PTPRO protein tyrosine phosphatase receptor type O [Homo sapiens (human)] - Gene

Summary

Official Symbol: PTPROprovided by HGNC
Official Full Name: protein tyrosine phosphatase receptor type Oprovided by HGNC
Primary source: HGNC:HGNC:9678
See related: Ensembl:ENSG00000151490 MIM:600579; AllianceGenome:HGNC:9678
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NPHS6; PTPU2; GLEPP1; PTP-OC; PTP-U2; PTPROT; R-PTP-O
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 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. [provided by RefSeq, May 2011]
Expression: Biased expression in kidney (RPKM 3.7), brain (RPKM 2.7) and 11 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12p12.3; 12p13-p12

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (15322508..15598331)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (15199775..15475561)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (15475442..15751265)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Protein tyrosine phosphatase PTPRO represses lung adenocarcinoma progression by inducing mitochondria-dependent apoptosis and restraining tumor metastasis.
Title: Protein tyrosine phosphatase PTPRO represses lung adenocarcinoma progression by inducing mitochondria-dependent apoptosis and restraining tumor metastasis.
PTPRO-related CD8(+) T-cell signatures predict prognosis and immunotherapy response in patients with breast cancer.
Title: PTPRO-related CD8(+) T-cell signatures predict prognosis and immunotherapy response in patients with breast cancer.
PTPRO activates TLR4/NF-kappaB signaling to intensify lipopolysaccharide-induced pneumonia cell injury.
Title: PTPRO activates TLR4/NF-κB signaling to intensify lipopolysaccharide-induced pneumonia cell injury.
MiR-6869-5p Induces M2 Polarization by Regulating PTPRO in Gestational Diabetes Mellitus.
Title: MiR-6869-5p Induces M2 Polarization by Regulating PTPRO in Gestational Diabetes Mellitus.
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.
Title: 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.
PTPRO exaggerates inflammation in ulcerative colitis through TLR4/NF-kappaB pathway.
Title: PTPRO exaggerates inflammation in ulcerative colitis through TLR4/NF-κB pathway.
IL-6 promotes PD-L1 expression in monocytes and macrophages by decreasing protein tyrosine phosphatase receptor type O expression in human hepatocellular carcinoma.
Title: IL-6 promotes PD-L1 expression in monocytes and macrophages by decreasing protein tyrosine phosphatase receptor type O expression in human hepatocellular carcinoma.
LncRNA HULC promotes lung squamous cell carcinoma by regulating PTPRO via NF-kappaB.
Title: LncRNA HULC promotes lung squamous cell carcinoma by regulating PTPRO via NF-κB.
PTPRO was significantly upregulated and negatively associated with miR-548c-5p in placental mononuclear cells in patients with preeclampsia.
Title: MiRNA-548c-5p downregulates inflammatory response in preeclampsia via targeting PTPRO.
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.
Title: Epigenetically silenced PTPRO functions as a prognostic marker and tumor suppressor in human lung squamous cell carcinoma.

Submit: New GeneRIF Correction See all GeneRIFs (39)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Nephrotic syndrome, type 6 MedGen: C3280100 OMIM: 614196 GeneReviews: Genetic Steroid-Resistant Nephrotic Syndrome Overview	Compare labs

EBI GWAS Catalog

Description
Genome-wide study identifies PTPRO and WDR72 and FOXQ1-SUMO1P1 interaction associated with neurocognitive function. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 induces CD4 association with lymphocyte surface molecules CD3, CD11a, CD27, CD45RA, CD45RB, CD45RO, CD49d, CD38, CD26, CD59, CD95 and class I MHC molecules	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G62268 (e-PCR)
- UniSTS:139300

G62341 (e-PCR)
- UniSTS:139307

G62271 (e-PCR)
- UniSTS:139310

D12S1571 (e-PCR)
- UniSTS:154203

A007I29 (e-PCR)
- UniSTS:22379

SHGC-68526 (e-PCR)
- UniSTS:182649

PTPRO_1364 (e-PCR)
- UniSTS:462475

PTPRO_v438 (e-PCR)
- UniSTS:462475

GDB:591927 (e-PCR)
- UniSTS:157898

SHGC-103008 (e-PCR)
- UniSTS:168911

SHGC-31637 (e-PCR)
- UniSTS:50683

D12S1303 (e-PCR), detects polymorphism
- UniSTS:12030

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables Wnt-protein binding	IBA Inferred from Biological aspect of Ancestor more info
enables Wnt-protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables cadherin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cadherin binding	IPI Inferred from Physical Interaction more info	PubMed
enables phosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein tyrosine phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein tyrosine phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein tyrosine phosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein tyrosine phosphatase activity	TAS Traceable Author Statement more info	PubMed
enables transmembrane receptor protein tyrosine phosphatase activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
involved_in axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in glomerulus development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lamellipodium assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in monocyte chemotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of canonical Wnt signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell-substrate adhesion	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of glomerular filtration	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of neuron projection development	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of retinal ganglion cell axon guidance	ISS Inferred from Sequence or Structural Similarity more info
involved_in peptidyl-tyrosine dephosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity	IEA Inferred from Electronic Annotation more info
involved_in podocyte differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in podocyte differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein dephosphorylation	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein dephosphorylation	TAS Traceable Author Statement more info	PubMed
involved_in regulation of glomerular filtration	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of glomerular filtration	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of synapse organization	IEA Inferred from Electronic Annotation more info
involved_in slit diaphragm assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in slit diaphragm assembly	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in apical plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in axon	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular exosome	HDA more info	PubMed
is_active_in glutamatergic synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in growth cone	ISS Inferred from Sequence or Structural Similarity more info
located_in lamellipodium	ISS Inferred from Sequence or Structural Similarity more info
located_in lateral plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	TAS Traceable Author Statement more info	PubMed
located_in neuron projection	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in postsynaptic density membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: receptor-type tyrosine-protein phosphatase O

Names: PTP phi; PTPase U2; glomerular epithelial protein 1; osteoclastic transmembrane protein-tyrosine phosphatase; phosphotyrosine phosphatase U2; protein tyrosine phosphatase PTP-U2

NP_002839.1

EC 3.1.3.48

NP_109592.1

EC 3.1.3.48

NP_109593.1

EC 3.1.3.48

NP_109594.1

EC 3.1.3.48

NP_109595.1

EC 3.1.3.48

NP_109596.1

EC 3.1.3.48

XP_016875214.1

EC 3.1.3.48

XP_054228699.1

EC 3.1.3.48

XP_054228700.1

EC 3.1.3.48

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_031857.1 RefSeqGene

Range

5252..281075

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002848.4 → NP_002839.1 receptor-type tyrosine-protein phosphatase O isoform b precursor

See identical proteins and their annotated locations for NP_002839.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region but maintains the reading frame, compared to variant 1. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AC007542, DR000351, U20489

Consensus CDS

CCDS8674.1

UniProtKB/TrEMBL

A8K169

Related

ENSP00000343434.2, ENST00000348962.7

Conserved Domains (4) summary

smart00194
Location:909 → 1164

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:937 → 1165

PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

cd00063
Location:434 → 526

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00041
Location:725 → 805

fn3; Fibronectin type III domain
NM_030667.3 → NP_109592.1 receptor-type tyrosine-protein phosphatase O isoform a precursor

See identical proteins and their annotated locations for NP_109592.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AC007542, BC126201, DR000351

Consensus CDS

CCDS8675.1

UniProtKB/Swiss-Prot

A0AV39, Q13101, Q16827, Q8IYG3, Q9UBF0, Q9UBT5

UniProtKB/TrEMBL

A8K169

Related

ENSP00000281171.4, ENST00000281171.9

Conserved Domains (3) summary

cd00047
Location:965 → 1193

PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

cd00063
Location:530 → 630

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00041
Location:435 → 521

fn3; Fibronectin type III domain
NM_030668.3 → NP_109593.1 receptor-type tyrosine-protein phosphatase O isoform d

See identical proteins and their annotated locations for NP_109593.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and has multiple differences in the coding region but maintains the reading frame, compared to variant 1. Variants 4 and 6 encode the same isoform (d), which is shorter than isoform a.

Source sequence(s)

AC007542, AF187044

Consensus CDS

CCDS53754.1

UniProtKB/TrEMBL

A0A6I8PRG8

Related

ENSP00000437571.1, ENST00000542557.5

Conserved Domains (1) summary

cd14614
Location:112 → 356

R-PTPc-O; catalytic domain of receptor-type tyrosine-protein phosphatase O
NM_030669.3 → NP_109594.1 receptor-type tyrosine-protein phosphatase O isoform c

See identical proteins and their annotated locations for NP_109594.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 3 and 5 encode the same isoform (c), which has a shorter N-terminus compared to isoform a.

Source sequence(s)

AC007542, AF187043

Consensus CDS

CCDS44837.1

UniProtKB/TrEMBL

A0A6I8PRG8

Related

ENSP00000501494.1, ENST00000674388.1

Conserved Domains (1) summary

cd00047
Location:154 → 382

PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...
NM_030670.3 → NP_109595.1 receptor-type tyrosine-protein phosphatase O isoform d

See identical proteins and their annotated locations for NP_109595.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) differs in the 5' UTR and 3' UTR, and has multiple differences in the coding region but maintains the reading frame, compared to variant 1. Variants 4 and 6 encode the same isoform (d), which is shorter than isoform a.

Source sequence(s)

AC007542, AF187042

Consensus CDS

CCDS53754.1

UniProtKB/TrEMBL

A0A6I8PRG8

Related

ENSP00000439234.1, ENST00000544244.5

Conserved Domains (1) summary

cd14614
Location:112 → 356

R-PTPc-O; catalytic domain of receptor-type tyrosine-protein phosphatase O
NM_030671.3 → NP_109596.1 receptor-type tyrosine-protein phosphatase O isoform c

See identical proteins and their annotated locations for NP_109596.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and 3' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants 3 and 5 encode the same isoform (c), which has a shorter N-terminus compared to isoform a.

Source sequence(s)

AC007542, AF152378

Consensus CDS

CCDS44837.1

UniProtKB/TrEMBL

A0A6I8PRG8

Related

ENSP00000393449.2, ENST00000445537.6

Conserved Domains (1) summary

cd00047
Location:154 → 382

PTPc; Protein tyrosine phosphatases (PTP) catalyze the dephosphorylation of phosphotyrosine peptides; they regulate phosphotyrosine levels in signal transduction pathways. The depth of the active site cleft renders the enzyme specific for phosphorylated Tyr ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

15322508..15598331

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017019725.3 → XP_016875214.1 receptor-type tyrosine-protein phosphatase O isoform X1

RNA

XR_931316.4 RNA Sequence
XR_007063106.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060936.1 Alternate T2T-CHM13v2.0

Range

15199775..15475561

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054372724.1 → XP_054228699.1 receptor-type tyrosine-protein phosphatase O isoform X1
XM_054372725.1 → XP_054228700.1 receptor-type tyrosine-protein phosphatase O isoform X2