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Aliases for PTPN3 Gene

Aliases for PTPN3 Gene

  • Protein Tyrosine Phosphatase, Non-Receptor Type 3 2 3 5
  • Protein-Tyrosine Phosphatase H1 3 4
  • PTP-H1 3 4
  • PTPH1 3 4
  • Cytoskeletal-Associated Protein Tyrosine Phosphatase 3
  • Tyrosine-Protein Phosphatase Non-Receptor Type 3 3
  • EC 4

External Ids for PTPN3 Gene

Previous GeneCards Identifiers for PTPN3 Gene

  • GC09M102938
  • GC09M103872
  • GC09M105597
  • GC09M107520
  • GC09M109220
  • GC09M111177
  • GC09M112138
  • GC09M081738

Summaries for PTPN3 Gene

Entrez Gene Summary for PTPN3 Gene

  • 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. [provided by RefSeq, Feb 2009]

GeneCards Summary for PTPN3 Gene

PTPN3 (Protein Tyrosine Phosphatase, Non-Receptor Type 3) is a Protein Coding gene. Diseases associated with PTPN3 include Cholangiocarcinoma and Non-Functioning Pituitary Adenoma. Among its related pathways are TNFR1 Pathway and Activation of cAMP-Dependent PKA. Gene Ontology (GO) annotations related to this gene include phosphatase activity and cytoskeletal protein binding. An important paralog of this gene is PTPN4.

UniProtKB/Swiss-Prot for PTPN3 Gene

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

Gene Wiki entry for PTPN3 Gene

Additional gene information for PTPN3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PTPN3 Gene

Genomics for PTPN3 Gene

GeneHancer (GH) Regulatory Elements for PTPN3 Gene

Promoters and enhancers for PTPN3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J109494 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 658.2 +40.8 40757 5.6 PKNOX1 ARID4B SIN3A DMAP1 ZNF48 GLIS2 ELK1 KLF13 SP3 SP5 PTPN3 GC09P109498 PALM2 YBX1P6 ENSG00000207329
GH09J109536 Enhancer 0.6 ENCODE dbSUPER 650.7 +0.7 672 2 GATA3 NFIA CUX1 PTPN3 YBX1P6
GH09J109472 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 22.6 +61.9 61917 7.5 PKNOX1 FOXA2 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZNF48 YY1 PTPN3 EPB41L4B PALM2 YBX1P6 GC09P109498 ENSG00000207329
GH09J109469 Enhancer 1.1 Ensembl ENCODE dbSUPER 12 +68.4 68412 1.6 ELF3 CTCF RAD21 YY1 TEAD3 ZFHX2 GATA3 EGR1 SMC3 ZNF143 PTPN3 EPB41L4B GC09P109498 ENSG00000207329
GH09J109440 Enhancer 1.3 Ensembl ENCODE dbSUPER 7.6 +97.5 97527 1.7 ATF1 FOXA2 SIN3A IRF4 ZNF143 ZFP91 FOS ATF7 RUNX3 RXRA EPB41L4B RNU6-984P PTPN3 GC09P109498 ENSG00000207329
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTPN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PTPN3 gene promoter:
  • E2F
  • POU6F1 (c2)
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • USF-1
  • USF1
  • Nkx2-5

Genomic Locations for PTPN3 Gene

Genomic Locations for PTPN3 Gene
162,888 bases
Minus strand
122,848 bases
Minus strand

Genomic View for PTPN3 Gene

Genes around PTPN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTPN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTPN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTPN3 Gene

Proteins for PTPN3 Gene

  • Protein details for PTPN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Tyrosine-protein phosphatase non-receptor type 3
    Protein Accession:
    Secondary Accessions:
    • A0AUW9
    • E7EN99
    • E9PGU7

    Protein attributes for PTPN3 Gene

    913 amino acids
    Molecular mass:
    103990 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PTPN3 Gene

    Alternative splice isoforms for PTPN3 Gene


neXtProt entry for PTPN3 Gene

Post-translational modifications for PTPN3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PTPN3 Gene

Domains & Families for PTPN3 Gene

Gene Families for PTPN3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily.
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily.
genes like me logo Genes that share domains with PTPN3: view

Function for PTPN3 Gene

Molecular function for PTPN3 Gene

UniProtKB/Swiss-Prot Function:
May act at junctions between the membrane and the cytoskeleton. Possesses tyrosine phosphatase activity.
UniProtKB/Swiss-Prot CatalyticActivity:
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
GENATLAS Biochemistry:
protein tyrosine phosphatase,non receptor type 3,(ERM) family member,responding and participating in reorganization of membrane-cytoplasmic interactions

Enzyme Numbers (IUBMB) for PTPN3 Gene

Phenotypes From GWAS Catalog for PTPN3 Gene

Gene Ontology (GO) - Molecular Function for PTPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001784 phosphotyrosine residue binding IPI 10364224
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004725 protein tyrosine phosphatase activity IEA,TAS --
GO:0005515 protein binding IEA,IPI 9341175
GO:0008092 cytoskeletal protein binding IEA --
genes like me logo Genes that share ontologies with PTPN3: view
genes like me logo Genes that share phenotypes with PTPN3: view

Human Phenotype Ontology for PTPN3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PTPN3 Gene

MGI Knock Outs for PTPN3:

Animal Model Products

  • Taconic Biosciences Mouse Models for PTPN3

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for PTPN3 Gene

Localization for PTPN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTPN3 Gene

Cell membrane; Peripheral membrane protein; Cytoplasmic side. Cytoplasm, cytoskeleton.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PTPN3 gene
Compartment Confidence
plasma membrane 5
cytoskeleton 5
cytosol 3
nucleus 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PTPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA,IDA 10940933
GO:0005856 cytoskeleton IEA --
GO:0005886 plasma membrane TAS --
GO:0009898 cytoplasmic side of plasma membrane IDA 10940933
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PTPN3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PTPN3 Gene

Pathways & Interactions for PTPN3 Gene

genes like me logo Genes that share pathways with PTPN3: view

SIGNOR curated interactions for PTPN3 Gene

Other effect:

Gene Ontology (GO) - Biological Process for PTPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IDA,IEA 10364224
GO:0016311 dephosphorylation IEA --
GO:0035335 peptidyl-tyrosine dephosphorylation IEA --
GO:0042059 negative regulation of epidermal growth factor receptor signaling pathway TAS --
GO:0045930 negative regulation of mitotic cell cycle IDA 10364224
genes like me logo Genes that share ontologies with PTPN3: view

Drugs & Compounds for PTPN3 Gene

(55) Drugs for PTPN3 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0

(41) Additional Compounds for PTPN3 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
genes like me logo Genes that share compounds with PTPN3: view

Transcripts for PTPN3 Gene

Unigene Clusters for PTPN3 Gene

Protein tyrosine phosphatase, non-receptor type 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PTPN3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15a · 15b ^ 16 ^
SP1: - - - - - - - -
SP2: - - - - - - - -
SP3: - - - -
SP4: - - - - -
SP5: - - - -
SP6: - - -
SP9: -

ExUns: 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27a · 27b · 27c · 27d ^ 28a · 28b ^ 29a · 29b ^ 30a · 30b · 30c
SP1: - - - -
SP2: - - -
SP3: - - - -
SP4: - - - -
SP9: - - - - - - - - - - - - -
SP12: -

Relevant External Links for PTPN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PTPN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PTPN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PTPN3 Gene

This gene is overexpressed in Muscle - Skeletal (x9.4), Liver (x4.9), and Heart - Left Ventricle (x4.1).

Protein differential expression in normal tissues from HIPED for PTPN3 Gene

This gene is overexpressed in Placenta (52.9) and Liver (11.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PTPN3 Gene

Protein tissue co-expression partners for PTPN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of PTPN3 Gene:


SOURCE GeneReport for Unigene cluster for PTPN3 Gene:


Evidence on tissue expression from TISSUES for PTPN3 Gene

  • Nervous system(4.8)
  • Intestine(4.3)
  • Liver(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PTPN3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • integumentary
  • urinary
  • biliary tract
  • gallbladder
  • kidney
  • liver
  • skin
genes like me logo Genes that share expression patterns with PTPN3: view

No data available for mRNA Expression by UniProt/SwissProt for PTPN3 Gene

Orthologs for PTPN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTPN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PTPN3 34 33
  • 99.53 (n)
(Canis familiaris)
Mammalia PTPN3 34 33
  • 91.68 (n)
(Bos Taurus)
Mammalia PTPN3 34 33
  • 90.72 (n)
(Rattus norvegicus)
Mammalia Ptpn3 33
  • 87.48 (n)
(Mus musculus)
Mammalia Ptpn3 16 34 33
  • 87.22 (n)
(Ornithorhynchus anatinus)
Mammalia PTPN3 34
  • 82 (a)
(Monodelphis domestica)
Mammalia PTPN3 34
  • 71 (a)
(Gallus gallus)
Aves PTPN3 34 33
  • 75.56 (n)
(Anolis carolinensis)
Reptilia PTPN3 34
  • 73 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ptpn3 33
  • 69.26 (n)
(Danio rerio)
Actinopterygii ptpn3 34 33
  • 61.96 (n)
fruit fly
(Drosophila melanogaster)
Insecta Ptpmeg 34 35
  • 35 (a)
(Caenorhabditis elegans)
Secernentea F36H1.3 35
  • 37 (a)
ptp-1 34 35
  • 35 (a)
F25H5.7 35
  • 35 (a)
K07F5.8 35
  • 35 (a)
F55F8.7 35
  • 35 (a)
T22C1.8 35
  • 35 (a)
C02B10.6 35
  • 33 (a)
F36H12.10 35
  • 33 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 41 (a)
Species where no ortholog for PTPN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PTPN3 Gene

Gene Tree for PTPN3 (if available)
Gene Tree for PTPN3 (if available)
Evolutionary constrained regions (ECRs) for PTPN3: view image

Paralogs for PTPN3 Gene

(35) SIMAP similar genes for PTPN3 Gene using alignment to 4 proteins:

  • B7Z8K9_HUMAN
  • B7Z9V1_HUMAN
  • J3KN34_HUMAN
genes like me logo Genes that share paralogs with PTPN3: view

Variants for PTPN3 Gene

Sequence variations from dbSNP and Humsavar for PTPN3 Gene

SNP ID Clin Chr 09 pos Variation AA Info Type
rs193920798 uncertain-significance, Malignant tumor of prostate 109,436,926(-) G/A coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs1000067520 -- 109,399,262(-) A/T intron_variant
rs1000070057 -- 109,424,100(-) G/T genic_upstream_transcript_variant, intron_variant
rs1000125312 -- 109,428,555(-) G/A genic_upstream_transcript_variant, intron_variant
rs1000126508 -- 109,467,796(-) G/A genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PTPN3 Gene

Variant ID Type Subtype PubMed ID
esv2759709 CNV loss 17122850
nsv1077172 CNV deletion 25765185
nsv1126917 CNV deletion 24896259
nsv831685 CNV gain 17160897
nsv8557 CNV loss 18304495

Variation tolerance for PTPN3 Gene

Residual Variation Intolerance Score: 17.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 11.57; 93.03% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTPN3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTPN3 Gene

Disorders for PTPN3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for PTPN3 Gene - From: HGMD, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
  • cholangiocarcinoma, susceptibility to
non-functioning pituitary adenoma
  • nfpa
scott syndrome
  • scts
functioning pituitary adenoma
  • secretory adenoma of the pituitary gland
diabetes mellitus, insulin-dependent
  • iddm
- elite association - COSMIC cancer census association via MalaCards
Search PTPN3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PTPN3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PTPN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTPN3 Gene

Publications for PTPN3 Gene

  1. Isolation of a cDNA clone encoding a human protein-tyrosine phosphatase with homology to the cytoskeletal-associated proteins band 4.1, ezrin, and talin. (PMID: 1648725) Yang Q … Tonks NK (Proceedings of the National Academy of Sciences of the United States of America 1991) 2 3 4 22 58
  2. Expression of cytoskeletal-associated protein tyrosine phosphatase PTPH1 mRNA in human hepatocellular carcinoma. (PMID: 7874267) Ikuta S … Yachi A (Journal of gastroenterology 1994) 3 4 22 58
  3. Large-scale structural analysis of the classical human protein tyrosine phosphatome. (PMID: 19167335) Barr AJ … Knapp S (Cell 2009) 3 4 58
  4. Candidate gene/loci studies in cleft lip/palate and dental anomalies finds novel susceptibility genes for clefts. (PMID: 18978678) Vieira AR … Marazita ML (Genetics in medicine : official journal of the American College of Medical Genetics 2008) 3 44 58
  5. Degradation of tyrosine phosphatase PTPN3 (PTPH1) by association with oncogenic human papillomavirus E6 proteins. (PMID: 17166906) Jing M … Vande Pol SB (Journal of virology 2007) 3 22 58

Products for PTPN3 Gene

Sources for PTPN3 Gene

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