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Aliases for PTPN13 Gene

Aliases for PTPN13 Gene

  • Protein Tyrosine Phosphatase, Non-Receptor Type 13 2 3 5
  • Protein Tyrosine Phosphatase, Non-Receptor Type 13 (APO-1/CD95 (Fas)-Associated Phosphatase) 2 3
  • Fas-Associated Protein-Tyrosine Phosphatase 1 3 4
  • Protein-Tyrosine Phosphatase PTPL1 3 4
  • Protein-Tyrosine Phosphatase 1E 3 4
  • PTP-BAS 3 4
  • HPTPE1 3 4
  • FAP-1 3 4
  • PTP1E 3 4
  • PTPL1 3 4
  • PNP1 3 4
  • Tyrosine-Protein Phosphatase Non-Receptor Type 13 3
  • APO-1/CD95 (Fas)-Associated Phosphatase 2
  • EC 4
  • PTP-BL 3
  • HPTP1E 3
  • PTP-E1 4
  • PTPLE 3

External Ids for PTPN13 Gene

Previous GeneCards Identifiers for PTPN13 Gene

  • GC04P087673
  • GC04P087817
  • GC04P087974
  • GC04P087873
  • GC04P087515
  • GC04P083259

Summaries for PTPN13 Gene

Entrez Gene Summary for PTPN13 Gene

  • The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP is a large intracellular protein. It has a catalytic PTP domain at its C-terminus and two major structural domains: a region with five PDZ domains and a FERM domain that binds to plasma membrane and cytoskeletal elements. This PTP was found to interact with, and dephosphorylate, Fas receptor and IkappaBalpha through the PDZ domains. This suggests it has a role in Fas mediated programmed cell death. This PTP was also shown to interact with GTPase-activating protein, and thus may function as a regulator of Rho signaling pathways. Four alternatively spliced transcript variants, which encode distinct proteins, have been reported. [provided by RefSeq, Oct 2008]

GeneCards Summary for PTPN13 Gene

PTPN13 (Protein Tyrosine Phosphatase, Non-Receptor Type 13) is a Protein Coding gene. Diseases associated with PTPN13 include Tropical Spastic Paraparesis. Among its related pathways are Immune response Fc epsilon RI pathway and Ephrin B reverse signaling. Gene Ontology (GO) annotations related to this gene include phosphatase activity and phosphatidylinositol 3-kinase regulatory subunit binding. An important paralog of this gene is FRMPD2.

UniProtKB/Swiss-Prot for PTPN13 Gene

  • Tyrosine phosphatase which regulates negatively FAS-induced apoptosis and NGFR-mediated pro-apoptotic signaling (PubMed:15611135). May regulate phosphoinositide 3-kinase (PI3K) signaling through dephosphorylation of PIK3R2 (PubMed:23604317).

Gene Wiki entry for PTPN13 Gene

Additional gene information for PTPN13 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PTPN13 Gene

Genomics for PTPN13 Gene

GeneHancer (GH) Regulatory Elements for PTPN13 Gene

Promoters and enhancers for PTPN13 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
GH04J086592 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 677.4 +0.4 358 4.9 HDGF PKNOX1 SMAD1 NEUROD1 SIN3A FEZF1 YBX1 ZNF2 ZBTB7B IRF4 PTPN13 MAPK10 LOC100419572 LOC260422 HSD17B13 GC04P086608
GH04J086599 Promoter 0.5 EPDnew 650.4 +5.2 5216 0.1 PTPN13 MAPK10 GC04P086608
GH04J086556 Enhancer 1.1 Ensembl ENCODE 39.1 -36.1 -36101 2.8 PKNOX1 INSM2 FEZF1 BATF ZNF2 YY1 ZNF213 ZNF350 ATF7 IKZF2 PTPN13 MAPK10 RPL6P13 NUDT9 MIR4452
GH04J086479 Enhancer 1.1 Ensembl ENCODE dbSUPER 33.2 -111.9 -111901 5.6 CTCF PKNOX1 NANOG CBFB MZF1 SIN3A ZNF384 FEZF1 ZIC2 ZNF664 PTPN13 MAPK10 SLC10A6 HSD17B13 MIR4452 RN7SKP96
GH04J086451 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 18.8 -141.4 -141407 3.1 PKNOX1 KLF17 ZIC2 YY1 CTBP1 GATA3 RCOR1 FOS FOSL2 SMARCE1 MAPK10 PTPN13 MIR4452 RN7SKP96
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTPN13 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PTPN13 gene promoter:
  • HFH-1
  • POU2F1a
  • POU2F1
  • GATA-1
  • MEF-2A
  • aMEF-2
  • Pbx1a
  • E4BP4

Genomic Locations for PTPN13 Gene

Genomic Locations for PTPN13 Gene
220,873 bases
Plus strand
220,862 bases
Plus strand

Genomic View for PTPN13 Gene

Genes around PTPN13 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTPN13 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTPN13 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTPN13 Gene

Proteins for PTPN13 Gene

  • Protein details for PTPN13 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Tyrosine-protein phosphatase non-receptor type 13
    Protein Accession:
    Secondary Accessions:
    • B2RTR0
    • Q15159
    • Q15263
    • Q15264
    • Q15265
    • Q15674
    • Q16826
    • Q8IWH7
    • Q9NYN9
    • Q9UDA8

    Protein attributes for PTPN13 Gene

    2485 amino acids
    Molecular mass:
    276906 Da
    Quaternary structure:
    • Interacts (via the first PDZ domain) with PLEKHA1 and PLEKHA2 (PubMed:14516276). Interacts (via the second PDZ domain) with TNFRSF6 (Fas receptor) (via C-terminus) (PubMed:10704206). Interacts (via the second PDZ domain) with TRIP6 (via the third LIM domain and C-terminus) (PubMed:10826496, PubMed:10400701). Interacts (via the third PDZ domain) with NGFR (via C-terminal SVP motif) and PKN2 (via C-terminus) (PubMed:10544233, PubMed:11356191). Interacts (via the second or fourth PDZ domains) with PDLIM4 (via C-terminus only or via combined C-terminus and LIM domain, but not LIM domain only). Found in a complex with PDLIM4 and TRIP6 (By similarity). Interacts with PDLIM4; this interaction results in dephosphorylation of SRC Tyr-419 by this protein leading to its inactivation (PubMed:19307596). Interacts with BRD7 (By similarity). Interacts with RAPGEF6 (PubMed:12095257). Interacts with ARHGAP29 (PubMed:9305890). Interacts with PIK3R2; dephosphorylates PIK3R2 (PubMed:23604317). Interacts with FBXL2 (PubMed:23604317). Interacts with SDCCAG3 (PubMed:23108400).
    • Sequence=AAH39610.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PTPN13 Gene

    Alternative splice isoforms for PTPN13 Gene


neXtProt entry for PTPN13 Gene

Post-translational modifications for PTPN13 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PTPN13 Gene

Domains & Families for PTPN13 Gene

Gene Families for PTPN13 Gene

Suggested Antigen Peptide Sequences for PTPN13 Gene

GenScript: Design optimal peptide antigens:

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 PTPN13: view

Function for PTPN13 Gene

Molecular function for PTPN13 Gene

UniProtKB/Swiss-Prot Function:
Tyrosine phosphatase which regulates negatively FAS-induced apoptosis and NGFR-mediated pro-apoptotic signaling (PubMed:15611135). May regulate phosphoinositide 3-kinase (PI3K) signaling through dephosphorylation of PIK3R2 (PubMed:23604317).
UniProtKB/Swiss-Prot CatalyticActivity:
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
GENATLAS Biochemistry:
protein tyrosine phosphatase,non receptor type 13,with a membrane binding region homologous to that found in cytoskeleton associated proteins,ezrin/moesin/radixin-like (ERM) family member,responding and participating in reorganization of membrane-cytoplasmic interactions

Enzyme Numbers (IUBMB) for PTPN13 Gene

Phenotypes From GWAS Catalog for PTPN13 Gene

Gene Ontology (GO) - Molecular Function for PTPN13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004725 protein tyrosine phosphatase activity IMP 23604317
GO:0005515 protein binding IPI 10918185
GO:0016787 hydrolase activity IEA --
GO:0016791 phosphatase activity IEA --
GO:0036312 phosphatidylinositol 3-kinase regulatory subunit binding IPI 23604317
genes like me logo Genes that share ontologies with PTPN13: view
genes like me logo Genes that share phenotypes with PTPN13: view

Animal Models for PTPN13 Gene

MGI Knock Outs for PTPN13:

Animal Model Products

CRISPR Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PTPN13 Gene

Localization for PTPN13 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTPN13 Gene

Cytoplasm, cytoskeleton. Nucleus. Cell projection, lamellipodium. Note=Colocalizes with F-actin (PubMed:10826496). Colocalizes with PKN2 in lamellipodia-like structure, regions of large actin turnover (PubMed:11356191). {ECO:0000269 PubMed:10826496, ECO:0000269 PubMed:11356191}.

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 PTPN13 gene
Compartment Confidence
plasma membrane 5
extracellular 5
nucleus 5
cytoskeleton 4
cytosol 4

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PTPN13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 11356191
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 14516276
GO:0005856 cytoskeleton IEA --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with PTPN13: view

Pathways & Interactions for PTPN13 Gene

genes like me logo Genes that share pathways with PTPN13: view

SIGNOR curated interactions for PTPN13 Gene


Gene Ontology (GO) - Biological Process for PTPN13 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IDA 17657516
GO:0006661 phosphatidylinositol biosynthetic process TAS --
GO:0014066 regulation of phosphatidylinositol 3-kinase signaling IDA 23604317
GO:0016311 dephosphorylation IEA --
GO:0035335 peptidyl-tyrosine dephosphorylation IMP 23604317
genes like me logo Genes that share ontologies with PTPN13: view

Drugs & Compounds for PTPN13 Gene

(5) Drugs for PTPN13 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

(5) Additional Compounds for PTPN13 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 PTPN13: view

Transcripts for PTPN13 Gene

mRNA/cDNA for PTPN13 Gene

Unigene Clusters for PTPN13 Gene

Protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase):
Representative Sequences:

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PTPN13 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25a ·
SP2: -
SP4: - - -

ExUns: 25b ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45 ^ 46 ^ 47 ^ 48a · 48b
SP1: -
SP2: -
SP4: -

Relevant External Links for PTPN13 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PTPN13 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PTPN13 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PTPN13 Gene

This gene is overexpressed in Retina (16.4), Bone marrow stromal cell (11.2), Cervix (9.4), Heart (9.0), and Urine (6.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PTPN13 Gene

NURSA nuclear receptor signaling pathways regulating expression of PTPN13 Gene:


SOURCE GeneReport for Unigene cluster for PTPN13 Gene:


mRNA Expression by UniProt/SwissProt for PTPN13 Gene:

Tissue specificity: Present in most tissues with the exception of the liver and skeletal muscle. Most abundant in lung, kidney and fetal brain.

Evidence on tissue expression from TISSUES for PTPN13 Gene

  • Nervous system(4.5)
  • Eye(4.3)
  • Pancreas(4.3)
  • Kidney(2.1)
  • Lung(2)
genes like me logo Genes that share expression patterns with PTPN13: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTPN13 Gene

Orthologs for PTPN13 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTPN13 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PTPN13 34 33
  • 99.45 (n)
(Canis familiaris)
Mammalia PTPN13 34 33
  • 91.38 (n)
(Bos Taurus)
Mammalia PTPN13 34 33
  • 89.57 (n)
(Mus musculus)
Mammalia Ptpn13 16 34 33
  • 81.39 (n)
(Ornithorhynchus anatinus)
Mammalia PTPN13 34
  • 81 (a)
(Rattus norvegicus)
Mammalia Ptpn13 33
  • 80.09 (n)
(Monodelphis domestica)
Mammalia PTPN13 34
  • 75 (a)
(Gallus gallus)
Aves PTPN13 34 33
  • 71.08 (n)
(Anolis carolinensis)
Reptilia PTPN13 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ptpn13 33
  • 63.78 (n)
(Danio rerio)
Actinopterygii ptpn13 34 33
  • 58.31 (n)
mchr2 33
(Caenorhabditis elegans)
Secernentea F55F8.7 35
  • 30 (a)
Y38C1AB.4 35
  • 30 (a)
frm-5.2 34
  • 21 (a)
frm-5.1 34
  • 19 (a)
Species where no ortholog for PTPN13 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)
  • fruit fly (Drosophila melanogaster)
  • 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 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)
  • wheat (Triticum aestivum)

Evolution for PTPN13 Gene

Gene Tree for PTPN13 (if available)
Gene Tree for PTPN13 (if available)
Evolutionary constrained regions (ECRs) for PTPN13: view image

Paralogs for PTPN13 Gene

Paralogs for PTPN13 Gene

(19) SIMAP similar genes for PTPN13 Gene using alignment to 4 proteins:

  • D6R9M4_HUMAN
  • D6R9X4_HUMAN
  • Q4W5F5_HUMAN
genes like me logo Genes that share paralogs with PTPN13: view

Variants for PTPN13 Gene

Sequence variations from dbSNP and Humsavar for PTPN13 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs1000009579 -- 86,698,101(+) T/A intron_variant
rs1000011765 -- 86,747,804(+) C/A/T intron_variant
rs1000057006 -- 86,624,765(+) A/T intron_variant
rs1000070988 -- 86,641,017(+) G/A/T intron_variant
rs1000072722 -- 86,606,120(+) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PTPN13 Gene

Variant ID Type Subtype PubMed ID
esv2653947 CNV deletion 19546169
esv2659040 CNV deletion 23128226
esv2759264 CNV loss 17122850
esv3564191 CNV deletion 23714750
esv3569571 CNV loss 25503493
esv3601257 CNV loss 21293372
esv3601258 CNV loss 21293372
esv3601259 CNV loss 21293372
esv3601260 CNV gain 21293372
esv3601263 CNV loss 21293372
esv999120 CNV deletion 20482838
nsv474128 CNV novel sequence insertion 20440878
nsv507180 OTHER sequence alteration 20534489
nsv508296 CNV deletion 20534489
nsv528327 CNV loss 19592680
nsv594786 CNV gain 21841781
nsv594787 CNV gain 21841781
nsv822635 CNV loss 20364138
nsv830001 CNV loss 17160897
nsv967770 CNV duplication 23825009

Variation tolerance for PTPN13 Gene

Residual Variation Intolerance Score: 98.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.44; 88.62% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTPN13 Gene

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

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTPN13 Gene

Disorders for PTPN13 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PTPN13 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
tropical spastic paraparesis
  • htlv-associated myelopathy
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PTPN13

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 PTPN13: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTPN13 Gene

Publications for PTPN13 Gene

  1. Molecular cloning of a novel protein-tyrosine phosphatase containing a membrane-binding domain and GLGF repeats. (PMID: 8287977) Maekawa K … Harada S (FEBS letters 1994) 2 3 4 22 58
  2. Genetic polymorphisms in the PTPN13 gene and risk of squamous cell carcinoma of head and neck. (PMID: 19892796) Niu J … Wei Q (Carcinogenesis 2009) 3 22 44 58
  3. Crystal structure of the PTPL1/FAP-1 human tyrosine phosphatase mutated in colorectal cancer: evidence for a second phosphotyrosine substrate recognition pocket. (PMID: 15611135) Villa F … van Aalten DM (The Journal of biological chemistry 2005) 3 4 22 58
  4. Interaction of the protein tyrosine phosphatase PTPL1 with the PtdIns(3,4)P2-binding adaptor protein TAPP1. (PMID: 14516276) Kimber WA … Alessi DR (The Biochemical journal 2003) 3 4 22 58
  5. Head-to-head juxtaposition of Fas-associated phosphatase-1 (FAP-1) and c-Jun NH2-terminal kinase 3 (JNK3) genes: genomic structure and seven polymorphisms of the FAP-1 gene. (PMID: 12436199) Yoshida S … Emi M (Journal of human genetics 2002) 3 4 22 58

Products for PTPN13 Gene

Sources for PTPN13 Gene

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