaffects expression1
CGP 52608affects binding, increases reaction1
pirfenidoneaffects binding, decreases reaction, increases reaction, decreases phosphorylation1
entinostatincreases expression1
cotylenin Adecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
clothianidinincreases expression1
belinostatdecreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL2401194BindingInhibition of recombinant PTPH1 (unknown origin) using pNPP as substrate by spectrophotometric analysisA potent and selective small-molecule inhibitor for the lymphoid-specific tyrosine phosphatase (LYP), a target associated with autoimmune diseases. — J Med Chem

Cellosaurus cell lines

6 cell lines: 6 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_1543NCI-H2228Cancer cell lineFemale
CVCL_4V13NCI-H2228-LucCancer cell lineFemale
CVCL_E3I6HyCyte NCI-H2228-LucCancer cell lineFemale
CVCL_E6DBNCI-H2228-ARYCancer cell lineFemale
CVCL_TH61HAP1 PTPN3 (-) 1Cancer cell lineMale
CVCL_TH62HAP1 PTPN3 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

600 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00000374PHASE4COMPLETEDTreatment for First-Episode Schizophrenia
NCT00001656PHASE4COMPLETEDComparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774PHASE4COMPLETEDTo Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001PHASE4COMPLETEDCATIE- Schizophrenia Trial
NCT00018668PHASE4COMPLETEDAntipsychotic Response in Schizophrenia
NCT00034801PHASE4COMPLETEDOlanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905PHASE4COMPLETEDA Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088PHASE4COMPLETEDOlanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187PHASE4COMPLETEDThe Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655PHASE4COMPLETEDSwitching Medication to Treat Schizophrenia
NCT00048828PHASE4COMPLETEDTreating Drug-Resistant Childhood Schizophrenia
NCT00053703PHASE4COMPLETEDTreatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498PHASE4COMPLETEDRisperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802PHASE4COMPLETEDEfficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327PHASE4COMPLETEDStudy of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049PHASE4COMPLETEDStudy of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012PHASE4COMPLETEDComparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776PHASE4COMPLETEDEfficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571PHASE4COMPLETEDOlanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368PHASE4COMPLETEDThe Effects of Risperidone and Olanzapine on Thinking
NCT00114595PHASE4COMPLETEDEthyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923PHASE4COMPLETEDRisperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020PHASE4COMPLETEDClinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166PHASE4COMPLETEDTreatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847PHASE4COMPLETEDNaltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564PHASE4COMPLETEDEnergy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715PHASE4COMPLETEDEfficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223PHASE4COMPLETEDEffectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081PHASE4COMPLETEDOne Year Drug Treatment in First-Episode Schizophrenia
NCT00159120PHASE4COMPLETEDMaintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133PHASE4COMPLETEDProdrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757PHASE4TERMINATED12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817PHASE4COMPLETEDEffect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026PHASE4TERMINATEDAlcoholism and Schizophrenia: Effects of Clozapine
NCT00169039PHASE4TERMINATEDClozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065PHASE4COMPLETEDEffectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091PHASE4TERMINATEDClozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423PHASE4COMPLETEDEfficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436PHASE4COMPLETEDAtomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008PHASE4COMPLETEDAripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety