PTPRO

gene
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Also known as PTPU2GLEPP1PTP-U2PTP-ocNPHS6

Summary

PTPRO (protein tyrosine phosphatase receptor type O, HGNC:9678) is a protein-coding gene on chromosome 12p12.3, encoding Receptor-type tyrosine-protein phosphatase O (Q16827). Possesses tyrosine phosphatase activity.

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 gene contains two distinct promoters, and alternatively spliced transcript variants encoding multiple isoforms have been observed. The encoded proteins may have multiple isoform-specific and tissue-specific functions, including the regulation of osteoclast production and activity, inhibition of cell proliferation and facilitation of apoptosis. This gene is a candidate tumor suppressor, and decreased expression of this gene has been observed in several types of cancer.

Source: NCBI Gene 5800 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): nephrotic syndrome, type 6 (Strong, GenCC) — +1 more curated relationship
  • Clinical variants (ClinVar): 527 total — 5 pathogenic, 5 likely-pathogenic
  • Druggable target: yes
  • MANE Select transcript: NM_030667

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9678
Approved symbolPTPRO
Nameprotein tyrosine phosphatase receptor type O
Location12p12.3
Locus typegene with protein product
StatusApproved
AliasesPTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6
Ensembl geneENSG00000151490
Ensembl biotypeprotein_coding
OMIM600579
Entrez5800

Gene structure

Transcript identifiers

Ensembl transcripts: 27 — 12 protein_coding, 8 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 3 retained_intron

ENST00000281171, ENST00000348962, ENST00000442921, ENST00000445537, ENST00000535311, ENST00000535322, ENST00000538907, ENST00000542557, ENST00000543886, ENST00000544244, ENST00000544706, ENST00000545023, ENST00000674186, ENST00000674188, ENST00000674220, ENST00000674261, ENST00000674286, ENST00000674316, ENST00000674352, ENST00000674354, ENST00000674385, ENST00000674388, ENST00000674391, ENST00000674392, ENST00000674434, ENST00000674483, ENST00000866319

RefSeq mRNA: 6 — MANE Select: NM_030667 NM_002848, NM_030667, NM_030668, NM_030669, NM_030670, NM_030671

CCDS: CCDS44837, CCDS53754, CCDS8674, CCDS8675

Canonical transcript exons

ENST00000281171 — 27 exons

ExonStartEnd
ENSE000009998811551549815515618
ENSE000009998851552020115520312
ENSE000011222041548397415484247
ENSE000011471411551676315516956
ENSE000011471461550857115508767
ENSE000011471521550390815504069
ENSE000011471601550162015502063
ENSE000011471651549944215499594
ENSE000011471711549724515497403
ENSE000016964781558945515589590
ENSE000017123301558689715587051
ENSE000017149291558167915581801
ENSE000017444361555155115551671
ENSE000017645661556019315560276
ENSE000017699931559493715595057
ENSE000017774011552614215526262
ENSE000017815851558069715580831
ENSE000017918531554656915546708
ENSE000022415491552481415524965
ENSE000023026131532250815322801
ENSE000034776221554909415549226
ENSE000035819691557885315578943
ENSE000035833021558003915580115
ENSE000036074901556559315565628
ENSE000036343631555745515557523
ENSE000036840681556941715569498
ENSE000038457131559609015598331

Expression profiles

Bgee: expression breadth ubiquitous, 214 present calls, max score 98.36.

FANTOM5 (CAGE): breadth broad, TPM avg 3.3795 / max 238.0984, expressed in 522 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1244880.7247163
1244920.6656225
1244910.4918152
1244930.4380139
1244840.4324132
1244890.4279128
1244860.077138
1244830.066039
1244850.029112
1244870.02708

Top tissues by expression

289 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
renal glomerulusUBERON:000007498.36gold quality
metanephric glomerulusUBERON:000473698.22gold quality
cortical plateUBERON:000534397.38gold quality
rectumUBERON:000105293.71gold quality
ganglionic eminenceUBERON:000402391.25gold quality
kidney epitheliumUBERON:000481987.83gold quality
middle temporal gyrusUBERON:000277187.39gold quality
adult mammalian kidneyUBERON:000008286.50gold quality
ventricular zoneUBERON:000305384.92gold quality
nucleus accumbensUBERON:000188284.84gold quality
prefrontal cortexUBERON:000045184.15gold quality
mucosa of transverse colonUBERON:000499183.76gold quality
metanephrosUBERON:000008183.55gold quality
kidneyUBERON:000211383.55gold quality
cortex of kidneyUBERON:000122582.91gold quality
monocyteCL:000057682.54gold quality
colonic epitheliumUBERON:000039782.38gold quality
Brodmann (1909) area 46UBERON:000648382.34gold quality
mononuclear cellCL:000084282.06gold quality
leukocyteCL:000073882.05gold quality
granulocyteCL:000009481.63gold quality
dorsolateral prefrontal cortexUBERON:000983481.46gold quality
calcaneal tendonUBERON:000370181.36gold quality
endothelial cellCL:000011581.32gold quality
frontal cortexUBERON:000187081.04gold quality
frontal lobeUBERON:001652581.02gold quality
neocortexUBERON:000195080.96gold quality
mucosa of sigmoid colonUBERON:000499380.66gold quality
thoracic aortaUBERON:000151580.63gold quality
ascending aortaUBERON:000149680.60gold quality

Single-cell (SCXA)

Detected in 8 experiment(s), a significant marker in 8.

ExperimentMarker?Max mean expression
E-GEOD-131882yes9874.95
E-CURD-119yes9566.57
E-GEOD-114530yes2043.25
E-CURD-135yes1441.69
E-HCAD-10yes1398.09
E-HCAD-35yes89.47
E-GEOD-125970yes21.56
E-ANND-3yes6.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

111 targeting PTPRO, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-3162-3P100.0065.37363
HSA-MIR-8485100.0077.574731
HSA-MIR-366299.9973.825684
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-186-5P99.9970.833707
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-480399.9871.993117
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-806899.9873.852376
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-302E99.9670.742669
HSA-MIR-185-3P99.9567.011743
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-302C-3P99.8971.201778
HSA-MIR-473999.8465.251832
HSA-MIR-202-3P99.8471.411290
HSA-MIR-132199.8465.301811
HSA-MIR-4756-5P99.8464.981809
HSA-MIR-607999.8468.541170

Literature-anchored findings (GeneRIF, showing 37)

  • conclude that an intronic promoter within the protein tyrosine phosphatase, receptor type(GLEPP1) gene drives the expression of the protein tyrosine phosphatase-osteoclast(PTP) in a cell type-specific manner (PMID:12949066)
  • overexpression of PTPROt inhibited BCR-triggered SYK tyrosyl phosphorylation, activation of the associated adaptor proteins SHC and BLNK, and downstream signaling events, and inhibition lymphoma cell proliferation and inducion of lymphoma cell apoptosis (PMID:16888096)
  • PTPRO methylation and silencing has a role in chronic lymphocytic leukemia tumorigenesis (PMID:17545520)
  • GLEPP1 expression may be a useful marker of podocyte injury in immunoglobulin A nephropathy, and may be predictive of clinical and pathological severity (PMID:17593862)
  • PTPRO gene is co-regulated by both E2F1 and miR-17-92. (PMID:18644370)
  • These data suggest that estrogen-mediated suppression of PTPRO is probably one of the early events in estrogen-induced tumorigenesis and that expression of PTPRO could facilitate endocrine therapy of breast cancer. (PMID:19095770)
  • Dimerization of neuronal type III receptor-protein tyrosine phosphatase PTPRO in living cells is regulated by disulfide linkages in the PTPRO intracellular domain. (PMID:19573017)
  • BCL6 repressed PTPROt transcription via a direct interaction with functional BCL6 binding sites in the PTPROt promoter (PMID:19855081)
  • The present study introduces mutations in PTPRO as another cause of autosomal-recessive nephrotic syndrome. (PMID:21722858)
  • These findings further substantiate the role of TCL1 in PTPROt suppression and its importance in the pathogenesis of chronic lymphocytic leukemia. (PMID:22001392)
  • hypermethylated PTPRO occurs frequently in esophageal squamous cell carcinoma (PMID:22099875)
  • Three intronic SNPs in PTPRO were associated with learning and memory. (PMID:22126837)
  • ErbB2 is a direct substrate of PTPRO and decreased expression of PTPRO predicts poor prognosis for ErbB2-positive breast cancer patients. (PMID:22851698)
  • methylation and downregulation of PTPRO in a subset of primary human HCC and establish VCP as a novel functionally important substrate of this tyrosine phosphatase that could be a potential molecular target for HCC therapy. (PMID:23533167)
  • PTPRO methylation is associated with poor survival only in HER2-positive patients. (PMID:24090193)
  • PTPRO level was decreased in the early phase but reversed in the late phase of hepatic ischemia reperfusion injury. (PMID:24128416)
  • Our study suggests an interesting PTPRO/TLR4/NF-kappaB signaling feedback loop in Hhepatocellular carcinomcarcinogenesis and progression (PMID:25034527)
  • Results highlight the PTPRO contribution in negative regulation of SRC/EGFR signaling in colon cancer. (PMID:25301722)
  • PTPRO was drastically decreased in fulminant hepatitis, and this was associated with enhanced beta-catenin accumulation but reduced IFN-gamma secretion. (PMID:25339662)
  • The optimal pH value of PTP-oc is approximately 7.0. (PMID:25462809)
  • Loss of PTPRO expression is associated with chronic lymphocytic leukemia. (PMID:25482129)
  • These observations confirm that PTPRO plays a critical role in liver fibrogenesis by affecting PDGF signaling in HSC activation and might be developed into a feasible therapeutic approach for the treatment of chronic fibrotic liver diseases. (PMID:25633279)
  • PTPRO truncated serves as an important tumor suppressor in hepatocellular carcinoma microenvironment. (PMID:26117839)
  • Single nucleotide polymorphism in PTPRO gene is associated with Acute Renal Graft Rejection. (PMID:27272414)
  • Results provide evidence that PTPRO inhibits ERBB2-driven breast cancer through dephosphorylation leading to dual effects of ERBB2 signaling suppression and endosomal internalization of ERBB2. (PMID:27345410)
  • PTPRO is a novel candidate gene in emphysema with severe airflow obstruction. (PMID:28199135)
  • the present study demonstrated that PTPRO inhibits tumor growth in vitro and in vivo, indicating the tumor suppressive function of PTPRO in LSCC. This study highlights PTPRO as an epigenetically silenced gene, and a candidate tumor-suppressor of LSCC. (PMID:28586036)
  • PTPRO was significantly upregulated and negatively associated with miR-548c-5p in placental mononuclear cells in patients with preeclampsia. (PMID:30443949)
  • LncRNA HULC promotes lung squamous cell carcinoma by regulating PTPRO via NF-kappaB. (PMID:31448453)
  • PTPRO exaggerates inflammation in ulcerative colitis through TLR4/NF-kappaB pathway. (PMID:31452237)
  • IL-6 promotes PD-L1 expression in monocytes and macrophages by decreasing protein tyrosine phosphatase receptor type O expression in human hepatocellular carcinoma. (PMID:32581055)
  • MiR-6869-5p Induces M2 Polarization by Regulating PTPRO in Gestational Diabetes Mellitus. (PMID:34007244)
  • Protein tyrosine phosphatase receptor type O (PTPRO) knockdown enhances the proliferative, invasive and angiogenic activities of trophoblast cells by suppressing ER resident protein 44 (ERp44) expression in preeclampsia. (PMID:34719307)
  • PTPRO activates TLR4/NF-kappaB signaling to intensify lipopolysaccharide-induced pneumonia cell injury. (PMID:35527665)
  • PTPRO-related CD8(+) T-cell signatures predict prognosis and immunotherapy response in patients with breast cancer. (PMID:36003382)
  • Protein tyrosine phosphatase PTPRO represses lung adenocarcinoma progression by inducing mitochondria-dependent apoptosis and restraining tumor metastasis. (PMID:38182570)
  • Protein tyrosine phosphatase receptor type O serves as a key regulator of insulin resistance-induced alpha-synuclein aggregation in Parkinson’s disease. (PMID:39276174)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_rerioptproENSDARG00000100422
danio_rerioENSDARG00000110470
mus_musculusPtproENSMUSG00000030223
rattus_norvegicusPtproENSRNOG00000006231
drosophila_melanogasterPtp4EFBGN0004368
drosophila_melanogasterPtp10DFBGN0004370
caenorhabditis_elegansWBGENE00009717

Paralogs (35): PTPRN (ENSG00000054356), PTPRU (ENSG00000060656), PTPN3 (ENSG00000070159), PTPN21 (ENSG00000070778), PTPN18 (ENSG00000072135), PTPN23 (ENSG00000076201), PTPRH (ENSG00000080031), PTPRC (ENSG00000081237), PTPN4 (ENSG00000088179), PTPRS (ENSG00000105426), PTPRZ1 (ENSG00000106278), PTPN5 (ENSG00000110786), PTPN6 (ENSG00000111679), PTPRB (ENSG00000127329), PTPN12 (ENSG00000127947), PTPRE (ENSG00000132334), PTPRA (ENSG00000132670), PTPN22 (ENSG00000134242), PTPRF (ENSG00000142949), PTPN7 (ENSG00000143851), PTPRG (ENSG00000144724), PTPRJ (ENSG00000149177), PTPN14 (ENSG00000152104), PTPRK (ENSG00000152894), PTPRR (ENSG00000153233), PTPRD (ENSG00000153707), PTPRN2 (ENSG00000155093), PTPN13 (ENSG00000163629), PTPN9 (ENSG00000169410), PTPRM (ENSG00000173482), PTPN2 (ENSG00000175354), PTPN11 (ENSG00000179295), PTPRT (ENSG00000196090), PTPN1 (ENSG00000196396), PTPN20 (ENSG00000204179)

Protein

Protein identifiers

Receptor-type tyrosine-protein phosphatase OQ16827 (reviewed: Q16827)

Alternative names: Glomerular epithelial protein 1, Protein tyrosine phosphatase U2

All UniProt accessions (10): Q16827, A0A6I8PIM6, A0A6I8PL17, A0A6I8PRB8, A0A6I8PRG8, A0A6I8PRZ5, A0A6I8PS48, A0A6I8PU14, H0YH11, H0YH60

UniProt curated annotations — full annotation on UniProt →

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

Subunit / interactions. Interacts (phosphorylated form) with FYN and GRB2.

Subcellular location. Membrane.

Tissue specificity. Glomerulus of kidney. Also detected in brain, lung and placenta.

Disease relevance. Nephrotic syndrome 6 (NPHS6) [MIM:614196] A form of nephrotic syndrome, a renal disease clinically characterized by severe proteinuria, resulting in complications such as hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. The disease is caused by variants affecting the gene represented in this entry.

Induction. By various differentiation-inducing agents.

Miscellaneous. Predominantly expressed in B-lymphoid tissues.

Similarity. Belongs to the protein-tyrosine phosphatase family. Receptor class 3 subfamily.

Isoforms (5)

UniProt IDNamesCanonical?
Q16827-11yes
Q16827-22
Q16827-33, PTPROt
Q16827-44
Q16827-55

RefSeq proteins (6): NP_002839, NP_109592, NP_109593, NP_109594, NP_109595, NP_109596 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000242PTP_catDomain
IPR000387Tyr_Pase_domDomain
IPR003595Tyr_Pase_catDomain
IPR003961FN3_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR016130Tyr_Pase_ASActive_site
IPR029021Prot-tyrosine_phosphatase-likeHomologous_superfamily
IPR036116FN3_sfHomologous_superfamily
IPR042996PTPROFamily
IPR058859Fn3_R-PTP-ODomain

Pfam: PF00041, PF00102, PF26586

Enzyme classification (BRENDA):

  • EC 3.1.3.48 — protein-tyrosine-phosphatase (BRENDA: 59 organisms, 501 substrates, 1326 inhibitors, 270 Km, 165 kcat entries)

Substrate kinetics (BRENDA)

70 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
4-NITROPHENYL PHOSPHATE0.0008–14884
6,8-DIFLUORO-4-METHYLUMBELLIFERYL PHOSPHATE0.0039–0.86227
P-NITROPHENYL PHOSPHATE0.0024–1020
DADEPYLIPQQG0.0003–0.112
PHOSPHOTYROSINE0.012–3011
LYSOZYME0.0003–0.0125
MYELIN BASIC PROTEIN0.0001–0.0225
ACETYL-DADEPY-NH20.0228–0.2194
ACETYL-DADEPYL-NH21.1–97.54
4,6,8-TRIMETHYL-2-OXO-2H-CHROMEN-7-YL DIHYDROGEN0.02–0.1563
SASASPYSASA0.53–2.33
1-NAPHTHYL PHOSPHATE1.19–1.882
3,6-FLUORESCEIN DIPHOSPHATE15–192
4-METHYLUMBELLIFERYL PHOSPHATE0.953–2.412
BOVINE SERUM ALBUMIN0.0001–0.00032

Catalyzed reactions (Rhea), 1 shown:

  • O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate (RHEA:10684)

UniProt features (80 total): glycosylation site 15, sequence conflict 15, strand 13, helix 10, domain 9, splice variant 4, binding site 3, turn 3, modified residue 2, topological domain 2, signal peptide 1, chain 1, active site 1, transmembrane region 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2GJTX-RAY DIFFRACTION2.15
2G59X-RAY DIFFRACTION2.19

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q16827-F177.550.34

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 1136 (phosphocysteine intermediate)

Ligand- & substrate-binding residues (3): 1102; 1136–1142; 1180

Post-translational modifications (2): 865, 1210

Glycosylation sites (15): 75, 154, 189, 201, 227, 278, 287, 323, 324, 370, 461, 490, 700, 712, 733

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9034015Signaling by NTRK3 (TRKC)

MSigDB gene sets: 403 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_REGULATION_OF_BLOOD_PRESSURE, GOBP_MYELOID_LEUKOCYTE_MIGRATION, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_CELL_CHEMOTAXIS, GOBP_RETINAL_GANGLION_CELL_AXON_GUIDANCE, GOBP_RENAL_SYSTEM_PROCESS_INVOLVED_IN_REGULATION_OF_BLOOD_VOLUME, MODULE_64, GOBP_REGULATION_OF_SYSTEMIC_ARTERIAL_BLOOD_PRESSURE, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_AXON_GUIDANCE, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, LHX3_01, GOBP_KIDNEY_EPITHELIUM_DEVELOPMENT

GO Biological Process (16): cell morphogenesis (GO:0000902), monocyte chemotaxis (GO:0002548), regulation of glomerular filtration (GO:0003093), negative regulation of glomerular filtration (GO:0003105), axon guidance (GO:0007411), negative regulation of cell-substrate adhesion (GO:0010812), negative regulation of neuron projection development (GO:0010977), lamellipodium assembly (GO:0030032), glomerulus development (GO:0032835), slit diaphragm assembly (GO:0036060), regulation of synapse organization (GO:0050807), podocyte differentiation (GO:0072112), negative regulation of canonical Wnt signaling pathway (GO:0090090), negative regulation of retinal ganglion cell axon guidance (GO:0090260), protein dephosphorylation (GO:0006470), dephosphorylation (GO:0016311)

GO Molecular Function (9): protein tyrosine phosphatase activity (GO:0004725), transmembrane receptor protein tyrosine phosphatase activity (GO:0005001), phosphatase activity (GO:0016791), Wnt-protein binding (GO:0017147), protein homodimerization activity (GO:0042803), cadherin binding (GO:0045296), phosphoprotein phosphatase activity (GO:0004721), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (13): plasma membrane (GO:0005886), membrane (GO:0016020), apical plasma membrane (GO:0016324), lateral plasma membrane (GO:0016328), lamellipodium (GO:0030027), axon (GO:0030424), growth cone (GO:0030426), neuron projection (GO:0043005), dendritic spine (GO:0043197), extracellular exosome (GO:0070062), postsynaptic density membrane (GO:0098839), glutamatergic synapse (GO:0098978), GABA-ergic synapse (GO:0098982)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Signaling by NTRKs1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
glomerular filtration2
cellular anatomical structure2
plasma membrane bounded cell projection2
synapse2
anatomical structure morphogenesis1
leukocyte chemotaxis1
mononuclear cell migration1
myeloid leukocyte migration1
regulation of renal system process1
regulation of glomerular filtration1
negative regulation of multicellular organismal process1
axonogenesis1
neuron projection guidance1
negative regulation of cell adhesion1
regulation of cell-substrate adhesion1
cell-substrate adhesion1
regulation of neuron projection development1
neuron projection development1
negative regulation of cell projection organization1
lamellipodium organization1
plasma membrane bounded cell projection assembly1
anatomical structure development1
nephron development1
filtration diaphragm assembly1
regulation of synapse structure or activity1
synapse organization1
regulation of cellular component organization1
renal filtration cell differentiation1
glomerular epithelial cell differentiation1
negative regulation of Wnt signaling pathway1
canonical Wnt signaling pathway1
regulation of canonical Wnt signaling pathway1
retinal ganglion cell axon guidance1
regulation of retinal ganglion cell axon guidance1
negative regulation of axon guidance1
dephosphorylation1
protein modification process1
phosphate-containing compound metabolic process1
phosphoprotein phosphatase activity1
protein tyrosine phosphatase activity1

Protein interactions and networks

STRING

1308 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PTPRONPHS1O60500664
PTPRONPHS2Q9NP85661
PTPROSYNPOQ8N3V7622
PTPROPTSQ03393609
PTPROFN1P02751607
PTPROPODXLO00592571
PTPROSLITRK2Q9H156557
PTPROSHISA4Q96DD7556
PTPROPLCE1Q9P212540
PTPROMYO1EQ12965532
PTPROCGB5P01233525
PTPROACTN4O43707514
PTPROWT1P19544507
PTPROINF2Q27J81507
PTPROCD2APQ9Y5K6507

IntAct

32 interactions, top by confidence:

ABTypeScore
PTPROPTPROpsi-mi:“MI:0407”(direct interaction)0.510
PTPROPTPROpsi-mi:“MI:0914”(association)0.510
PTPROGTF2IRD1psi-mi:“MI:0915”(physical association)0.400
DPPA4PTPROpsi-mi:“MI:0915”(physical association)0.370
DPYSL4PTPROpsi-mi:“MI:0915”(physical association)0.370
PTPROSH3GL1psi-mi:“MI:0915”(physical association)0.370
SH3GL3PTPROpsi-mi:“MI:0915”(physical association)0.370
PTPROYWHAZpsi-mi:“MI:0915”(physical association)0.370
PTPROPLXNB2psi-mi:“MI:0914”(association)0.350
PTPROCDH2psi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROTECpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROERBB2psi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROPDGFRBpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROMETpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROPXNpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROLCKpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROCTNNB1psi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROINSRpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROCSKpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROGAB1psi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPRONTRK1psi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROPDPK1psi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPRONSFpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROEPORpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROMAPK3psi-mi:“MI:0203”(dephosphorylation reaction)0.000
TEKPTPROpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROTEKpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROWASpsi-mi:“MI:0203”(dephosphorylation reaction)0.000
PTPROCBLpsi-mi:“MI:0203”(dephosphorylation reaction)0.000

BioGRID (180): PTPRO (Affinity Capture-MS), SDF2 (Affinity Capture-MS), ERLEC1 (Affinity Capture-MS), NGLY1 (Affinity Capture-MS), SDF2L1 (Affinity Capture-MS), DNAJC30 (Affinity Capture-MS), GOLIM4 (Affinity Capture-MS), TMEM246 (Affinity Capture-MS), LGALS3 (Affinity Capture-MS), TXNDC12 (Affinity Capture-MS), PDIA4 (Affinity Capture-MS), PDIA3 (Affinity Capture-MS), SEL1L (Affinity Capture-MS), CALR (Affinity Capture-MS), OS9 (Affinity Capture-MS)

ESM2 similar proteins: A0A0A6YXX9, A0A1Z2R986, B8RJM0, E9Q555, E9Q612, G5E8Q8, O35664, O88393, P09258, P0DP43, P13374, P20746, P22596, P22650, P22651, P26342, P33500, P35054, P48749, P68325, Q03167, Q14CH0, Q16827, Q2TAV2, Q2YDM0, Q56A20, Q5BKX0, Q5R7R7, Q5RBQ2, Q5U228, Q68FB2, Q6NU22, Q6NU51, Q6P995, Q6S6Q5, Q6UC88, Q76B58, Q77NN4, Q7SXB3, Q8K1M8

Diamond homologs: A0A6I8TCE0, A1L1L3, A2ALK8, A4IFW2, B0V2N1, B0X4T2, B1AUH1, B2GV87, B2RU80, B3DK56, B9EKR1, E9Q0N2, E9Q612, F1NWE3, G5EC24, G5EGJ9, H2KZM6, O02695, O08617, O13016, O35239, O55082, P06800, P16620, P17706, P18031, P18052, P18433, P20417, P23467, P23468, P23469, P23470, P23471, P26045, P28191, P29074, P29350, P29351, P29352

SIGNOR signaling

6 interactions.

AEffectBMechanism
PTPRO“down-regulates quantity by destabilization”ERBB2dephosphorylation
PTPRO“down-regulates activity”SRCdephosphorylation
PTPRO“down-regulates activity”STAT3dephosphorylation
PTPRO“down-regulates activity”VCPdephosphorylation
PTPRO“down-regulates activity”LYNdephosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 27 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Bacterial Infection Pathways567.2×8e-07
PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling727.1×6e-07
Constitutive Signaling by Aberrant PI3K in Cancer525.4×6e-05
PIP3 activates AKT signaling821.4×4e-07
Signaling by Receptor Tyrosine Kinases918.6×2e-07
RAF/MAP kinase cascade614.7×1e-04
Signaling by Interleukins512.8×1e-03
Diseases of signal transduction by growth factor receptors and second messengers511.4×1e-03

GO biological processes:

GO termPartnersFoldFDR
epidermal growth factor receptor signaling pathway545.9×1e-05
cell surface receptor protein tyrosine kinase signaling pathway638.6×5e-06
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction720.3×1e-05
protein phosphorylation717.6×1e-05
positive regulation of MAPK cascade514.9×1e-03
angiogenesis613.9×4e-04
intracellular signal transduction79.9×4e-04
negative regulation of apoptotic process67.7×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

527 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic5
Likely pathogenic5
Uncertain significance254
Likely benign142
Benign78

Top pathogenic / likely-pathogenic (10)

Variant IDHGVSClassification
2110028NM_030667.3(PTPRO):c.1241C>G (p.Ser414Ter)Pathogenic
2110029NM_030667.3(PTPRO):c.1949del (p.Ser650fs)Pathogenic
30110NM_030667.3(PTPRO):c.2627+1G>TPathogenic
30111NM_030667.3(PTPRO):c.2829+1G>APathogenic
3656259NM_030667.3(PTPRO):c.2803_2806del (p.Asp935fs)Pathogenic
1068336NM_030667.3(PTPRO):c.2712-2delLikely pathogenic
2116990NM_030667.3(PTPRO):c.2305-1G>CLikely pathogenic
3574470NM_030667.3(PTPRO):c.1758del (p.Val587fs)Likely pathogenic
3574482NM_030667.3(PTPRO):c.2027del (p.Lys676fs)Likely pathogenic
3574503NM_030667.3(PTPRO):c.2712-1G>ALikely pathogenic

SpliceAI

4787 predictions. Top by Δscore:

VariantEffectΔscore
12:15483965:A:AGacceptor_gain1.0000
12:15499439:CA:Cacceptor_loss1.0000
12:15499440:A:AGacceptor_gain1.0000
12:15499440:A:ATacceptor_loss1.0000
12:15499441:G:GAacceptor_gain1.0000
12:15499591:ACTGG:Adonor_loss1.0000
12:15499592:CTGGT:Cdonor_loss1.0000
12:15499593:TGG:Tdonor_loss1.0000
12:15499594:GGTAA:Gdonor_loss1.0000
12:15499595:G:GGdonor_gain1.0000
12:15499595:GTA:Gdonor_loss1.0000
12:15499596:TAA:Tdonor_loss1.0000
12:15499597:AA:Adonor_loss1.0000
12:15501618:A:AGacceptor_gain1.0000
12:15501619:G:GGacceptor_gain1.0000
12:15501619:GCC:Gacceptor_gain1.0000
12:15501619:GCCCC:Gacceptor_gain1.0000
12:15501941:G:GGdonor_gain1.0000
12:15501951:G:GTdonor_gain1.0000
12:15503900:T:Gacceptor_gain1.0000
12:15504070:G:GGdonor_gain1.0000
12:15516761:A:AGacceptor_gain1.0000
12:15516762:G:GGacceptor_gain1.0000
12:15524943:G:GTdonor_gain1.0000
12:15524944:A:Tdonor_gain1.0000
12:15524961:AGAGT:Adonor_gain1.0000
12:15524962:GAGT:Gdonor_gain1.0000
12:15524962:GAGTG:Gdonor_gain1.0000
12:15524964:GT:Gdonor_gain1.0000
12:15524966:G:GGdonor_gain1.0000

AlphaMissense

8058 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:15516825:T:AW550R1.000
12:15516825:T:CW550R1.000
12:15551601:A:CS830R1.000
12:15551603:C:AS830R1.000
12:15551603:C:GS830R1.000
12:15569493:T:CF942L1.000
12:15569495:T:AF942L1.000
12:15569495:T:GF942L1.000
12:15578921:C:AN966K1.000
12:15578921:C:GN966K1.000
12:15578922:C:AR967S1.000
12:15578933:C:AN970K1.000
12:15578933:C:GN970K1.000
12:15580106:C:AN996K1.000
12:15580106:C:GN996K1.000
12:15580725:C:AA1009D1.000
12:15580733:G:AG1012R1.000
12:15580733:G:CG1012R1.000
12:15580733:G:TG1012W1.000
12:15580763:T:AW1022R1.000
12:15580763:T:CW1022R1.000
12:15580800:T:AV1034D1.000
12:15580806:T:CL1036P1.000
12:15581682:A:GK1046E1.000
12:15581684:A:CK1046N1.000
12:15581684:A:TK1046N1.000
12:15581685:T:CC1047R1.000
12:15581687:T:GC1047W1.000
12:15581697:T:AW1051R1.000
12:15581697:T:CW1051R1.000

dbSNP variants (sampled 300 via entrez): RS1000008393 (12:15589152 G>A), RS1000009567 (12:15500709 G>A,T), RS1000036998 (12:15467608 A>G), RS1000047294 (12:15582035 G>C), RS1000050846 (12:15455218 T>C), RS1000053787 (12:15423914 A>G), RS1000055993 (12:15575887 G>A), RS1000056355 (12:15547976 G>A), RS1000072749 (12:15494041 G>T), RS1000074454 (12:15597433 G>A), RS1000084026 (12:15377491 A>T), RS1000094123 (12:15467464 A>C), RS1000121868 (12:15535522 G>A), RS1000124902 (12:15493763 A>G), RS1000149791 (12:15378644 C>T)

Disease associations

OMIM: gene MIM:600579 | disease phenotypes: MIM:614196, MIM:614800, MIM:616483

GenCC curated gene-disease

DiseaseClassificationInheritance
nephrotic syndrome, type 6StrongAutosomal recessive
familial idiopathic steroid-resistant nephrotic syndromeSupportiveAutosomal dominant

Mondo (5): nephrotic syndrome, type 6 (MONDO:0013619), short stature-optic atrophy-Pelger-Huët anomaly syndrome (MONDO:0013889), infantile liver failure syndrome 2 (MONDO:0014659), focal segmental glomerulosclerosis (MONDO:0100313), familial idiopathic steroid-resistant nephrotic syndrome (MONDO:0019006)

Orphanet (2): Hereditary steroid-resistant nephrotic syndrome (Orphanet:656), Short stature-optic atrophy-Pelger-Huët anomaly syndrome (Orphanet:391677)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D005923Glomerulosclerosis, Focal SegmentalC12.050.351.968.419.570.363.640; C12.200.777.419.570.363.660; C12.950.419.570.363.640

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105749 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: catalytic receptor — Receptor tyrosine phosphatase (RTP) family

ChEMBL bioactivities

2 potent at pChembl≥5 of 6 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
6.91Ki123nMCHEMBL4063482
6.25IC50560nMSODIUM ORTHOVANAD

PubChem BioAssay actives

1 with measured affinity, of 8 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
5-[[4-[2-(4-butylphenyl)ethynyl]phenyl]methyl-hexylamino]-2-hydroxybenzoic acid1930714: Binding affinity to GLEPP1 (unknown origin) assessed as inhibition constantki0.1230uM

CTD chemical–gene interactions

48 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Estradiolaffects reaction, decreases expression, affects cotreatment, increases expression3
Valproic Aciddecreases expression, increases expression3
methylmercuric chloridedecreases expression, increases expression2
bisphenol Adecreases expression, affects reaction, affects cotreatment, decreases methylation2
entinostatdecreases expression, affects cotreatment2
Panobinostatdecreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Cadmium Chloridedecreases reaction, increases abundance, increases palmitoylation, increases expression2
triphenyl phosphateaffects expression1
lead acetateincreases expression, affects cotreatment1
terbufosincreases methylation1
zinc protoporphyrinaffects cotreatment, increases expression1
cobaltous chloridedecreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
cupric chloridedecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, affects cotreatment, decreases expression1
diallyl trisulfideincreases expression1
di-n-butylphosphoric acidaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
clothianidindecreases expression1
abrineincreases expression1
dorsomorphindecreases expression, affects cotreatment1
(+)-JQ1 compounddecreases expression1
Arsenic Trioxidedecreases expression1
Fulvestrantaffects cotreatment, decreases methylation, increases methylation1
Acetaminophenincreases expression1
Allergensdecreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Cadmiumdecreases reaction, increases abundance, increases palmitoylation1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL3991951BindingInhibition of human recombinant Glepp-1 catalytic domain using DiFMUP as substrate after 30 mins by fluorescence assayGLEPP-1 inhibitors in the treatment of autoimmune and/or inflammatory disorders

Clinical trials (associated diseases)

76 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT01129557PHASE4TERMINATEDAldosterone Breakthrough During Diovan, Tekturna, and Combination Therapy in Patients With Proteinuric Kidney Disease
NCT02399462PHASE4WITHDRAWNActhar for Treatment of Post-transplant FSGS
NCT02585804PHASE4COMPLETEDTreating to Reduce Albuminuria and Normalize Hemodynamic Function in Focal ScLerosis With dApagliflozin Trial Effects
NCT02633046PHASE4COMPLETEDActhar for Treatment-Resistant or Treatment-Intolerant Proteinuria
NCT07219121PHASE4RECRUITINGSparsentan in Posttransplant Immunoglobulin A Nephropathy or Focal Segmental Glomerulosclerosis
NCT01164098PHASE3TERMINATEDRituximab to Prevent Recurrence of Proteinuria
NCT02683889PHASE3COMPLETEDUse of Acthar in Patients With FSGS That Will be Undergoing Renal Transplantation
NCT03298698PHASE3UNKNOWNEfficacy of Rituximab in Comparison to Continued Corticosteroid Treatment in Idiopathic Nephrotic Syndrome
NCT03493685PHASE3COMPLETEDStudy of Sparsentan in Patients With Primary Focal Segmental Glomerulosclerosis (FSGS)
NCT05183646PHASE3RECRUITINGA Study of the Efficacy and Safety of DMX-200 in Patients With FSGS Who Are Receiving an ARB
NCT07220083PHASE3RECRUITINGA Study to Find Out if BI 764198 Helps Adults and Adolescents With a Kidney Condition Called Focal Segmental Glomerulosclerosis (FSGS)
NCT00550342PHASE2WITHDRAWNRituximab Treatment of Focal Segmental Glomerulosclerosis
NCT00814255PHASE2COMPLETEDNovel Therapies for Resistant FSGS (FONTII): Phase II Clinical Trial
NCT01613118PHASE2COMPLETEDRandomized, Double-Blind, Safety and Efficacy Study of RE-021 (Sparsentan) in Focal Segmental Glomerulosclerosis
NCT02592798PHASE2COMPLETEDPilot Study to Evaluate the Safety and Efficacy of Abatacept in Adults and Children 6 Years and Older With Excessive Loss of Protein in the Urine Due to Either Focal Segmental Glomerulosclerosis (FSGS) or Minimal Change Disease (MCD)
NCT03366337PHASE2COMPLETEDA Phase 2 Trial of the Safety and Efficacy of Bardoxolone Methyl in Patients With Rare Chronic Kidney Diseases - PHOENIX
NCT03448692PHASE2TERMINATEDA Study to Evaluate PF-06730512 in Adults With Focal Segmental Glomerulosclerosis (FSGS)
NCT03536754PHASE2COMPLETEDA Study of CCX140-B in Subjects With FSGS
NCT03598036PHASE2TERMINATEDDose-Exploration Evaluating the Efficacy and Safety of Voclosporin in Subjects With Focal Segmental Glomerulosclerosis
NCT03649152PHASE2COMPLETEDSafety and Effectiveness of Propagermanium in Focal Segmental Glomerulosclerosis Participants Receiving Irbesartan
NCT03703908PHASE2TERMINATEDA Study of CCX140-B in Subjects With Primary FSGS and Nephrotic Syndrome
NCT04009668PHASE2COMPLETEDTumor Necrosis Factor Inhibition in Focal Segmental Glomerulosclerosis and Treatment Resistant Minimal Change Disease
NCT04573920PHASE2ACTIVE_NOT_RECRUITINGAtrasentan in Patients With Proteinuric Glomerular Diseases
NCT05003986PHASE2RECRUITINGStudy of Sparsentan Treatment in Pediatrics With Proteinuric Glomerular Diseases
NCT05267262PHASE2COMPLETEDStudy to Evaluate R3R01 in Patients With Alport Syndrome and Patients With Focal Segmental Glomerulosclerosis
NCT05441826PHASE2TERMINATEDEfficacy and Safety of VB119 in Subjects With Minimal Change Disease (MCD) and Focal Segmental Glomerulosclerosis (FSGS)
NCT06500702PHASE2RECRUITINGA Study to Evaluate the Efficacy and Safety of Frexalimab, Brivekimig, or Rilzabrutinib in Participants Aged 16 to 75 Years With Primary Focal Segmental Glomerulosclerosis or Minimal Change Disease
NCT06664814PHASE2RECRUITINGAn Open-Label Phase 2 Study of N-Acetyl-D-Mannosamine (ManNAc) in Subjects With Primary Focal Segmental Glomerulosclerosis
NCT06983028PHASE2RECRUITINGAtacicept in Multiple Glomerular Diseases
NCT07268638PHASE2RECRUITINGA Study of Praliciguat in Participants With Focal Segmental Glomerulosclerosis (FSGS)
NCT07614477PHASE2RECRUITINGEvaluate the Efficacy, Safety, Pharmacokinetics, and Pharmacodynamics of EVER001 in Participants With Selected Proteinuric Glomerular Diseases
NCT00464321PHASE1COMPLETEDSafety Study of GC1008 in Patients With Focal Segmental Glomerulosclerosis (FSGS) of Single Doses of GC1008 in Patients With Treatment Resistant Idiopathic FSGS
NCT00782561PHASE1TERMINATEDSafety and Pharmacokinetics of FG-3019 in Adolescents and Adults With Focal Segmental Glomerulosclerosis (FSGS)
NCT00816478PHASE1TERMINATEDEffect of Oral Galactose on Focal Segmental Glomerulosclerosis (FSGS) Permeability Factor
NCT00816504PHASE1WITHDRAWNEffect of Galactose on Permeblity Factor in Patients With FSGS and CKD Stage 5
NCT02382874PHASE1UNKNOWNAllogenic AD-MSC Transplantation in Idiopathic Nephrotic Syndrome (Focal Segmental Glomerulosclerosis)
NCT02693366PHASE1COMPLETEDStem Cell Therapy for Patients With Focal Segmental Glomerulosclerosis
NCT05942625PHASE1RECRUITINGA First in Human Study to Evaluate Safety, Tolerability, Pharmacology of HS-10390 in Healthy Subjects
NCT05955872PHASE1COMPLETEDA Study Evaluating the Relative Bioavailability and Food Effect of a Tablet Formulation of VX-147
NCT06529796PHASE1COMPLETEDEvaluation of the Pharmacokinetics and Safety of Inaxaplin in Participants With Mild or Moderate Hepatic Impairment