PTPRT protein tyrosine phosphatase receptor type T [Homo sapiens (human)] - Gene

Summary

Official Symbol: PTPRTprovided by HGNC
Official Full Name: protein tyrosine phosphatase receptor type Tprovided by HGNC
Primary source: HGNC:HGNC:9682
See related: Ensembl:ENSG00000196090 MIM:608712; AllianceGenome:HGNC:9682
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: R-PTP-T; RPTPrho; RPTP-rho
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 intracellular catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP (MAM) domain, Ig-like and fibronectin type III-like repeats. The protein domain structure and the expression pattern of the mouse counterpart of this PTP suggest its roles in both signal transduction and cellular adhesion in the central nervous system. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]
Expression: Biased expression in brain (RPKM 9.9) and placenta (RPKM 1.1) See more
Orthologs: mouse all
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Genomic context

Location:: 20q12-q13.11

Exon count:: 36

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (42031890..43189906, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (43763752..44923941, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (40701396..41818546, complement)

Chromosome 20 - NC_000020.11 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
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?

Downregulation of PTPRT elevates the expression of survivin and promotes the proliferation, migration, and invasion of lung adenocarcinoma.
Title: Downregulation of PTPRT elevates the expression of survivin and promotes the proliferation, migration, and invasion of lung adenocarcinoma.
Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
Title: Novel genetic variants linked to prelabor rupture of membranes among Chinese pregnant women.
Association of PTPRT Mutations with Cancer Metastasis in Multiple Cancer Types.
Title: Association of PTPRT Mutations with Cancer Metastasis in Multiple Cancer Types.
PTPRT Could Be a Treatment Predictive and Prognostic Biomarker for Breast Cancer.
Title: PTPRT Could Be a Treatment Predictive and Prognostic Biomarker for Breast Cancer.
PTPRT epigenetic silencing defines lung cancer with STAT3 activation and can direct STAT3 targeted therapies.
Title: PTPRT epigenetic silencing defines lung cancer with STAT3 activation and can direct STAT3 targeted therapies.
Study revealed a significantly higher prevalence of PTPRT and JAK2 mutations in lung adenocarcinomas among African Americans compared with European Americans. Patients carrying these mutations have a concomitant increase in IL-6/STAT3 signaling and miR-21 expression.
Title: Recurrent PTPRT/JAK2 mutations in lung adenocarcinoma among African Americans.
A novel de novo 20q13.11q13.12 microdeletion was found in a boy with neurodevelopmental disorders. The established function of the PTPRT gene suggests that haploinsuficiency of this gene may result in the clinical features observed in our patient: stereotype movements, nervous tics, social and emotional disturbances and attention-span deficits.
Title: A novel de novo 20q13.11q13.12 microdeletion in a boy with neurodevelopmental disorders - case report.
The single cell genotyping not only confirmed the co-occurrence of the PTPRT, CAND1 and DOCK6 mutations in the same AML clone but also revealed a clonal hierarchy, as the PTPRT mutation was likely acquired after the CAND1 and DOCK6 mutations.
Title: Single cell genotyping of exome sequencing-identified mutations to characterize the clonal composition and evolution of inv(16) AML in a CBL mutated clonal hematopoiesis.
PTPRT promoter methylation is significantly associated with sensitivity to STAT3 inhibition in HNSCC cells, suggesting that PTPRT promoter methylation may serve as a predictive biomarker for responsiveness to STAT3 inhibitors in clinical development
Title: Frequent promoter hypermethylation of PTPRT increases STAT3 activation and sensitivity to STAT3 inhibition in head and neck cancer.
Data reported evidence that rs2866943 polymorphism in PTPRT 3'-UTR was involved in the occurrence of esophageal squamous cell carcinoma by acting as a protective factor while rs6029959 acts as a risk factor.
Title: The Functional Variant in the 3'UTR of PTPRT with the Risk of Esophageal Squamous Cell Carcinoma in a Chinese Population.

Submit: New GeneRIF Correction See all GeneRIFs (23)

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

EBI GWAS Catalog

Description
Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of chronic periodontitis in a general German population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies in multiethnic Asians identifies two loci for age-related nuclear cataract. 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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH120053 (e-PCR)
- UniSTS:133377

AL031489 (e-PCR)
- UniSTS:47378

AL030967 (e-PCR)
- UniSTS:33558

D20S110 (e-PCR)
- UniSTS:55842

D20S591E (e-PCR)
- UniSTS:60724

G62595 (e-PCR)
- UniSTS:139575

Z94519 (e-PCR)
- UniSTS:30776

WI-10350 (e-PCR)
- UniSTS:56645

SHGC-68781 (e-PCR)
- UniSTS:100682

Z94358 (e-PCR)
- UniSTS:69973

D20S110 (e-PCR)
- UniSTS:79445

G31023 (e-PCR)
- UniSTS:46687

RH66086 (e-PCR)
- UniSTS:51297

Z94343 (e-PCR)
- UniSTS:5989

G42933 (e-PCR)
- UniSTS:94828

SHGC-148173 (e-PCR)
- UniSTS:176241

PTPRT_1775 (e-PCR)
- UniSTS:277629

D20S108 (e-PCR), detects polymorphism
- UniSTS:66174

D20S598 (e-PCR)
- UniSTS:21893

AL031487 (e-PCR)
- UniSTS:74375

D20S499 (e-PCR)
- UniSTS:905

RH120169 (e-PCR)
- UniSTS:132236

RH122575 (e-PCR)
- UniSTS:138639

SHGC-105606 (e-PCR)
- UniSTS:169362

SHGC-150658 (e-PCR)
- UniSTS:173206

Z94543 (e-PCR)
- UniSTS:53671

RH120697 (e-PCR)
- UniSTS:132778

D20S46 (e-PCR)
- UniSTS:146859

D20S108 (e-PCR), detects polymorphism
- UniSTS:3759

D20S46 (e-PCR)
- UniSTS:146872

Z94437 (e-PCR)
- UniSTS:30911

RH104430 (e-PCR)
- UniSTS:98755

G62746 (e-PCR)
- UniSTS:139723

RH121112 (e-PCR)
- UniSTS:134107

Z94641 (e-PCR)
- UniSTS:49633

AL023697 (e-PCR)
- UniSTS:59107

D20S899 (e-PCR), detects polymorphism
- UniSTS:11239

AL022351 (e-PCR)
- UniSTS:54762

D20S858 (e-PCR), detects polymorphism
- UniSTS:73964

D20S466 (e-PCR)
- UniSTS:149231

Z94342 (e-PCR)
- UniSTS:4345

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables STAT family protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables alpha-actinin binding	IEA Inferred from Electronic Annotation more info
enables alpha-catenin binding	IDA Inferred from Direct Assay more info	PubMed
enables beta-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
enables cadherin binding	IPI Inferred from Physical Interaction more info	PubMed
enables delta-catenin binding	IPI Inferred from Physical Interaction more info	PubMed
enables gamma-catenin binding	IDA Inferred from Direct Assay more info	PubMed
enables histone H2AXY142 phosphatase activity	IEA Inferred from Electronic Annotation more info
enables non-membrane spanning protein tyrosine phosphatase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein phosphatase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein tyrosine phosphatase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein tyrosine phosphatase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein tyrosine phosphatase activity, metal-dependent	IEA Inferred from Electronic Annotation more info
enables thiolester hydrolase activity	IEA Inferred from Electronic Annotation more info
enables transmembrane receptor protein tyrosine phosphatase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in cell adhesion	NAS Non-traceable Author Statement more info	PubMed
involved_in cell surface receptor protein tyrosine kinase signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to interleukin-6	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in homophilic cell adhesion via plasma membrane adhesion molecules	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of receptor signaling pathway via STAT	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of receptor signaling pathway via STAT	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron projection development	IBA Inferred from Biological aspect of Ancestor more info
involved_in peptidyl-tyrosine dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in protein dephosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of synapse organization	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
located_in membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay 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 T

Names: receptor protein tyrosine phosphatase; receptor-type tyrosine-protein phosphatase rho

NP_001380953.1

EC 3.1.3.48

NP_001380954.1

EC 3.1.3.48

NP_001380955.1

EC 3.1.3.48

NP_008981.4

EC 3.1.3.48

NP_573400.3

EC 3.1.3.48

XP_016883100.1

EC 3.1.3.48

XP_016883101.1

EC 3.1.3.48

XP_016883102.1

EC 3.1.3.48

XP_047295802.1

EC 3.1.3.48

XP_047295803.1

EC 3.1.3.48

XP_047295804.1

EC 3.1.3.48

XP_054178850.1

EC 3.1.3.48

XP_054178851.1

EC 3.1.3.48

XP_054178852.1

EC 3.1.3.48

XP_054178853.1

EC 3.1.3.48

XP_054178854.1

EC 3.1.3.48

XP_054178855.1

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_033880.3 RefSeqGene

Range

5000..1122150

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001394024.1 → NP_001380953.1 receptor-type tyrosine-protein phosphatase T isoform 3 precursor

Status: REVIEWED

Source sequence(s)

AL021395, AL022239, AL024473, AL031656, AL035459, AL049812, AL121763, AL136461, Z93942

UniProtKB/TrEMBL

B1AJR9

Related

ENSP00000362280.1, ENST00000373184.5

Conserved Domains (5) summary

smart00060
Location:289 → 360

FN3; Fibronectin type 3 domain

smart00137
Location:29 → 189

MAM; Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others)

cd00063
Location:502 → 584

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 ...

cd14630
Location:909 → 1165

R-PTPc-T-1; catalytic domain of receptor-type tyrosine-protein phosphatase T, repeat 1

cd14634
Location:1250 → 1455

R-PTPc-T-2; PTP domain of receptor-type tyrosine-protein phosphatase T, repeat 2
NM_001394025.1 → NP_001380954.1 receptor-type tyrosine-protein phosphatase T isoform 4 precursor

Status: REVIEWED

Source sequence(s)

AL021395, AL022239, AL024473, AL031656, AL035459, AL049812, AL121763, AL136461, Z93942

UniProtKB/TrEMBL

B1AJR8

Related

ENSP00000348408.2, ENST00000356100.6

Conserved Domains (5) summary

smart00060
Location:289 → 360

FN3; Fibronectin type 3 domain

smart00137
Location:29 → 189

MAM; Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others)

cd00063
Location:502 → 584

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 ...

cd14630
Location:918 → 1154

R-PTPc-T-1; catalytic domain of receptor-type tyrosine-protein phosphatase T, repeat 1

cd14634
Location:1239 → 1444

R-PTPc-T-2; PTP domain of receptor-type tyrosine-protein phosphatase T, repeat 2
NM_001394026.1 → NP_001380955.1 receptor-type tyrosine-protein phosphatase T isoform 5 precursor

Status: REVIEWED

Source sequence(s)

AL021395, AL022239, AL024473, AL031656, AL035459, AL121763, AL136461, Z93942

UniProtKB/TrEMBL

B1AJR6

Conserved Domains (5) summary

smart00060
Location:289 → 360

FN3; Fibronectin type 3 domain

smart00137
Location:29 → 189

MAM; Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others)

smart00194
Location:1173 → 1278

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00063
Location:502 → 584

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 ...

cd14630
Location:909 → 1145

R-PTPc-T-1; catalytic domain of receptor-type tyrosine-protein phosphatase T, repeat 1
NM_007050.6 → NP_008981.4 receptor-type tyrosine-protein phosphatase T isoform 2 precursor

See identical proteins and their annotated locations for NP_008981.4

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks a fragment within the coding region when compared to variant 1. The translation remains in-frame, and thus encodes a protein that lacks an internal segment, as compared to isoform 1.

Source sequence(s)

AL021395, AL022239, AL024473, AL031656, AL035459, AL049812, AL121763, AL136461, Z93942

Consensus CDS

CCDS42874.1

UniProtKB/Swiss-Prot

A8E4R6, O14522, O43655, O75664, Q5W0X9, Q5W0Y1, Q9BR24, Q9BR28, Q9H0Y8, Q9NTL1, Q9NU72, Q9UBD2, Q9UJL7

UniProtKB/TrEMBL

B1AJR6

Related

ENSP00000362283.1, ENST00000373187.6

Conserved Domains (7) summary

cd06263
Location:32 → 189

MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...

smart00137
Location:29 → 189

MAM; Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others)

smart00194
Location:888 → 1142

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:915 → 1142

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:502 → 584

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:294 → 360

fn3; Fibronectin type III domain

cl11960
Location:196 → 281

Ig; Immunoglobulin domain
NM_133170.4 → NP_573400.3 receptor-type tyrosine-protein phosphatase T isoform 1 precursor

See identical proteins and their annotated locations for NP_573400.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AL021395, AL022239, AL024473, AL031656, AL035459, AL049812, AL121763, AL136461, Z93942

Consensus CDS

CCDS68127.1

UniProtKB/TrEMBL

A0A075B6H0, B1AJR8

Related

ENSP00000362294.4, ENST00000373198.8

Conserved Domains (7) summary

cd06263
Location:32 → 189

MAM; Meprin, A5 protein, and protein tyrosine phosphatase Mu (MAM) domain. MAM is an extracellular domain which mediates protein-protein interactions and is found in a diverse set of proteins, many of which are known to function in cell adhesion. Members ...

smart00137
Location:29 → 189

MAM; Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others)

smart00194
Location:907 → 1161

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:934 → 1161

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:502 → 584

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:294 → 360

fn3; Fibronectin type III domain

cl11960
Location:196 → 281

Ig; Immunoglobulin domain

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_000020.11 Reference GRCh38.p14 Primary Assembly

Range

42031890..43189906 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047439848.1 → XP_047295804.1 receptor-type tyrosine-protein phosphatase T isoform X5
XM_047439846.1 → XP_047295802.1 receptor-type tyrosine-protein phosphatase T isoform X2
XM_017027611.2 → XP_016883100.1 receptor-type tyrosine-protein phosphatase T isoform X1

UniProtKB/TrEMBL

B1AJR9
XM_047439847.1 → XP_047295803.1 receptor-type tyrosine-protein phosphatase T isoform X4
XM_017027612.2 → XP_016883101.1 receptor-type tyrosine-protein phosphatase T isoform X3

UniProtKB/TrEMBL

B1AJR8
XM_017027613.2 → XP_016883102.1 receptor-type tyrosine-protein phosphatase T isoform X6

UniProtKB/TrEMBL

B1AJS0

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

43763752..44923941 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054322879.1 → XP_054178854.1 receptor-type tyrosine-protein phosphatase T isoform X5
XM_054322876.1 → XP_054178851.1 receptor-type tyrosine-protein phosphatase T isoform X2
XM_054322875.1 → XP_054178850.1 receptor-type tyrosine-protein phosphatase T isoform X1
XM_054322878.1 → XP_054178853.1 receptor-type tyrosine-protein phosphatase T isoform X4
XM_054322877.1 → XP_054178852.1 receptor-type tyrosine-protein phosphatase T isoform X3
XM_054322880.1 → XP_054178855.1 receptor-type tyrosine-protein phosphatase T isoform X6