Free for academic non-profit institutions. Other users need a Commercial license

Aliases for PTPN9 Gene

Aliases for PTPN9 Gene

  • Protein Tyrosine Phosphatase, Non-Receptor Type 9 2 3 5
  • Protein-Tyrosine Phosphatase MEG2 3 4
  • Tyrosine-Protein Phosphatase Non-Receptor Type 9 3
  • PTPase-MEG2 3
  • PTPase MEG2 4
  • EC 4
  • PTPMEG2 3
  • MEG2 3

External Ids for PTPN9 Gene

Previous GeneCards Identifiers for PTPN9 Gene

  • GC15M071637
  • GC15M068850
  • GC15M073335
  • GC15M073475
  • GC15M073546
  • GC15M075759
  • GC15M052517

Summaries for PTPN9 Gene

Entrez Gene Summary for PTPN9 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 PTP contains an N-terminal domain that shares a significant similarity with yeast SEC14, which is a protein that has phosphatidylinositol transfer activity and is required for protein secretion through the Golgi complex in yeast. This PTP was found to be activated by polyphosphoinositide, and is thought to be involved in signaling events regulating phagocytosis. [provided by RefSeq, Jul 2008]

GeneCards Summary for PTPN9 Gene

PTPN9 (Protein Tyrosine Phosphatase, Non-Receptor Type 9) is a Protein Coding gene. Among its related pathways are PAK Pathway. Gene Ontology (GO) annotations related to this gene include phosphatase activity and non-membrane spanning protein tyrosine phosphatase activity. An important paralog of this gene is PTPRB.

UniProtKB/Swiss-Prot for PTPN9 Gene

  • Protein-tyrosine phosphatase that could participate in the transfer of hydrophobic ligands or in functions of the Golgi apparatus.

Gene Wiki entry for PTPN9 Gene

Additional gene information for PTPN9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PTPN9 Gene

Genomics for PTPN9 Gene

GeneHancer (GH) Regulatory Elements for PTPN9 Gene

Promoters and enhancers for PTPN9 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
GH15J075577 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +0.6 569 3 PKNOX1 ARID4B SIN3A DMAP1 ZNF48 GLIS2 ZFP91 ATF7 RUNX3 MXD4 PTPN9 MAN2C1 SNUPN LOC441728 DNM1P35 ENSG00000260269 ENSG00000259931
GH15J074888 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 19.8 +688.7 688662 4 HDGF MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B ZNF766 MPI RPP25 SIN3A ENSG00000203392 SNX33 ISLR PTPN9 GOLGA6D LOC105370902 LOC732265
GH15J074613 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 11.1 +963.0 962977 4.9 MLX DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC ZNF610 CLK3 ENSG00000260919 LOC102723750 SIN3A EDC3 MAN2C1 ENSG00000260274 UBL7-AS1 FAM219B LOC101929333
GH15J075366 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 11.8 +210.5 210536 3.8 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 MAN2C1 ENSG00000260274 SIN3A DNM1P35 EDC3 LOC441728 FBXO22 SNUPN CLK3 COMMD4
GH15J074841 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10.5 +735.4 735432 5 HDGF PKNOX1 SMAD1 ZFP64 ARID4B NEUROD1 SIN3A DMAP1 ZNF2 ZBTB7B ULK3 SIN3A EDC3 RPP25 ENSG00000260274 MAN2C1 SNUPN MPI SCAMP2 SNX33
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTPN9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PTPN9 gene promoter:
  • MZF-1
  • NF-1/L
  • NF-1
  • Arnt
  • AhR
  • p53
  • Spz1
  • RP58
  • Pax-5
  • AREB6

Genomic Locations for PTPN9 Gene

Genomic Locations for PTPN9 Gene
116,041 bases
Minus strand
112,169 bases
Minus strand

Genomic View for PTPN9 Gene

Genes around PTPN9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTPN9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTPN9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTPN9 Gene

Proteins for PTPN9 Gene

  • Protein details for PTPN9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Tyrosine-protein phosphatase non-receptor type 9
    Protein Accession:
    Secondary Accessions:
    • Q53XR9

    Protein attributes for PTPN9 Gene

    593 amino acids
    Molecular mass:
    68020 Da
    Quaternary structure:
    No Data Available

    Three dimensional structures from OCA and Proteopedia for PTPN9 Gene

neXtProt entry for PTPN9 Gene

Post-translational modifications for PTPN9 Gene

  • Ubiquitination at posLast=185185
  • Modification sites at PhosphoSitePlus

Other Protein References for PTPN9 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PTPN9 Gene

Domains & Families for PTPN9 Gene

Gene Families for PTPN9 Gene

Suggested Antigen Peptide Sequences for PTPN9 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class 3 subfamily.
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class 3 subfamily.
genes like me logo Genes that share domains with PTPN9: view

Function for PTPN9 Gene

Molecular function for PTPN9 Gene

UniProtKB/Swiss-Prot Function:
Protein-tyrosine phosphatase that could participate in the transfer of hydrophobic ligands or in functions of the Golgi apparatus.
UniProtKB/Swiss-Prot CatalyticActivity:
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.

Enzyme Numbers (IUBMB) for PTPN9 Gene

Phenotypes From GWAS Catalog for PTPN9 Gene

Gene Ontology (GO) - Molecular Function for PTPN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004725 protein tyrosine phosphatase activity IDA,IEA 19167335
GO:0004726 non-membrane spanning protein tyrosine phosphatase activity TAS 1557404
GO:0005515 protein binding IPI 12907755
GO:0016787 hydrolase activity IEA --
GO:0016791 phosphatase activity IEA --
genes like me logo Genes that share ontologies with PTPN9: view
genes like me logo Genes that share phenotypes with PTPN9: view

Animal Models for PTPN9 Gene

MGI Knock Outs for PTPN9:

Animal Model Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PTPN9 Gene

Localization for PTPN9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTPN9 Gene


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 PTPN9 gene
Compartment Confidence
cytosol 3
nucleus 2
plasma membrane 1
mitochondrion 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PTPN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 10940933
GO:0044306 neuron projection terminus IDA 27655914
genes like me logo Genes that share ontologies with PTPN9: view

Pathways & Interactions for PTPN9 Gene

SuperPathways for PTPN9 Gene

SuperPathway Contained pathways
1 PAK Pathway
genes like me logo Genes that share pathways with PTPN9: view

Pathways by source for PTPN9 Gene

1 Qiagen pathway for PTPN9 Gene

SIGNOR curated interactions for PTPN9 Gene


Gene Ontology (GO) - Biological Process for PTPN9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA,TAS 1557404
GO:0010977 negative regulation of neuron projection development IDA 27655914
GO:0016311 dephosphorylation IEA --
GO:0035335 peptidyl-tyrosine dephosphorylation IEA,IDA 27655914
GO:0071345 cellular response to cytokine stimulus TAS --
genes like me logo Genes that share ontologies with PTPN9: view

Drugs & Compounds for PTPN9 Gene

(3) Drugs for PTPN9 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

(3) Additional Compounds for PTPN9 Gene - From: HMDB and Novoseek

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 PTPN9: view

Transcripts for PTPN9 Gene

mRNA/cDNA for PTPN9 Gene

Unigene Clusters for PTPN9 Gene

Protein tyrosine phosphatase, non-receptor type 9:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PTPN9 Gene

No ASD Table

Relevant External Links for PTPN9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PTPN9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PTPN9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PTPN9 Gene

This gene is overexpressed in Breast (7.4) and Peripheral blood mononuclear cells (6.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PTPN9 Gene

Protein tissue co-expression partners for PTPN9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PTPN9 Gene:


SOURCE GeneReport for Unigene cluster for PTPN9 Gene:


Evidence on tissue expression from TISSUES for PTPN9 Gene

  • Pancreas(4.2)
  • Nervous system(2.7)
  • Lung(2.1)
genes like me logo Genes that share expression patterns with PTPN9: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTPN9 Gene

Orthologs for PTPN9 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTPN9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PTPN9 34 33
  • 95.16 (n)
(Canis familiaris)
Mammalia PTPN9 34 33
  • 93.72 (n)
(Bos Taurus)
Mammalia PTPN9 34 33
  • 92.47 (n)
(Rattus norvegicus)
Mammalia Ptpn9 33
  • 91.91 (n)
(Mus musculus)
Mammalia Ptpn9 16 34 33
  • 91.62 (n)
(Monodelphis domestica)
Mammalia PTPN9 34
  • 86 (a)
(Ornithorhynchus anatinus)
Mammalia PTPN9 34
  • 77 (a)
(Gallus gallus)
Aves PTPN9 34 33
  • 72.92 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC52584 33
(Danio rerio)
Actinopterygii ptpn9a 34 33
  • 67.43 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001109 33
  • 52.55 (n)
fruit fly
(Drosophila melanogaster)
Insecta l(1)G0232 34
  • 33 (a)
(Caenorhabditis elegans)
Secernentea M04G7.2 35
  • 34 (a)
F36H12.10 35
  • 33 (a)
ZK616.7 35
  • 33 (a)
C02B10.6 35
  • 33 (a)
F25H5.7 35
  • 33 (a)
F55F8.7 35
  • 33 (a)
C17H12.3 35
  • 32 (a)
F36H1.3 35
  • 32 (a)
F47B3.1 35
  • 32 (a)
F47B3.6 35
  • 32 (a)
K07F5.8 35
  • 31 (a)
Species where no ortholog for PTPN9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • lizard (Anolis carolinensis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for PTPN9 Gene

Gene Tree for PTPN9 (if available)
Gene Tree for PTPN9 (if available)
Evolutionary constrained regions (ECRs) for PTPN9: view image

Paralogs for PTPN9 Gene

Paralogs for PTPN9 Gene

(10) SIMAP similar genes for PTPN9 Gene using alignment to 3 proteins:

  • Q6IQ43_HUMAN Pseudogenes for PTPN9 Gene

genes like me logo Genes that share paralogs with PTPN9: view

Variants for PTPN9 Gene

Sequence variations from dbSNP and Humsavar for PTPN9 Gene

SNP ID Clin Chr 15 pos Variation AA Info Type
rs1000017487 -- 75,566,393(-) C/T intron_variant
rs1000021063 -- 75,468,031(-) T/C 3_prime_UTR_variant
rs1000038656 -- 75,487,004(-) C/A intron_variant
rs1000043610 -- 75,541,348(-) GCTGGGAT/GCTGGGATGCTGGGAT intron_variant
rs1000096268 -- 75,521,908(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PTPN9 Gene

Variant ID Type Subtype PubMed ID
esv1056937 CNV insertion 17803354
esv1178689 CNV deletion 17803354
esv1611493 CNV insertion 17803354
esv1633101 CNV deletion 17803354
esv1664478 CNV insertion 17803354
esv2480100 CNV deletion 19546169
esv2675670 CNV deletion 23128226
esv2749894 CNV deletion 23290073
esv2749895 CNV deletion 23290073
esv2749897 CNV deletion 23290073
esv3552694 CNV deletion 23714750
esv3892713 CNV loss 25118596
nsv1116463 OTHER inversion 24896259
nsv1131203 CNV deletion 24896259
nsv1138388 CNV deletion 24896259
nsv1138389 CNV deletion 24896259
nsv1138390 CNV deletion 24896259
nsv472885 CNV novel sequence insertion 20440878
nsv819520 CNV loss 19587683
nsv827390 CNV gain 20364138
nsv957960 CNV deletion 24416366
nsv977738 CNV duplication 23825009

Variation tolerance for PTPN9 Gene

Residual Variation Intolerance Score: 19.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.99; 20.38% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTPN9 Gene

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 PTPN9 Gene

Disorders for PTPN9 Gene

Additional Disease Information for PTPN9

No disorders were found for PTPN9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PTPN9 Gene

Publications for PTPN9 Gene

  1. Cloning and expression of a cytosolic megakaryocyte protein-tyrosine-phosphatase with sequence homology to retinaldehyde-binding protein and yeast SEC14p. (PMID: 1557404) Gu M … Majerus PW (Proceedings of the National Academy of Sciences of the United States of America 1992) 2 3 4 22 58
  2. A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci. (PMID: 20189936) Okada Y … Kamatani N (Human molecular genetics 2010) 3 44 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. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. Homotypic secretory vesicle fusion induced by the protein tyrosine phosphatase MEG2 depends on polyphosphoinositides in T cells. (PMID: 14662869) Huynh H … Mustelin T (Journal of immunology (Baltimore, Md. : 1950) 2003) 3 22 58

Products for PTPN9 Gene

Sources for PTPN9 Gene

Loading form....