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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
  • EC 4 58
  • 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
  • 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 Amyloidosis, Hereditary, Transthyretin-Related and Tropical Spastic Paraparesis. Among its related pathways are Metabolism and Ectoderm Differentiation. 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

Regulatory Elements for PTPN13 Gene

Enhancers for PTPN13 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04H086556 1.2 Ensembl ENCODE 39.1 -36.1 -36102 2.8 PKNOX1 INSM2 FEZF1 BATF ZNF2 ZNF350 ATF7 ZNF391 RUNX3 CREM PTPN13 MAPK10 RPL6P13 NUDT9 MIR4452
GH04H086479 1.2 Ensembl ENCODE dbSUPER 33.2 -111.9 -111901 5.6 CTCF PKNOX1 CBFB FEZF1 ZNF384 ZIC2 ETS1 ZNF664 POLR2A GLIS1 PTPN13 MAPK10 SLC10A6 HSD17B13 MIR4452 RN7SKP96
GH04H086592 1.3 ENCODE dbSUPER 27.4 +0.4 358 4.9 HDGF PKNOX1 SIN3A FEZF1 YBX1 GLI4 ZNF2 ZBTB7B ZNF121 GLIS2 PTPN13 LOC260422 MAPK10 HSD17B13 GC04P086608
GH04H086585 1.2 Ensembl ENCODE dbSUPER 27.1 -7.7 -7725 3.1 PKNOX1 KLF1 EBF1 GATA3 EED ATF7 PRDM10 ETV6 IKZF2 DPF2 PTPN13 MAPK10 HSD17B13 MIR4452
GH04H086496 0.7 ENCODE 37.1 -97.4 -97387 1 SMARCE1 CTCF DPF2 RAD21 RFX5 GATA3 EED SCRT2 IKZF1 SMC3 PTPN13 MAPK10 SLC10A6 MIR4452 RN7SKP96
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PTPN13 on UCSC Golden Path with GeneCards custom track

Promoters for PTPN13 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Locations for PTPN13 Gene

Genomic Locations for PTPN13 Gene
220,873 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 with TRIP6 and TNFRSF6 (Fas receptor) through its second PDZ domain. Interacts with the C-terminal SVP motif of NGFR through its third PDZ domain. Interacts with the LIM domain of PDLIM4 through its second and fourth PDZ domains. Binds PLEKHA1 and PLEKHA2 through its first PDZ domain. Interacts with BRD7. Interacts with ARHGAP29. Interacts (via PDZ 3 domain) with PKN2 (via C-terminus). 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

Selected DME Specific Peptides for PTPN13 Gene


Post-translational modifications for PTPN13 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & 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

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
UniProtKB/Swiss-Prot CatalyticActivity:
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
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).

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

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 PKN2 in lamellipodia-like structure, regions of large actin turnover.

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 IDA,IEA 11356191
GO:0005737 cytoplasm IDA,IEA 14516276
GO:0005856 cytoskeleton IEA --
GO:0005886 plasma membrane TAS --
GO:0030027 lamellipodium IEA,IDA 11356191
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
  • NFB Orthophosphate
  • O-Phosphoric acid
  • Ortho-phosphate
  • Orthophosphate (PO43-)
  • Orthophosphate(3-)
genes like me logo Genes that share compounds with PTPN13: view

Transcripts for PTPN13 Gene

Unigene Clusters for PTPN13 Gene

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

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, PaxDb, 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 33 34
  • 99.45 (n)
(Canis familiaris)
Mammalia PTPN13 33 34
  • 91.38 (n)
(Bos Taurus)
Mammalia PTPN13 33 34
  • 89.57 (n)
(Mus musculus)
Mammalia Ptpn13 33 16 34
  • 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 33 34
  • 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 33 34
  • 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)

Paralogs for PTPN13 Gene

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 Sequence Context AA Info Type
rs1000009579 -- 86,698,101(+) AGCAA(A/T)AATGT intron-variant
rs1000011765 -- 86,747,804(+) GTCTG(A/C)CTGTT intron-variant
rs1000057006 -- 86,624,765(+) CCATG(A/T)TCATG intron-variant
rs1000070988 -- 86,641,017(+) TATTT(A/G/T)GAGGA intron-variant
rs1000072722 -- 86,606,120(+) CTATT(A/G)ATTGA intron-variant

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

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

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)

Relevant External Links 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

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

Disorder Aliases PubMed IDs
amyloidosis, hereditary, transthyretin-related
  • transthyretin amyloidosis
tropical spastic paraparesis
  • htlv-associated myelopathy
colorectal cancer
  • colorectal cancer, somatic
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for PTPN13

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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 60
  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 45 60
  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 60
  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 60
  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 60

Products for PTPN13 Gene

Sources for PTPN13 Gene

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