Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Associated diseases
Entrez ID	5800
Gene name	Protein tyrosine phosphatase receptor type O
Gene symbol	PTPRO
Synonyms (NCBI Gene)	GLEPP1NPHS6PTP-OCPTP-U2PTPROTPTPU2R-PTP-O
Chromosome	12
Chromosome location	12p12.3\|12p13-p12
Summary	This gene encodes a member of the R3 subtype family of receptor-type protein tyrosine phosphatases. These proteins are localized to the apical surface of polarized cells and may have tissue-specific functions through activation of Src family kinases. This

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SNP ID	Visualize variation	Clinical significance	Consequence
rs1591750243	G>A	Pathogenic	Splice donor variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT000977	hsa-miR-17-5p	Luciferase reporter assayWestern blot	18644370
MIRT000977	hsa-miR-17-5p	Luciferase reporter assay	18644370
MIRT029550	hsa-miR-26b-5p	Microarray	19088304
MIRT000977	hsa-miR-17-5p	Luciferase reporter assay	27720936
MIRT732856	hsa-miR-6869-5p	Luciferase reporter assayqRT-PCRFlow cytometryELISA	34007244
MIRT1276365	hsa-miR-1343	CLIP-seq
MIRT1276366	hsa-miR-194	CLIP-seq
MIRT1276367	hsa-miR-2467-5p	CLIP-seq
MIRT1276368	hsa-miR-3115	CLIP-seq
MIRT1276369	hsa-miR-3159	CLIP-seq
MIRT1276370	hsa-miR-361-5p	CLIP-seq
MIRT1276371	hsa-miR-3667-3p	CLIP-seq
MIRT1276372	hsa-miR-3675-5p	CLIP-seq
MIRT1276373	hsa-miR-3690	CLIP-seq
MIRT1276374	hsa-miR-3908	CLIP-seq
MIRT1276375	hsa-miR-3919	CLIP-seq
MIRT1276376	hsa-miR-3925-5p	CLIP-seq
MIRT1276377	hsa-miR-3973	CLIP-seq
MIRT1276378	hsa-miR-4254	CLIP-seq
MIRT1276379	hsa-miR-4283	CLIP-seq
MIRT1276380	hsa-miR-4302	CLIP-seq
MIRT1276381	hsa-miR-4489	CLIP-seq
MIRT1276382	hsa-miR-4502	CLIP-seq
MIRT1276383	hsa-miR-4528	CLIP-seq
MIRT1276384	hsa-miR-4656	CLIP-seq
MIRT1276385	hsa-miR-4747-5p	CLIP-seq
MIRT1276386	hsa-miR-4773	CLIP-seq
MIRT1276387	hsa-miR-486-5p	CLIP-seq
MIRT1276388	hsa-miR-548a-5p	CLIP-seq
MIRT1276389	hsa-miR-548ab	CLIP-seq
MIRT1276390	hsa-miR-548ak	CLIP-seq
MIRT1276391	hsa-miR-548b-5p	CLIP-seq
MIRT1276392	hsa-miR-548c-5p	CLIP-seq
MIRT1276393	hsa-miR-548d-5p	CLIP-seq
MIRT1276394	hsa-miR-548h	CLIP-seq
MIRT1276395	hsa-miR-548i	CLIP-seq
MIRT1276396	hsa-miR-548j	CLIP-seq
MIRT1276397	hsa-miR-548w	CLIP-seq
MIRT1276398	hsa-miR-548y	CLIP-seq
MIRT1276399	hsa-miR-559	CLIP-seq
MIRT1276400	hsa-miR-642b	CLIP-seq
MIRT1276401	hsa-miR-665	CLIP-seq
MIRT1276402	hsa-miR-671-5p	CLIP-seq
MIRT1276403	hsa-miR-802	CLIP-seq
MIRT1276404	hsa-miR-873	CLIP-seq
MIRT1276405	hsa-miR-1323	CLIP-seq
MIRT1276406	hsa-miR-137	CLIP-seq
MIRT1276407	hsa-miR-15a	CLIP-seq
MIRT1276408	hsa-miR-15b	CLIP-seq
MIRT1276409	hsa-miR-16	CLIP-seq
MIRT1276410	hsa-miR-195	CLIP-seq
MIRT1276411	hsa-miR-25	CLIP-seq
MIRT1276412	hsa-miR-3122	CLIP-seq
MIRT1276413	hsa-miR-3124-3p	CLIP-seq
MIRT1276414	hsa-miR-3182	CLIP-seq
MIRT1276415	hsa-miR-3194-3p	CLIP-seq
MIRT1276416	hsa-miR-32	CLIP-seq
MIRT1276370	hsa-miR-361-5p	CLIP-seq
MIRT1276417	hsa-miR-363	CLIP-seq
MIRT1276418	hsa-miR-367	CLIP-seq
MIRT1276419	hsa-miR-3686	CLIP-seq
MIRT1276420	hsa-miR-3913-5p	CLIP-seq
MIRT1276421	hsa-miR-3921	CLIP-seq
MIRT1276377	hsa-miR-3973	CLIP-seq
MIRT1276422	hsa-miR-424	CLIP-seq
MIRT1276423	hsa-miR-4303	CLIP-seq
MIRT1276424	hsa-miR-4325	CLIP-seq
MIRT1276425	hsa-miR-4468	CLIP-seq
MIRT1276426	hsa-miR-4653-5p	CLIP-seq
MIRT1276427	hsa-miR-4742-3p	CLIP-seq
MIRT1276428	hsa-miR-4782-5p	CLIP-seq
MIRT1276429	hsa-miR-497	CLIP-seq
MIRT1276388	hsa-miR-548a-5p	CLIP-seq
MIRT1276389	hsa-miR-548ab	CLIP-seq
MIRT1276390	hsa-miR-548ak	CLIP-seq
MIRT1276391	hsa-miR-548b-5p	CLIP-seq
MIRT1276392	hsa-miR-548c-5p	CLIP-seq
MIRT1276393	hsa-miR-548d-5p	CLIP-seq
MIRT1276394	hsa-miR-548h	CLIP-seq
MIRT1276395	hsa-miR-548i	CLIP-seq
MIRT1276396	hsa-miR-548j	CLIP-seq
MIRT1276430	hsa-miR-548o	CLIP-seq
MIRT1276397	hsa-miR-548w	CLIP-seq
MIRT1276398	hsa-miR-548y	CLIP-seq
MIRT1276399	hsa-miR-559	CLIP-seq
MIRT1276400	hsa-miR-642b	CLIP-seq
MIRT1276404	hsa-miR-873	CLIP-seq
MIRT1276431	hsa-miR-92a	CLIP-seq
MIRT1276432	hsa-miR-92b	CLIP-seq
MIRT1276433	hsa-miR-944	CLIP-seq
MIRT2081303	hsa-miR-3117-5p	CLIP-seq
MIRT2081304	hsa-miR-514	CLIP-seq
MIRT2081305	hsa-miR-514b-3p	CLIP-seq
MIRT2439712	hsa-miR-208a	CLIP-seq
MIRT2439713	hsa-miR-208b	CLIP-seq
MIRT2439714	hsa-miR-3617	CLIP-seq
MIRT2439715	hsa-miR-499-5p	CLIP-seq
MIRT2439716	hsa-miR-641	CLIP-seq

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Transcription factor	Regulation	Reference
E2F1	Unknown	18644370

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000902	Process	Cell morphogenesis	IEA
GO:0000902	Process	Cell morphogenesis	ISS
GO:0002548	Process	Monocyte chemotaxis	IMP	19233845
GO:0003093	Process	Regulation of glomerular filtration	IBA
GO:0003093	Process	Regulation of glomerular filtration	IEA
GO:0003093	Process	Regulation of glomerular filtration	ISS
GO:0003105	Process	Negative regulation of glomerular filtration	IEA
GO:0003105	Process	Negative regulation of glomerular filtration	ISS
GO:0004721	Function	Phosphoprotein phosphatase activity	IEA
GO:0004725	Function	Protein tyrosine phosphatase activity	IBA
GO:0004725	Function	Protein tyrosine phosphatase activity	IDA	19167335
GO:0004725	Function	Protein tyrosine phosphatase activity	IEA
GO:0004725	Function	Protein tyrosine phosphatase activity	IMP	19233845
GO:0004725	Function	Protein tyrosine phosphatase activity	TAS	10498613
GO:0005001	Function	Transmembrane receptor protein tyrosine phosphatase activity	NAS	7665166
GO:0005515	Function	Protein binding	IPI	19167335, 28330616
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	NAS	7665166
GO:0007411	Process	Axon guidance	IBA
GO:0007411	Process	Axon guidance	IEA
GO:0007411	Process	Axon guidance	ISS
GO:0010812	Process	Negative regulation of cell-substrate adhesion	ISS
GO:0010977	Process	Negative regulation of neuron projection development	ISS
GO:0016020	Component	Membrane	IEA
GO:0016020	Component	Membrane	TAS	10498613
GO:0016324	Component	Apical plasma membrane	IEA
GO:0016324	Component	Apical plasma membrane	ISS
GO:0016328	Component	Lateral plasma membrane	IEA
GO:0016328	Component	Lateral plasma membrane	ISS
GO:0016787	Function	Hydrolase activity	IEA
GO:0016791	Function	Phosphatase activity	ISS
GO:0017147	Function	Wnt-protein binding	IBA
GO:0017147	Function	Wnt-protein binding	IEA
GO:0017147	Function	Wnt-protein binding	ISS
GO:0030027	Component	Lamellipodium	ISS
GO:0030032	Process	Lamellipodium assembly	IEA
GO:0030032	Process	Lamellipodium assembly	ISS
GO:0030424	Component	Axon	ISS
GO:0030426	Component	Growth cone	ISS
GO:0032835	Process	Glomerulus development	IEA
GO:0032835	Process	Glomerulus development	IMP	21722858
GO:0036060	Process	Slit diaphragm assembly	IEA
GO:0036060	Process	Slit diaphragm assembly	ISS
GO:0036060	Process	Slit diaphragm assembly	NAS	20633639
GO:0042803	Function	Protein homodimerization activity	IEA
GO:0042803	Function	Protein homodimerization activity	ISS
GO:0043005	Component	Neuron projection	ISS
GO:0043197	Component	Dendritic spine	IEA
GO:0043197	Component	Dendritic spine	ISS
GO:0045296	Function	Cadherin binding	IBA
GO:0045296	Function	Cadherin binding	IPI	28926625
GO:0050807	Process	Regulation of synapse organization	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0072112	Process	Podocyte differentiation	IBA
GO:0072112	Process	Podocyte differentiation	IEA
GO:0072112	Process	Podocyte differentiation	ISS
GO:0090090	Process	Negative regulation of canonical Wnt signaling pathway	IBA
GO:0090090	Process	Negative regulation of canonical Wnt signaling pathway	IEA
GO:0090090	Process	Negative regulation of canonical Wnt signaling pathway	ISS
GO:0090260	Process	Negative regulation of retinal ganglion cell axon guidance	ISS
GO:0098839	Component	Postsynaptic density membrane	IEA
GO:0098978	Component	Glutamatergic synapse	IBA
GO:0098978	Component	Glutamatergic synapse	IEA
GO:0098982	Component	GABA-ergic synapse	IBA
GO:0098982	Component	GABA-ergic synapse	IEA

MIM	HGNC	e!Ensembl
600579	9678	ENSG00000151490

Q16827

Protein name

Receptor-type tyrosine-protein phosphatase O (R-PTP-O) (EC 3.1.3.48) (Glomerular epithelial protein 1) (Protein tyrosine phosphatase U2) (PTP-U2) (PTPase U2)

Protein function

Possesses tyrosine phosphatase activity. Plays a role in regulating the glomerular pressure/filtration rate relationship through an effect on podocyte structure and function (By similarity).

PDB

2G59 , 2GJT

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00041	fn3	434 → 521	Fibronectin type III domain	Domain
PF00041	fn3	724 → 805	Fibronectin type III domain	Domain
PF00102	Y_phosphatase	962 → 1194	Protein-tyrosine phosphatase	Domain

Tissue specificity

TISSUE SPECIFICITY: Glomerulus of kidney. Also detected in brain, lung and placenta. {ECO:0000269|PubMed:10498613}.

Sequence

MGHLPTGIHGARRLLPLLWLFVLFKNATAFHVTVQDDNNIVVSLEASDVISPASVYVVKI
TGESKNYFFEFEEFNSTLPPPVIFKASYHGLYYIITLVVVNGNVVTKPSRSITVLTKPLP
VTSVSIYDYKPSPETGVLFEIHYPEKYNVFTRVNISYWEGKDFRTMLYKDFFKGKTVFNH
WLPGMCYSNITFQLVSEATFNKSTLVEYSGVSHEPKQHRTAPYPPQNISVRIVNLNKNNW
EEQSGNFPEESFMRSQDTIGKEKLFHFTEETPEIPSGNISSGWPDFNSSDYETTSQPYWW
DSASAAPESEDEFVSVLPMEYENNSTLSETEKSTSGSFSFFPVQMILTWLPPKPPTAFDG
FHIHIEREENFTEYLMVDEEAHEFVAELKEPGKYKLSVTTFSSSGSCETRKSQSAKSLSF
YISPSGEWIEELTEKPQHVSVHVLSSTTALMSWTSSQENYNSTIVSVVSLTCQKQKESQR
LEKQYCTQVNSSKPIIENLVPGAQYQVVIYLRKGPLIGPPSDPVTFAIVPTGIKDLMLYP
LGPTAVVLSWTRPYLGVFRKYVVEMFYFNPATMTSEWTTYYEIAATVSLTASVRIANLLP
AWYYNFRVTMVTWGDPELSCCDSSTISFITAPVAPEITSVEYFNSLLYISWTYGDDTTDL
SHSRMLHWMVVAEGKKKIKKSVTRNVMTAILSLPPGDIYNLSVTACTERGSNTSMLRLVK
LEPAPPKSLFAVNKTQTSVTLLWVEEGVADFFEVFCQQVGSSQKTKLQEPVAVSSHVVTI
SSLLPATAYNCSVTSFSHDSPSVPTFIAVSTMVTEMNPNVVVISVLAILSTLLIGLLLVT
LIILRKKHLQMARECGAGTFVNFASLERDGKLPYNWRRSIFAFLTLLPSCLWTDYLLAFY
INPWSKNGLKKRKLTNPVQLDDFDAYIKDMAKDSDYKFSLQFEELKLIGLDIPHFAADLP
LNRCKNRYTNILPYDFSRVRLVSMNEEEGADYINANYIPGYNSPQEYIATQGPLPETRND
FWKMVLQQKSQIIVMLTQCNEKRRVKCDHYWPFTEEPIAYGDITVEMISEEEQDDWACRH
FRINYADEMQDVMHFNYTAWPDHGVPTANAAESILQFVHMVRQQATKSKGPMIIHCSAGV
GRTGTFIALDRLLQHIRDHEFVDILGLVSEMRSYRMSMVQTEEQYIFIHQCVQLMWMKKK
QQFCISDVIYENVSKS

Sequence length

1216

Interactions

View interactions

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Nephrotic syndrome, type 6	Pathogenic	rs1591732280, rs1591750243	RCV000023015 RCV000023016	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (38)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANTIPHOSPHOLIPID SYNDROME	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Corticosteroids response	drug response; Benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ENDOMETRIOSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL IDIOPATHIC STEROID-RESISTANT NEPHROTIC SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FOCAL GLOMERULOSCLEROSIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROESOPHAGEAL REFLUX DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GENETIC STEROID-RESISTANT NEPHROTIC SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY STEROID-RESISTANT NEPHROTIC SYNDROME	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPEROPIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER CIRRHOSIS, EXPERIMENTAL	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LIVER NEOPLASMS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MELANOMA	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUTROPENIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PTPRO-related disorder	Benign; Likely benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

PTPRO (protein tyrosine phosphatase receptor type O)