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PTPRN2 protein tyrosine phosphatase receptor type N2 [ Homo sapiens (human) ]

Gene ID: 5799, updated on 22-Sep-2022

Summary

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Official Symbol
PTPRN2provided by HGNC
Official Full Name
protein tyrosine phosphatase receptor type N2provided by HGNC
Primary source
HGNC:HGNC:9677
See related
Ensembl:ENSG00000155093 MIM:601698; AllianceGenome:HGNC:9677
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
IAR; ICAAR; PTPRP; IA-2beta; R-PTP-N2
Summary
This gene encodes a protein with sequence similarity to receptor-like protein tyrosine phosphatases. However, tyrosine phosphatase activity has not been experimentally validated for this protein. Studies of the rat ortholog suggest that the encoded protein may instead function as a phosphatidylinositol phosphatase with the ability to dephosphorylate phosphatidylinositol 3-phosphate and phosphatidylinositol 4,5-diphosphate, and this function may be involved in the regulation of insulin secretion. This protein has been identified as an autoantigen in insulin-dependent diabetes mellitus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]
Expression
Broad expression in brain (RPKM 7.2), stomach (RPKM 4.9) and 18 other tissues See more
Orthologs
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Genomic context

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See PTPRN2 in Genome Data Viewer
Location:
7q36.3
Exon count:
29
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (157539056..158587823, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (158727687..159797184, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (157331750..158380515, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927914 Neighboring gene Sharpr-MPRA regulatory region 4962 Neighboring gene uncharacterized LOC105375610 Neighboring gene uncharacterized LOC105375615 Neighboring gene uncharacterized LOC105375614 Neighboring gene microRNA 153-2 Neighboring gene PTPRN2 antisense RNA 1 Neighboring gene uncharacterized LOC105375613 Neighboring gene Sharpr-MPRA regulatory region 9311 Neighboring gene Sharpr-MPRA regulatory region 9999 Neighboring gene Sharpr-MPRA regulatory region 5343 Neighboring gene D7S22 minisatellite repeat instability region Neighboring gene Sharpr-MPRA regulatory region 11620 Neighboring gene uncharacterized LOC124901793 Neighboring gene Sharpr-MPRA regulatory region 10119 Neighboring gene microRNA 595 Neighboring gene long intergenic non-protein coding RNA 1022 Neighboring gene microRNA 5707 Neighboring gene THAP domain containing 5 pseudogene 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. The association of genetically controlled CpG methylation (cg158269415) of protein tyrosine phosphatase, receptor type N2 (PTPRN2) with childhood obesity. Lee S. Sci Rep, 2019 Mar 19. PMID 30890718, Free PMC Article
  2. Aberrant Expression of proPTPRN2 in Cancer Cells Confers Resistance to Apoptosis. Sorokin AV, et al. Cancer Res, 2015 May 1. PMID 25877877, Free PMC Article
  3. X-ray structure of the mature ectodomain of phogrin. Noguera ME, et al. J Struct Funct Genomics, 2015 Mar. PMID 25421040
  4. Coherent somatic mutation in autoimmune disease. Ross KA. PLoS One, 2014. PMID 24988487, Free PMC Article
  5. DNA hypermethylation and DNA hypomethylation is present at different loci in chronic kidney disease. Smyth LJ, et al. Epigenetics, 2014 Mar. PMID 24253112, Free PMC Article

See all (57) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Rab35 regulates insulin secretion via phogrin in pancreatic beta cells.
    Title: Rab35 regulates insulin secretion via phogrin in pancreatic β cells.
  2. HOXD13 promotes the malignant progression of colon cancer by upregulating PTPRN2.
    Title: HOXD13 promotes the malignant progression of colon cancer by upregulating PTPRN2.
  3. The association of genetically controlled CpG methylation (cg158269415) of protein tyrosine phosphatase, receptor type N2 (PTPRN2) with childhood obesity.
    Title: The association of genetically controlled CpG methylation (cg158269415) of protein tyrosine phosphatase, receptor type N2 (PTPRN2) with childhood obesity.
  4. Copy-number variations are enriched for PTPRN2 and other neurodevelopmental genes in children with developmental coordination disorder.
    Title: Copy-number variations are enriched for neurodevelopmental genes in children with developmental coordination disorder.
  5. Haplotype-dependent allele-specific methylation of PTPRN2 gene is associated with neurological disorders.
    Title: Mechanisms and Disease Associations of Haplotype-Dependent Allele-Specific DNA Methylation.
  6. Reduction in plasma membrane PI(4,5)P2 abundance by PTPRN2 and PLCbeta1 releases the PI(4,5)P2-binding protein cofilin from its inactive membrane-associated state into the cytoplasm where it mediates actin turnover dynamics.
    Title: PTPRN2 and PLCβ1 promote metastatic breast cancer cell migration through PI(4,5)P2-dependent actin remodeling.
  7. Data indicate the X-ray structure of the mature ectodomain of mature ectodomain of phogrin/IA-2beta (PTPRN2) (ME phogrin) at pH 7.4 and 4.6.
    Title: X-ray structure of the mature ectodomain of phogrin.
  8. ProPTPRN2 elicited these effects through direct interaction with TRAF2.
    Title: Aberrant Expression of proPTPRN2 in Cancer Cells Confers Resistance to Apoptosis.
  9. While PTPRN2 shares sequence similarity with protein tyrosine phosphatases, this study in rat suggests that this protein instead functions as a membrane bound phosphatidylinositol phosphatase.
    Title: The neurosecretory vesicle protein phogrin functions as a phosphatidylinositol phosphatase to regulate insulin secretion.
  10. The findings in this patient raise the possibility that PTPRN2 may be active during early development of the human brainstem and that its overexpression may cause bilateral Duane retraction syndrome as occurs in patients with homozygous HOXA1 mutations.
    Title: Partial chromosome 7 duplication with a phenotype mimicking the HOXA1 spectrum disorder.
Submit: New GeneRIF Correction See all GeneRIFs (16)

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
A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
EBI GWAS Catalog
Case-case genome-wide association analysis shows markers differentially associated with schizophrenia and bipolar disorder and implicates calcium channel genes.
EBI GWAS Catalog
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of protein tyrosine phosphatase, receptor type, N polypeptide 2 (PTPRN2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables transmembrane receptor protein tyrosine phosphatase activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in insulin secretion involved in cellular response to glucose stimulus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in insulin secretion involved in cellular response to glucose stimulus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in lipid metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in neurotransmitter secretion ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein dephosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of secretion IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Component Evidence Code Pubs
located_in ficolin-1-rich granule membrane TAS
Traceable Author Statement
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
part_of receptor complex IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in secretory granule IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in secretory granule membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in synaptic vesicle membrane ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
receptor-type tyrosine-protein phosphatase N2
Names
IAR/receptor-like protein-tyrosine phosphatase
islet cell autoantigen-related protein
phogrin
protein tyrosine phosphatase receptor pi
protein tyrosine phosphatase, receptor type, N polypeptide 2
tyrosine phosphatase IA-2 beta
NP_001295196.1
NP_001295197.1
NP_002838.2
NP_570857.2
NP_570858.2
XP_011514748.1
XP_011514749.1
XP_011514750.1
XP_011514751.1
XP_016867964.1
XP_016867965.1
XP_047276634.1
XP_047276635.1
XP_047276636.1

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

  1. NG_029966.2 RefSeqGene

    Range
    5000..1053767
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001308267.2 → NP_001295196.1  receptor-type tyrosine-protein phosphatase N2 isoform 4 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.
    Source sequence(s)
    AC005481, AC006372, AC011899, AC078942, AC093662, AC093856
    Consensus CDS
    CCDS78294.1
    UniProtKB/Swiss-Prot
    Q92932
    UniProtKB/TrEMBL
    E7EM83, I6L9F8
    Related
    ENSP00000387114.1, ENST00000409483.5
    Conserved Domains (4) summary
    smart00194
    Location:707 → 966
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:734 → 966
    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:474 → 559
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:55 → 100
    RESP18; RESP18 domain

  2. NM_001308268.2 → NP_001295197.1  receptor-type tyrosine-protein phosphatase N2 isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' terminal exon, and it thus differs in the 5' UTR and 5' coding region, compared to variant 1. The encoded isoform (5) has a distinct N-terminus and is longer than isoform 1.
    Source sequence(s)
    AC005481, AC006372, AC011899, AC019043, AC078942, AC093856
    UniProtKB/Swiss-Prot
    Q92932
    UniProtKB/TrEMBL
    I6L9F8
    Conserved Domains (4) summary
    smart00194
    Location:768 → 1027
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:795 → 1027
    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:535 → 620
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:82 → 161
    RESP18; RESP18 domain

  3. NM_002847.5 → NP_002838.2  receptor-type tyrosine-protein phosphatase N2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_002838.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC005481, AC006372, AC011899, AC019043, AC078942, AC093662, AC093856
    Consensus CDS
    CCDS5947.1
    UniProtKB/Swiss-Prot
    Q92932, Q9Y4I6
    UniProtKB/TrEMBL
    I6L9F8
    Related
    ENSP00000374069.4, ENST00000389418.9
    Conserved Domains (4) summary
    smart00194
    Location:745 → 1004
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:772 → 1004
    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:512 → 597
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:59 → 138
    RESP18; RESP18 domain

  4. NM_130842.4 → NP_570857.2  receptor-type tyrosine-protein phosphatase N2 isoform 2 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    AC005481, AC006372, AC011899, AC019043, AC093662, AC093856
    Consensus CDS
    CCDS5948.1
    UniProtKB/Swiss-Prot
    Q92932
    Related
    ENSP00000374067.4, ENST00000389416.8
    Conserved Domains (4) summary
    smart00194
    Location:728 → 987
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:755 → 987
    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:495 → 580
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:42 → 121
    RESP18; RESP18 domain

  5. NM_130843.4 → NP_570858.2  receptor-type tyrosine-protein phosphatase N2 isoform 3 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
    Source sequence(s)
    AC005481, AC006372, AC011899, AC019043, AC078942, AC093662, AC093856
    Consensus CDS
    CCDS5949.1
    UniProtKB/Swiss-Prot
    Q92932
    Related
    ENSP00000374064.3, ENST00000389413.7
    Conserved Domains (4) summary
    smart00194
    Location:716 → 975
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:743 → 975
    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:516 → 568
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:59 → 138
    RESP18; RESP18 domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    157539056..158587823 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420678.1 → XP_047276634.1  receptor-type tyrosine-protein phosphatase N2 isoform X1

  2. XM_047420679.1 → XP_047276635.1  receptor-type tyrosine-protein phosphatase N2 isoform X3

  3. XM_017012475.1 → XP_016867964.1  receptor-type tyrosine-protein phosphatase N2 isoform X2

  4. XM_011516446.2 → XP_011514748.1  receptor-type tyrosine-protein phosphatase N2 isoform X5

    Conserved Domains (3) summary
    pfam11548
    Location:512 → 597
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:59 → 138
    RESP18; RESP18 domain
    cl21483
    Location:772 → 832
    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 ...

  5. XM_017012476.2 → XP_016867965.1  receptor-type tyrosine-protein phosphatase N2 isoform X4

  6. XM_011516447.3 → XP_011514749.1  receptor-type tyrosine-protein phosphatase N2 isoform X6

    Conserved Domains (2) summary
    pfam11548
    Location:512 → 575
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:59 → 138
    RESP18; RESP18 domain

  7. XM_047420680.1 → XP_047276636.1  receptor-type tyrosine-protein phosphatase N2 isoform X8

  8. XM_011516448.4 → XP_011514750.1  receptor-type tyrosine-protein phosphatase N2 isoform X7

    Conserved Domains (2) summary
    pfam11548
    Location:512 → 575
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:59 → 138
    RESP18; RESP18 domain

  9. XM_011516449.3 → XP_011514751.1  receptor-type tyrosine-protein phosphatase N2 isoform X9

    Conserved Domains (2) summary
    pfam11548
    Location:512 → 563
    Receptor_IA-2; Protein-tyrosine phosphatase receptor IA-2
    pfam14948
    Location:59 → 138
    RESP18; RESP18 domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    158727687..159797184 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92932.2 GenPept UniProtKB/Swiss-Prot:Q92932

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