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Aliases for PTPRF Gene

Aliases for PTPRF Gene

  • Protein Tyrosine Phosphatase, Receptor Type F 2 3 5
  • Leukocyte Common Antigen Related 3 4
  • LAR 3 4
  • Protein Tyrosine Phosphatase, Receptor Type, F Polypeptide 3
  • Receptor-Linked Protein-Tyrosine Phosphatase LAR 3
  • Leukocyte Antigen-Related Tyrosine Phosphatase 3
  • Leukocyte Antigen-Related (LAR) PTP Receptor 3
  • Receptor-Type Tyrosine-Protein Phosphatase F 3
  • LCA-Homolog 3
  • EC 4
  • BNAH2 3

External Ids for PTPRF Gene

Previous HGNC Symbols for PTPRF Gene

  • LAR

Previous GeneCards Identifiers for PTPRF Gene

  • GC01P043874
  • GC01P042996
  • GC01P043426
  • GC01P043409
  • GC01P043665
  • GC01P043769
  • GC01P043990
  • GC01P042115

Summaries for PTPRF Gene

Entrez Gene Summary for PTPRF 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 possesses an extracellular region, a single transmembrane region, and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains three Ig-like domains, and nine non-Ig like domains similar to that of neural-cell adhesion molecule. This PTP was shown to function in the regulation of epithelial cell-cell contacts at adherents junctions, as well as in the control of beta-catenin signaling. An increased expression level of this protein was found in the insulin-responsive tissue of obese, insulin-resistant individuals, and may contribute to the pathogenesis of insulin resistance. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]

CIViC summary for PTPRF Gene

GeneCards Summary for PTPRF Gene

PTPRF (Protein Tyrosine Phosphatase, Receptor Type F) is a Protein Coding gene. Diseases associated with PTPRF include Breasts And/Or Nipples, Aplasia Or Hypoplasia Of, 2 and Isolated Congenital Breast Hypoplasia/Aplasia. Among its related pathways are Regulation of lipid metabolism Insulin signaling-generic cascades and Adherens junction. Gene Ontology (GO) annotations related to this gene include phosphatase activity. An important paralog of this gene is PTPRD.

UniProtKB/Swiss-Prot for PTPRF Gene

  • Possible cell adhesion receptor. It possesses an intrinsic protein tyrosine phosphatase activity (PTPase) and dephosphorylates EPHA2 regulating its activity.

  • The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one.

Gene Wiki entry for PTPRF Gene

Additional gene information for PTPRF Gene

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

Genomics for PTPRF Gene

GeneHancer (GH) Regulatory Elements for PTPRF Gene

Promoters and enhancers for PTPRF 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
GH01J043529 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 657 +11.5 11502 9.2 HDGF PKNOX1 CLOCK SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF213 PTPRF KDM4A-AS1 ST3GAL3 ARTN IPO13 LOC101929609 HYI MED8 GC01M043545
GH01J043522 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 652.2 +1.8 1796 3.4 HDGF PKNOX1 SMAD1 FOXA2 ARNT SIN3A YBX1 ZNF766 E2F8 FOS PTPRF SZT2 P3H1 MED8 KDM4A HYI PPIH ZNF691 KDM4A-AS1 DMAP1
GH01J043598 Promoter 0.5 EPDnew 660.7 +75.9 75895 0.1 PTPRF ST3GAL3 KDM4A-AS1 LOC101929592 SZT2 IPO13 LOC101929609 GC01M043617 GC01M043545
GH01J043521 Enhancer 0.3 dbSUPER 650.7 -0.2 -162 0.4 ELF1 PTPRF GC01M043427
GH01J043539 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 18.2 +25.2 25246 15.4 FOXA2 MLX ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 YY1 SLC30A9 GC01M043545 LOC101929592 PTPRF MED8 YBX1 SZT2 ST3GAL3 KDM4A-AS1 IPO13 LOC101929609
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTPRF on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PTPRF gene promoter:
  • GR-beta
  • GR-alpha
  • GR
  • CREB
  • deltaCREB

Genomic Locations for PTPRF Gene

Genomic Locations for PTPRF Gene
101,435 bases
Plus strand
98,486 bases
Plus strand

Genomic View for PTPRF Gene

Genes around PTPRF on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PTPRF Gene

Proteins for PTPRF Gene

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

    Protein Symbol:
    Recommended name:
    Receptor-type tyrosine-protein phosphatase F
    Protein Accession:
    Secondary Accessions:
    • D3DPX6
    • D3DPX7
    • Q5T021
    • Q5T022
    • Q5W9G2
    • Q86WS0

    Protein attributes for PTPRF Gene

    1907 amino acids
    Molecular mass:
    212879 Da
    Quaternary structure:
    • Interacts with GRIP1 (By similarity). Interacts with PPFIA1, PPFIA2 and PPFIA3. Interacts with INSR.
    • Sequence=BAD66835.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=CAA68754.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PTPRF Gene

    Alternative splice isoforms for PTPRF Gene


neXtProt entry for PTPRF Gene

Post-translational modifications for PTPRF Gene

  • Glycosylation at Asn966, Asn959, posLast=721721, posLast=295295, posLast=250250, and posLast=117117
  • Ubiquitination at posLast=13031303
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PTPRF Gene

Domains & Families for PTPRF Gene

Gene Families for PTPRF Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted membrane proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for PTPRF Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the protein-tyrosine phosphatase family. Receptor class 2A subfamily.
  • Belongs to the protein-tyrosine phosphatase family. Receptor class 2A subfamily.
genes like me logo Genes that share domains with PTPRF: view

Function for PTPRF Gene

Molecular function for PTPRF Gene

UniProtKB/Swiss-Prot Function:
Possible cell adhesion receptor. It possesses an intrinsic protein tyrosine phosphatase activity (PTPase) and dephosphorylates EPHA2 regulating its activity.
UniProtKB/Swiss-Prot Function:
The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one.
UniProtKB/Swiss-Prot CatalyticActivity:
Protein tyrosine phosphate + H(2)O = protein tyrosine + phosphate.
GENATLAS Biochemistry:
protein tyrosine phosphatase,receptor-type II,f polypeptide,involved in axon guidance and mammary gland development

Enzyme Numbers (IUBMB) for PTPRF Gene

Phenotypes From GWAS Catalog for PTPRF Gene

Gene Ontology (GO) - Molecular Function for PTPRF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004725 protein tyrosine phosphatase activity IMP,IEA 23358419
GO:0005001 transmembrane receptor protein tyrosine phosphatase activity TAS 8995282
GO:0005515 protein binding IEA --
GO:0008201 heparin binding IEA --
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PTPRF: view
genes like me logo Genes that share phenotypes with PTPRF: view

Human Phenotype Ontology for PTPRF Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PTPRF Gene

MGI Knock Outs for PTPRF:

Animal Model Products

miRNA for PTPRF Gene

miRTarBase miRNAs that target PTPRF

Clone Products

  • Addgene plasmids for PTPRF

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

Localization for PTPRF Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTPRF Gene

Membrane; Single-pass type I membrane protein.

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 PTPRF gene
Compartment Confidence
plasma membrane 5
extracellular 5
endoplasmic reticulum 2
golgi apparatus 2
cytoskeleton 1
peroxisome 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Golgi apparatus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PTPRF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 2972792
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0043005 neuron projection IEA --
genes like me logo Genes that share ontologies with PTPRF: view

Pathways & Interactions for PTPRF Gene

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

Pathways by source for PTPRF Gene

1 GeneGo (Thomson Reuters) pathway for PTPRF Gene
1 Qiagen pathway for PTPRF Gene
1 Cell Signaling Technology pathway for PTPRF Gene

SIGNOR curated interactions for PTPRF Gene


Gene Ontology (GO) - Biological Process for PTPRF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA --
GO:0007155 cell adhesion TAS,IEA --
GO:0007185 transmembrane receptor protein tyrosine phosphatase signaling pathway TAS 8995282
GO:0010975 regulation of neuron projection development IEA --
GO:0016311 dephosphorylation IEA --
genes like me logo Genes that share ontologies with PTPRF: view

Drugs & Compounds for PTPRF Gene

(7) Drugs for PTPRF 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 PTPRF 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 PTPRF: view

Transcripts for PTPRF Gene

Unigene Clusters for PTPRF Gene

Protein tyrosine phosphatase, receptor type, F:
Representative Sequences:

Clone Products

  • Addgene plasmids for PTPRF

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

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ·
SP1: - -
SP5: - -
SP6: -
SP9: - -
SP10: - -
SP12: - -

ExUns: 16c ^ 17a · 17b ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22 ^ 23 ^ 24a · 24b ^ 25a · 25b · 25c ^ 26 ^ 27 ^ 28a · 28b ^ 29a · 29b ^ 30a · 30b · 30c ^ 31a · 31b ^
SP1: - - - - - - - -
SP2: - - - - - - -
SP3: - - - - - - -
SP4: - - - -
SP13: - -
SP14: -
SP15: -
SP17: -

ExUns: 32a · 32b ^ 33a · 33b ^ 34 ^ 35a · 35b ^ 36 ^ 37 ^ 38 ^ 39
SP1: -
SP2: -
SP3: -

Relevant External Links for PTPRF Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PTPRF Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PTPRF Gene

This gene is overexpressed in Serum (34.9).

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

NURSA nuclear receptor signaling pathways regulating expression of PTPRF Gene:


SOURCE GeneReport for Unigene cluster for PTPRF Gene:


Evidence on tissue expression from TISSUES for PTPRF Gene

  • Nervous system(4.9)
  • Liver(4.4)
  • Bone marrow(4)
  • Intestine(3.4)
  • Lung(3.4)
  • Eye(2.5)

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

Germ Layers:
  • ectoderm
  • integumentary
  • skeleton
Head and neck:
  • ear
  • face
  • head
  • lip
  • nose
  • outer ear
  • skull
  • breast
  • skin
genes like me logo Genes that share expression patterns with PTPRF: view

No data available for mRNA differential expression in normal tissues , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for PTPRF Gene

Orthologs for PTPRF Gene

This gene was present in the common ancestor of animals.

Orthologs for PTPRF Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PTPRF 34 33
  • 99.26 (n)
(Bos Taurus)
Mammalia PTPRF 34 33
  • 91.82 (n)
(Canis familiaris)
Mammalia PTPRF 34 33
  • 91.38 (n)
(Rattus norvegicus)
Mammalia Ptprf 33
  • 89.36 (n)
(Mus musculus)
Mammalia Ptprf 16 34 33
  • 89.02 (n)
(Ornithorhynchus anatinus)
Mammalia PTPRF 34
  • 86 (a)
(Gallus gallus)
Aves PTPRF 34 33
  • 78.1 (n)
(Anolis carolinensis)
Reptilia PTPRF 34
  • 82 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ptprf 33
  • 72.1 (n)
African clawed frog
(Xenopus laevis)
Amphibia XPTP-LAR 33
(Danio rerio)
Actinopterygii ptprfa 34
  • 76 (a)
ptprfb 34 33
  • 72.67 (n)
fruit fly
(Drosophila melanogaster)
Insecta Lar 34 35
  • 47 (a)
Ptp52F 35
  • 42 (a)
Ptp69D 35
  • 34 (a)
(Caenorhabditis elegans)
Secernentea Y48G9A.9 35
  • 36 (a)
F47B3.7 35
  • 36 (a)
F25H5.7 35
  • 35 (a)
F55F8.7 35
  • 35 (a)
K04D7.4 35
  • 33 (a)
C17H12.3 35
  • 32 (a)
T22C1.8 35
  • 32 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1998 34
  • 45 (a)
Species where no ortholog for PTPRF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • oppossum (Monodelphis domestica)
  • 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 PTPRF Gene

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

Paralogs for PTPRF Gene

Paralogs for PTPRF Gene

(39) SIMAP similar genes for PTPRF Gene using alignment to 8 proteins:

  • A2A437_HUMAN
  • F2Z3B8_HUMAN
  • G1UI20_HUMAN
  • H0Y380_HUMAN
  • H0Y4H1_HUMAN
  • H0Y6Z7_HUMAN
  • H0Y7Z9_HUMAN
genes like me logo Genes that share paralogs with PTPRF: view

Variants for PTPRF Gene

Sequence variations from dbSNP and Humsavar for PTPRF Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000014440 -- 43,623,410(+) G/C 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1000017414 -- 43,525,744(+) G/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000049349 -- 43,593,847(+) G/A intron_variant
rs1000070143 -- 43,613,344(+) C/T intron_variant
rs1000096127 -- 43,560,611(+) C/T intron_variant

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

Variant ID Type Subtype PubMed ID
dgv157n100 CNV gain 25217958
dgv158n100 CNV gain 25217958
dgv77n106 CNV deletion 24896259
dgv78n106 OTHER inversion 24896259
dgv82e59 CNV duplication 20981092
esv2600447 OTHER inversion 19546169
esv2659684 CNV deletion 23128226
esv2678218 CNV deletion 23128226
esv3326720 OTHER inversion 20981092
esv3364493 CNV duplication 20981092
esv3439174 OTHER inversion 20981092
esv3445133 CNV duplication 20981092
esv3585869 CNV loss 21293372
esv3585870 OTHER inversion 21293372
esv7506 OTHER inversion 19470904
nsv1077759 OTHER inversion 25765185
nsv1078379 CNV deletion 25765185
nsv1137756 CNV deletion 24896259
nsv513636 OTHER inversion 21212237
nsv519570 CNV loss 19592680
nsv822487 CNV loss 20364138

Variation tolerance for PTPRF Gene

Residual Variation Intolerance Score: 0.343% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.46; 54.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTPRF 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 PTPRF Gene

Disorders for PTPRF Gene

MalaCards: The human disease database

(6) MalaCards diseases for PTPRF Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PTPRF in MalaCards View complete list of genes associated with diseases


  • Aplasia or hypoplasia of the breasts and/or nipples 2 (BNAH2) [MIM:616001]: A group of congenital deformities encompassing total absence of breasts and nipple (amastia), absence of the nipple (athelia), and absence of the mammary gland (amazia). {ECO:0000269 PubMed:24781087}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PTPRF

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

No data available for Genatlas for PTPRF Gene

Publications for PTPRF Gene

  1. Functional association between the insulin receptor and the transmembrane protein-tyrosine phosphatase LAR in intact cells. (PMID: 8995282) Ahmad F … Goldstein BJ (The Journal of biological chemistry 1997) 3 4 22 58
  2. Distinct functional roles of the two intracellular phosphatase like domains of the receptor-linked protein tyrosine phosphatases LCA and LAR. (PMID: 1695146) Streuli M … Saito H (The EMBO journal 1990) 3 4 22 58
  3. Homozygous truncating PTPRF mutation causes athelia. (PMID: 24781087) Borck G … Basel-Vanagaite L (Human genetics 2014) 3 4 58
  4. Receptor protein tyrosine phosphatase-receptor tyrosine kinase substrate screen identifies EphA2 as a target for LAR in cell migration. (PMID: 23358419) Lee H … Bennett AM (Molecular and cellular biology 2013) 3 4 58
  5. Trans-synaptic adhesions between netrin-G ligand-3 (NGL-3) and receptor tyrosine phosphatases LAR, protein-tyrosine phosphatase delta (PTPdelta), and PTPsigma via specific domains regulate excitatory synapse formation. (PMID: 20139422) Kwon SK … Kim E (The Journal of biological chemistry 2010) 3 22 58

Products for PTPRF Gene

Sources for PTPRF Gene

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