PTPRN protein tyrosine phosphatase receptor type N [Homo sapiens (human)] - Gene

Summary

Official Symbol: PTPRNprovided by HGNC
Official Full Name: protein tyrosine phosphatase receptor type Nprovided by HGNC
Primary source: HGNC:HGNC:9676
See related: Ensembl:ENSG00000054356 MIM:601773; AllianceGenome:HGNC:9676
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: IA2; IA-2; ICA512; R-PTP-N; IA-2/PTP
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 a single catalytic domain, and thus represents a receptor-type PTP. This PTP was found to be an autoantigen that is reactive with insulin-dependent diabetes mellitus (IDDM) patient sera, and thus may be a potential target of autoimmunity in diabetes mellitus. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Dec 2010]
Expression: Biased expression in brain (RPKM 53.0), adrenal (RPKM 12.2) and 2 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q35

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (219289623..219309401, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (219774379..219794153, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (220154345..220174123, complement)

Chromosome 2 - NC_000002.12 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
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?

Glutamic Acid Decarboxylase and Tyrosine Phosphatase-Related Islet Antigen-2 Positivity among Children and Adolescents with Diabetes in Korea.
Title: Glutamic Acid Decarboxylase and Tyrosine Phosphatase-Related Islet Antigen-2 Positivity among Children and Adolescents with Diabetes in Korea.
Seroreactivity Against Tyrosine Phosphatase PTPRN Links Type 2 Diabetes and Colorectal Cancer and Identifies a Potential Diagnostic and Therapeutic Target.
Title: Seroreactivity Against Tyrosine Phosphatase PTPRN Links Type 2 Diabetes and Colorectal Cancer and Identifies a Potential Diagnostic and Therapeutic Target.
Different interaction of onset age and duration of type 1 diabetes on the dynamics of autoantibodies to insulinoma-associated antigen-2 and zinc transporter 8.
Title: Different interaction of onset age and duration of type 1 diabetes on the dynamics of autoantibodies to insulinoma-associated antigen-2 and zinc transporter 8.
PTPN12, PTPRN and PTPN18 were independent prognostic factors in Hepatocellular Carcinoma.
Title: Prognostic Value of Phosphotyrosine Phosphatases in Hepatocellular Carcinoma.
E. coli GI724 strain emerged as a handy source of recombinant IA-2ic, achieving high levels of expression as a thioredoxin fusion protein, adequately validated and applicable to the development of innovative and cost-effective immunoassays for IA-2A detection in most laboratories.
Title: Novel prokaryotic expression of thioredoxin-fused insulinoma associated protein tyrosine phosphatase 2 (IA-2), its characterization and immunodiagnostic application.
Identification of amino acids contributing to distinct epitopes on IA-2, with both HLA-DR and HLA-DQ alleles influencing epitope specificity.
Title: Influence of HLA-DR and -DQ alleles on autoantibody recognition of distinct epitopes within the juxtamembrane domain of the IA-2 autoantigen in type 1 diabetes.
RESP18HD is required for efficient sorting of ICA512 to secretory granules: RESP18HD is a key determinant for ICA512 granule targeting.
Title: Biochemical, biophysical, and functional properties of ICA512/IA-2 RESP18 homology domain.
The binding of CREB to the promoter region, -216 to +115, enhanced IA-2 transcription by more than fivefold.
Title: The minimal promoter region of the dense-core vesicle protein IA-2: transcriptional regulation by CREB.
Kaplan-Meier survival curves estimated a worst pancreas graft survival for patients with positive IA-2 antibodies versus those patients with negative auto-antibodies and GAD65+ auto-antibodies after simultaneous pancreas kidney transplantation.
Title: Tyrosine-phosphatase and glutamate-decarboxylase antibodies after simultaneous pancreas kidney transplantation: do they have an impact on pancreas graft survival?
Humoral responses to islet antigen-2 and zinc transporter 8 are attenuated in patients carrying HLA-A*24 alleles at the onset of type 1 diabetes.
Title: Humoral responses to islet antigen-2 and zinc transporter 8 are attenuated in patients carrying HLA-A*24 alleles at the onset of type 1 diabetes.

Submit: New GeneRIF Correction See all GeneRIFs (35)

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

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

MARC_8095-8096:996688286:1 (e-PCR)
- UniSTS:269893

RH80635 (e-PCR)
- UniSTS:86612

RH70260 (e-PCR)
- UniSTS:25696

PTPRN_1350 (e-PCR)
- UniSTS:277628

PTPRN_v432 (e-PCR)
- UniSTS:277628

RH93957 (e-PCR)
- UniSTS:88992

RH69021 (e-PCR)
- UniSTS:4515

RH80862 (e-PCR)
- UniSTS:84131

X74438 (e-PCR)
- UniSTS:163252

GDB:452693 (e-PCR)
- UniSTS:157408

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
NOT enables protein tyrosine phosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables spectrin binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription factor binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-like protein ligase binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in dense core granule maturation	IGI Inferred from Genetic Interaction more info	PubMed
involved_in insulin secretion	IGI Inferred from Genetic Interaction more info	PubMed
involved_in insulin secretion involved in cellular response to glucose stimulus	IBA Inferred from Biological aspect of Ancestor more info
involved_in insulin secretion involved in cellular response to glucose stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in luteinization	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of type B pancreatic cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of secretion	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to reactive oxygen species	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
located_in axon terminus	ISS Inferred from Sequence or Structural Similarity more info
located_in endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perikaryon	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in secretory granule	IBA Inferred from Biological aspect of Ancestor more info
located_in secretory granule	ISS Inferred from Sequence or Structural Similarity more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	ISS Inferred from Sequence or Structural Similarity more info
NOT located_in synaptic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in transport vesicle membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: receptor-type tyrosine-protein phosphatase-like N

Names: ICA 512; PTP IA-2; insulinoma-associated tyrosine-phosphatase-like protein; islet cell antigen 2; islet cell antigen 512; islet cell autoantigen 3; protein tyrosine phosphatase-like N

NP_001186692.1

EC 3.1.3.48

NP_001186693.1

EC 3.1.3.48

NP_002837.1

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_029546.1 RefSeqGene

Range

5173..24951

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001199763.2 → NP_001186692.1 receptor-type tyrosine-protein phosphatase-like N isoform 2 precursor

See identical proteins and their annotated locations for NP_001186692.1

Status: REVIEWED

Description

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

Source sequence(s)

AC114803, BC070053, DC344431

Consensus CDS

CCDS56168.1

UniProtKB/TrEMBL

A8K604

Related

ENSP00000386638.3, ENST00000409251.7

Conserved Domains (4) summary

smart00194
Location:680 → 939

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:707 → 939

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 ...

pfam11548
Location:476 → 528

Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2

pfam14948
Location:60 → 138

RESP18; RESP18 domain
NM_001199764.2 → NP_001186693.1 receptor-type tyrosine-protein phosphatase-like N isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences causes translation initiation at a downstream AUG and results an isoform (3) with a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AC114803, AK296335, BC070053

Consensus CDS

CCDS56167.1

UniProtKB/TrEMBL

Q96IA0

Related

ENSP00000392598.2, ENST00000423636.6

Conserved Domains (4) summary

smart00194
Location:619 → 878

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:646 → 878

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 ...

pfam11548
Location:382 → 467

Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2

pfam14948
Location:1 → 48

RESP18; RESP18 domain
NM_002846.4 → NP_002837.1 receptor-type tyrosine-protein phosphatase-like N isoform 1 precursor

See identical proteins and their annotated locations for NP_002837.1

Status: REVIEWED

Description

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

Source sequence(s)

BC007713, L18983, X62899

Consensus CDS

CCDS2440.1

UniProtKB/Swiss-Prot

B4DK12, F5GZS3, Q08319, Q16849, Q53QD6, Q6NSL1

UniProtKB/TrEMBL

A0A4Y5WWT4

Related

ENSP00000295718.2, ENST00000295718.7

Conserved Domains (4) summary

smart00194
Location:709 → 968

PTPc; Protein tyrosine phosphatase, catalytic domain

cd00047
Location:736 → 968

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 ...

pfam11548
Location:472 → 557

Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2

pfam14948
Location:60 → 138

RESP18; RESP18 domain