PTPRF (protein tyrosine phosphatase receptor type F)

Gene

• Entrez ID: 5792
• Gene name: Protein tyrosine phosphatase receptor type F
• Gene symbol: PTPRF
• Synonyms: BNAH2, LAR
• Chromosome: 1
• Chromosome location: 1p34.2
• Summary: 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]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1131692054	TG>-	Pathogenic	Intron variant, coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT001340	hsa-miR-1-3p	pSILAC, Proteomics;Other	18668040
MIRT035527	hsa-miR-24-3p	Luciferase reporter assay	23418360
MIRT035797	hsa-miR-1914-5p	CLASH	23622248
MIRT036277	hsa-miR-1229-3p	CLASH	23622248
MIRT037603	hsa-miR-744-5p	CLASH	23622248
MIRT037821	hsa-miR-455-3p	CLASH	23622248
MIRT037821	hsa-miR-455-3p	PAR-CLIP	23592263
MIRT037821	hsa-miR-455-3p	PAR-CLIP	20371350
MIRT037821	hsa-miR-455-3p	HITS-CLIP	23313552
MIRT037821	hsa-miR-455-3p	PAR-CLIP	26701625
MIRT038659	hsa-miR-15b-3p	CLASH	23622248
MIRT046964	hsa-miR-221-3p	CLASH	23622248
MIRT052751	hsa-miR-1260b	CLASH	23622248
MIRT469934	hsa-miR-4665-5p	PAR-CLIP	23592263
MIRT469935	hsa-miR-1275	PAR-CLIP	23592263
MIRT469936	hsa-miR-4662a-5p	PAR-CLIP	23592263
MIRT469937	hsa-miR-4472	PAR-CLIP	23592263
MIRT469938	hsa-miR-4447	PAR-CLIP	23592263
MIRT469939	hsa-miR-3190-3p	PAR-CLIP	23592263
MIRT469940	hsa-miR-5010-5p	PAR-CLIP	23592263
MIRT469941	hsa-miR-4525	PAR-CLIP	23592263
MIRT469942	hsa-miR-6870-5p	PAR-CLIP	23592263
MIRT469943	hsa-miR-7111-5p	PAR-CLIP	23592263
MIRT469944	hsa-miR-5698	PAR-CLIP	23592263
MIRT469945	hsa-miR-4723-5p	PAR-CLIP	23592263
MIRT469946	hsa-miR-625-5p	PAR-CLIP	23592263
MIRT469947	hsa-miR-3175	PAR-CLIP	23592263
MIRT469948	hsa-miR-6878-5p	PAR-CLIP	23592263
MIRT469949	hsa-miR-4795-5p	PAR-CLIP	23592263
MIRT469950	hsa-miR-1296-3p	PAR-CLIP	23592263
MIRT469951	hsa-miR-575	PAR-CLIP	23592263
MIRT469952	hsa-miR-6858-3p	PAR-CLIP	23592263
MIRT469952	hsa-miR-6858-3p	HITS-CLIP	19536157
MIRT469953	hsa-miR-4676-5p	PAR-CLIP	23592263
MIRT469954	hsa-miR-6516-5p	PAR-CLIP	23592263
MIRT469954	hsa-miR-6516-5p	PAR-CLIP	20371350
MIRT469954	hsa-miR-6516-5p	HITS-CLIP	23313552
MIRT469954	hsa-miR-6516-5p	PAR-CLIP	26701625
MIRT469955	hsa-miR-1273e	PAR-CLIP	23592263
MIRT469955	hsa-miR-1273e	PAR-CLIP	21572407
MIRT469955	hsa-miR-1273e	PAR-CLIP	20371350
MIRT469955	hsa-miR-1273e	HITS-CLIP	23313552
MIRT469955	hsa-miR-1273e	PAR-CLIP	26701625
MIRT469956	hsa-miR-6885-5p	PAR-CLIP	23592263
MIRT469956	hsa-miR-6885-5p	PAR-CLIP	21572407
MIRT469956	hsa-miR-6885-5p	PAR-CLIP	20371350
MIRT469956	hsa-miR-6885-5p	HITS-CLIP	23313552
MIRT469956	hsa-miR-6885-5p	PAR-CLIP	26701625
MIRT469957	hsa-miR-328-5p	PAR-CLIP	23592263
MIRT469957	hsa-miR-328-5p	PAR-CLIP	21572407
MIRT469957	hsa-miR-328-5p	PAR-CLIP	20371350
MIRT469957	hsa-miR-328-5p	HITS-CLIP	23313552
MIRT469957	hsa-miR-328-5p	PAR-CLIP	26701625
MIRT469958	hsa-miR-486-3p	PAR-CLIP	23592263
MIRT469958	hsa-miR-486-3p	PAR-CLIP	21572407
MIRT469958	hsa-miR-486-3p	PAR-CLIP	20371350
MIRT469958	hsa-miR-486-3p	HITS-CLIP	23313552
MIRT469958	hsa-miR-486-3p	PAR-CLIP	26701625
MIRT469959	hsa-miR-6499-3p	PAR-CLIP	23592263
MIRT469959	hsa-miR-6499-3p	PAR-CLIP	20371350
MIRT469959	hsa-miR-6499-3p	HITS-CLIP	23313552
MIRT469959	hsa-miR-6499-3p	PAR-CLIP	26701625
MIRT469960	hsa-miR-2467-3p	PAR-CLIP	23592263
MIRT469960	hsa-miR-2467-3p	PAR-CLIP	21572407
MIRT469960	hsa-miR-2467-3p	PAR-CLIP	20371350
MIRT469960	hsa-miR-2467-3p	HITS-CLIP	23313552
MIRT469960	hsa-miR-2467-3p	PAR-CLIP	26701625
MIRT469961	hsa-miR-298	PAR-CLIP	23592263
MIRT469961	hsa-miR-298	PAR-CLIP	21572407
MIRT469961	hsa-miR-298	PAR-CLIP	20371350
MIRT469962	hsa-miR-6086	PAR-CLIP	23592263
MIRT469962	hsa-miR-6086	PAR-CLIP	20371350
MIRT469962	hsa-miR-6086	HITS-CLIP	23313552
MIRT469962	hsa-miR-6086	PAR-CLIP	26701625
MIRT469963	hsa-miR-377-5p	PAR-CLIP	23592263
MIRT469963	hsa-miR-377-5p	PAR-CLIP	20371350
MIRT469963	hsa-miR-377-5p	HITS-CLIP	23313552
MIRT469963	hsa-miR-377-5p	PAR-CLIP	26701625
MIRT469964	hsa-miR-4537	PAR-CLIP	23592263
MIRT469964	hsa-miR-4537	HITS-CLIP	23313552
MIRT469964	hsa-miR-4537	PAR-CLIP	26701625
MIRT469965	hsa-miR-219b-3p	PAR-CLIP	23592263
MIRT469965	hsa-miR-219b-3p	PAR-CLIP	21572407
MIRT469965	hsa-miR-219b-3p	PAR-CLIP	20371350
MIRT469965	hsa-miR-219b-3p	HITS-CLIP	23313552
MIRT469965	hsa-miR-219b-3p	PAR-CLIP	26701625
MIRT469966	hsa-miR-4532	PAR-CLIP	23592263
MIRT469966	hsa-miR-4532	PAR-CLIP	21572407
MIRT469966	hsa-miR-4532	PAR-CLIP	20371350
MIRT469966	hsa-miR-4532	HITS-CLIP	23313552
MIRT469966	hsa-miR-4532	PAR-CLIP	26701625
MIRT469967	hsa-miR-4257	PAR-CLIP	23592263
MIRT469967	hsa-miR-4257	PAR-CLIP	20371350
MIRT469967	hsa-miR-4257	PAR-CLIP	26701625
MIRT469968	hsa-miR-6511a-5p	PAR-CLIP	23592263
MIRT469969	hsa-miR-1910-3p	PAR-CLIP	23592263
MIRT469970	hsa-miR-302f	PAR-CLIP	23592263
MIRT469970	hsa-miR-302f	PAR-CLIP	21572407
MIRT469970	hsa-miR-302f	PAR-CLIP	20371350
MIRT469970	hsa-miR-302f	HITS-CLIP	23313552
MIRT469970	hsa-miR-302f	PAR-CLIP	26701625
MIRT469971	hsa-miR-3714	PAR-CLIP	23592263
MIRT469972	hsa-miR-4484	PAR-CLIP	23592263
MIRT469973	hsa-miR-6768-3p	PAR-CLIP	23592263
MIRT469974	hsa-miR-548an	PAR-CLIP	23592263
MIRT569277	hsa-miR-4730	PAR-CLIP	20371350
MIRT569278	hsa-miR-608	PAR-CLIP	20371350
MIRT569279	hsa-miR-4651	PAR-CLIP	20371350
MIRT569280	hsa-miR-6842-5p	PAR-CLIP	20371350
MIRT569281	hsa-miR-7110-5p	PAR-CLIP	20371350
MIRT569282	hsa-miR-6752-5p	PAR-CLIP	20371350
MIRT569283	hsa-miR-25-5p	PAR-CLIP	20371350
MIRT569284	hsa-miR-658	PAR-CLIP	20371350
MIRT569285	hsa-miR-4787-5p	PAR-CLIP	20371350
MIRT645711	hsa-miR-493-5p	HITS-CLIP	23824327
MIRT645712	hsa-let-7g-3p	HITS-CLIP	23824327
MIRT645713	hsa-let-7a-2-3p	HITS-CLIP	23824327
MIRT645714	hsa-let-7c-3p	HITS-CLIP	23824327
MIRT645715	hsa-miR-542-3p	HITS-CLIP	23824327
MIRT645716	hsa-miR-4504	HITS-CLIP	23824327
MIRT645717	hsa-miR-2115-5p	HITS-CLIP	23824327
MIRT645718	hsa-miR-4679	HITS-CLIP	23824327
MIRT645719	hsa-miR-4677-3p	HITS-CLIP	23824327
MIRT700483	hsa-miR-4684-5p	HITS-CLIP	23313552
MIRT700484	hsa-miR-1268b	HITS-CLIP	23313552
MIRT700485	hsa-miR-1268a	HITS-CLIP	23313552
MIRT700486	hsa-miR-585-3p	HITS-CLIP	23313552
MIRT700487	hsa-miR-4486	HITS-CLIP	23313552
MIRT700488	hsa-miR-939-3p	HITS-CLIP	23313552
MIRT700489	hsa-miR-6827-3p	HITS-CLIP	23313552
MIRT700490	hsa-miR-340-3p	HITS-CLIP	23313552
MIRT700491	hsa-miR-7851-3p	HITS-CLIP	23313552
MIRT700492	hsa-miR-619-3p	HITS-CLIP	23313552
MIRT700493	hsa-miR-6771-3p	HITS-CLIP	23313552
MIRT717384	hsa-miR-425-3p	HITS-CLIP	19536157
MIRT717385	hsa-miR-3157-5p	HITS-CLIP	19536157
MIRT717386	hsa-miR-7106-3p	HITS-CLIP	19536157
MIRT717387	hsa-miR-4660	HITS-CLIP	19536157
MIRT717388	hsa-miR-4655-3p	HITS-CLIP	19536157
MIRT717389	hsa-miR-4469	HITS-CLIP	19536157
MIRT717390	hsa-miR-6803-3p	HITS-CLIP	19536157
MIRT717391	hsa-miR-4530	HITS-CLIP	19536157
MIRT717392	hsa-miR-6736-3p	HITS-CLIP	19536157
MIRT717393	hsa-miR-4691-3p	HITS-CLIP	19536157
MIRT717394	hsa-miR-646	HITS-CLIP	19536157

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004725	Function	Protein tyrosine phosphatase activity	IBA	21873635
GO:0004725	Function	Protein tyrosine phosphatase activity	IDA	10338209
GO:0004725	Function	Protein tyrosine phosphatase activity	IMP	23358419
GO:0005001	Function	Transmembrane receptor protein tyrosine phosphatase activity	TAS	8995282
GO:0005886	Component	Plasma membrane	TAS
GO:0005887	Component	Integral component of plasma membrane	TAS	2972792
GO:0006470	Process	Protein dephosphorylation	IBA	21873635
GO:0007155	Process	Cell adhesion	TAS	7665159
GO:0007185	Process	Transmembrane receptor protein tyrosine phosphatase signaling pathway	TAS	8995282
GO:0008201	Function	Heparin binding	IEA
GO:0016477	Process	Cell migration	IMP	23358419
GO:0031102	Process	Neuron projection regeneration	IEA
GO:0035335	Process	Peptidyl-tyrosine dephosphorylation	IBA	21873635
GO:0035335	Process	Peptidyl-tyrosine dephosphorylation	IMP	23358419
GO:0035373	Function	Chondroitin sulfate proteoglycan binding	IEA
GO:0043005	Component	Neuron projection	IEA
GO:0043025	Component	Neuronal cell body	IEA
GO:0044877	Function	Protein-containing complex binding	IEA
GO:0048679	Process	Regulation of axon regeneration	IEA
GO:0050839	Function	Cell adhesion molecule binding	IPI	23986473
GO:0070062	Component	Extracellular exosome	HDA	19199708
GO:0099560	Process	Synaptic membrane adhesion	IBA	21873635
GO:0099560	Process	Synaptic membrane adhesion	IDA	26321637
GO:0099560	Process	Synaptic membrane adhesion	IMP	26321637
GO:1900121	Process	Negative regulation of receptor binding	IMP	23358419

Other IDs

• MIM: 179590
• HGNC: 9670
• e!Ensembl: ENSG00000142949

Protein

• UniProt ID: P10586
• Protein name: Receptor-type tyrosine-protein phosphatase F (EC 3.1.3.48) (Leukocyte common antigen related) (LAR)
• Protein function: 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.
• PDB: 1LAR, 2DJU, 2DN7, 2EDX, 2EDY, 2YD5, 2YD8, 4N5U, 6KR4, 6TPT, 6TPU, 6TPV, 6TPW
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF07679	I-set	33 → 124	Immunoglobulin I-set domain	Domain
  PF07679	I-set	135 → 225	Immunoglobulin I-set domain	Domain
  PF07679	I-set	232 → 315	Immunoglobulin I-set domain	Domain
  PF00041	fn3	320 → 401	Fibronectin type III domain	Domain
  PF00041	fn3	415 → 500	Fibronectin type III domain	Domain
  PF00041	fn3	513 → 594	Fibronectin type III domain	Domain
  PF00041	fn3	608 → 696	Fibronectin type III domain	Domain
  PF00041	fn3	710 → 809	Fibronectin type III domain	Domain
  PF00041	fn3	823 → 903	Fibronectin type III domain	Domain
  PF00041	fn3	917 → 1000	Fibronectin type III domain	Domain
  PF00102	Y_phosphatase	1375 → 1606	Protein-tyrosine phosphatase	Domain
  PF00102	Y_phosphatase	1664 → 1897	Protein-tyrosine phosphatase	Domain

• Sequence:

  MAPEPAPGRTMVPLVPALVMLGLVAGAHGDSKPVFIKVPEDQTGLSGGVASFVCQATGEP
  KPRITWMKKGKKVSSQRFEVIEFDDGAGSVLRIQPLRVQRDEAIYECTATNSLGEINTSA
  KLSVLEEEQLPPGFPSIDMGPQLKVVEKARTATMLCAAGGNPDPEISWFKDFLPVDPATS
  NGRIKQLRSGALQIESSEESDQGKYECVATNSAGTRYSAPANLYVRVRRVAPRFSIPPSS
  QEVMPGGSVNLTCVAVGAPMPYVKWMMGAEELTKEDEMPVGRNVLELSNVVRSANYTCVA
  ISSLGMIEATAQVTVKALPKPPIDLVVTETTATSVTLTWDSGNSEPVTYYGIQYRAAGTE
  GPFQEVDGVATTRYSIGGLSPFSEYAFRVLAVNSIGRGPPSEAVRARTGEQAPSSPPRRV
  QARMLSASTMLVQWEPPEEPNGLVRGYRVYYTPDSRRPPNAWHKHNTDAGLLTTVGSLLP
  GITYSLRVLAFTAVGDGPPSPTIQVKTQQGVPAQPADFQAEVESDTRIQLSWLLPPQERI
  IMYELVYWAAEDEDQQHKVTFDPTSSYTLEDLKPDTLYRFQLAARSDMGVGVFTPTIEAR
  TAQSTPSAPPQKVMCVSMGSTTVRVSWVPPPADSRNGVITQYSVAYEAVDGEDRGRHVVD
  GISREHSSWDLVGLEKWTEYRVWVRAHTDVGPGPESSPVLVRTDEDVPSGPPRKVEVEPL
  NSTAVHVYWKLPVPSKQHGQIRGYQVTYVRLENGEPRGLPIIQDVMLAEAQWRPEESEDY
  ETTISGLTPETTYSVTVAAYTTKGDGARSKPKIVTTTGAVPGRPTMMISTTAMNTALLQW
  HPPKELPGELLGYRLQYCRADEARPNTIDFGKDDQHFTVTGLHKGTTYIFRLAAKNRAGL
  GEEFEKEIRTPEDLPSGFPQNLHVTGLTTSTTELAWDPPVLAERNGRIISYTVVFRDINS
  QQELQNITTDTRFTLTGLKPDTTYDIKVRAWTSKGSGPLSPSIQSRTMPVEQVFAKNFRV
  AAAMKTSVLLSWEVPDSYKSAVPFKILYNGQSVEVDGHSMRKLIADLQPNTEYSFVLMNR
  GSSAGGLQHLVSIRTAPDLLPHKPLPASAYIEDGRFDLSMPHVQDPSLVRWFYIVVVPID
  RVGGSMLTPRWSTPEELELDELLEAIEQGGEEQRRRRRQAERLKPYVAAQLDVLPETFTL
  GDKKNYRGFYNRPLSPDLSYQCFVLASLKEPMDQKRYASSPYSDEIVVQVTPAQQQEEPE
  MLWVTGPVLAVILIILIVIAILLFKRKRTHSPSSKDEQSIGLKDSLLAHSSDPVEMRRLN
  YQTPGMRDHPPIPITDLADNIERLKANDGLKFSQEYESIDPGQQFTWENSNLEVNKPKNR
  YANVIAYDHSRVILTSIDGVPGSDYINANYIDGYRKQNAYIATQGPLPETMGDFWRMVWE
  QRTATVVMMTRLEEKSRVKCDQYWPARGTETCGLIQVTLLDTVELATYTVRTFALHKSGS
  SEKRELRQFQFMAWPDHGVPEYPTPILAFLRRVKACNPLDAGPMVVHCSAGVGRTGCFIV
  IDAMLERMKHEKTVDIYGHVTCMRSQRNYMVQTEDQYVFIHEALLEAATCGHTEVPARNL
  YAHIQKLGQVPPGESVTAMELEFKLLASSKAHTSRFISANLPCNKFKNRLVNIMPYELTR
  VCLQPIRGVEGSDYINASFLDGYRQQKAYIATQGPLAESTEDFWRMLWEHNSTIIVMLTK
  LREMGREKCHQYWPAERSARYQYFVVDPMAEYNMPQYILREFKVTDARDGQSRTIRQFQF
  TDWPEQGVPKTGEGFIDFIGQVHKTKEQFGQDGPITVHCSAGVGRTGVFITLSIVLERMR
  YEGVVDMFQTVKTLRTQRPAMVQTEDQYQLCYRAALEYLGSFDHYAT

• Sequence length: 1907