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

Summary

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: mouse all
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Genomic context

Location:: 7q36.3

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (157539056..158587823, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (158727687..159797184, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (157331750..158380515, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions of genetic variations in FAS, GJB2 and PTPRN2 are associated with noise-induced hearing loss: a case-control study in China.
Title: Interactions of genetic variations in FAS, GJB2 and PTPRN2 are associated with noise-induced hearing loss: a case-control study in China.
Rab35 regulates insulin secretion via phogrin in pancreatic beta cells.
Title: Rab35 regulates insulin secretion via phogrin in pancreatic β cells.
HOXD13 promotes the malignant progression of colon cancer by upregulating PTPRN2.
Title: HOXD13 promotes the malignant progression of colon cancer by upregulating PTPRN2.
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.
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.
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.
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.
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.
ProPTPRN2 elicited these effects through direct interaction with TRAF2.
Title: Aberrant Expression of proPTPRN2 in Cancer Cells Confers Resistance to Apoptosis.
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.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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

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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

GDB:4585755 (e-PCR)
- UniSTS:2054

D7S2423 (e-PCR)
- UniSTS:39942

SHGC-147446 (e-PCR)
- UniSTS:172808

GDB:1317804 (e-PCR)
- UniSTS:46346

D7S98 (e-PCR)
- UniSTS:66607

GDB:4585269 (e-PCR)
- UniSTS:5685

G19707 (e-PCR)
- UniSTS:7228

A001W14 (e-PCR)
- UniSTS:7229

GDB:4585294 (e-PCR)
- UniSTS:16962

D7S467 (e-PCR)
- UniSTS:70216

RH47765 (e-PCR)
- UniSTS:28517

G17166 (e-PCR)
- UniSTS:21350

GDB:4584949 (e-PCR)
- UniSTS:17255

GDB:4585471 (e-PCR)
- UniSTS:38504

PTPRN2_240 (e-PCR)
- UniSTS:277627

SHGC-147330 (e-PCR)
- UniSTS:175746

D7S1476 (e-PCR)
- UniSTS:58243

D7S54 (e-PCR)
- UniSTS:40075

SHGC-144805 (e-PCR)
- UniSTS:172428

SHGC-53826 (e-PCR)
- UniSTS:11407

G20053 (e-PCR)
- UniSTS:48018

GDB:4585135 (e-PCR)
- UniSTS:28564

RH119650 (e-PCR)
- UniSTS:133019

GDB:1317982 (e-PCR)
- UniSTS:22177

D7S3168 (e-PCR)
- UniSTS:225953

D7S1759 (e-PCR)
- UniSTS:50084

D7S2423 (e-PCR)
- UniSTS:39601

D7S22 (e-PCR)
- UniSTS:71095

RH65458 (e-PCR)
- UniSTS:15033

RH12041 (e-PCR)
- UniSTS:65474

SHGC-142152 (e-PCR)
- UniSTS:174024

RH93077 (e-PCR)
- UniSTS:90569

GDB:4584967 (e-PCR)
- UniSTS:40655

SHGC-148672 (e-PCR)
- UniSTS:184534

WI-19502 (e-PCR)
- UniSTS:48856

SHGC-144451 (e-PCR)
- UniSTS:172252

SHGC-81751 (e-PCR)
- UniSTS:103917

NoName (e-PCR)
- UniSTS:17906

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
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 tyrosine phosphatase activity, metal-dependent	IEA Inferred from Electronic Annotation more info
enables transmembrane receptor protein tyrosine phosphatase activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
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 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	TAS Traceable Author Statement more info	PubMed
involved_in regulation of secretion	IBA Inferred from Biological aspect of Ancestor more info

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
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
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

EC 3.1.3.48

NP_001295197.1

EC 3.1.3.48

NP_002838.2

EC 3.1.3.48

NP_570857.2

EC 3.1.3.48

NP_570858.2

EC 3.1.3.48

XP_011514748.1

EC 3.1.3.48

XP_011514749.1

EC 3.1.3.48

XP_011514750.1

EC 3.1.3.48

XP_011514751.1

EC 3.1.3.48

XP_016867964.1

EC 3.1.3.48

XP_016867965.1

EC 3.1.3.48

XP_047276634.1

EC 3.1.3.48

XP_047276635.1

EC 3.1.3.48

XP_047276636.1

EC 3.1.3.48

XP_054214712.1

EC 3.1.3.48

XP_054214713.1

EC 3.1.3.48

XP_054214714.1

EC 3.1.3.48

XP_054214715.1

EC 3.1.3.48

XP_054214716.1

EC 3.1.3.48

XP_054214717.1

EC 3.1.3.48

XP_054214718.1

EC 3.1.3.48

XP_054214719.1

EC 3.1.3.48

XP_054214720.1

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_029966.2 RefSeqGene

Range

5000..1053767

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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/TrEMBL

E7EM83, Q9Y4I9

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
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/TrEMBL

Q9Y4I9

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
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

E9PC57, Q8N4I5, Q92662, Q92932, Q9Y4F8, Q9Y4I6

UniProtKB/TrEMBL

Q9Y4I9

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
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/TrEMBL

Q9Y4I9

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
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/TrEMBL

Q9Y4I9

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: 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_000007.14 Reference GRCh38.p14 Primary Assembly

Range

157539056..158587823 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

Q9Y4I9
XM_047420679.1 → XP_047276635.1 receptor-type tyrosine-protein phosphatase N2 isoform X3

UniProtKB/TrEMBL

Q9Y4I9
XM_017012475.1 → XP_016867964.1 receptor-type tyrosine-protein phosphatase N2 isoform X2

UniProtKB/TrEMBL

Q9Y4I9
XM_011516446.2 → XP_011514748.1 receptor-type tyrosine-protein phosphatase N2 isoform X5

UniProtKB/TrEMBL

Q9Y4I9

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

UniProtKB/TrEMBL

Q9Y4I9
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
XM_047420680.1 → XP_047276636.1 receptor-type tyrosine-protein phosphatase N2 isoform X8
XM_011516448.4 → XP_011514750.1 receptor-type tyrosine-protein phosphatase N2 isoform X7

UniProtKB/TrEMBL

I6L9F8

Conserved Domains (2) summary

pfam11548
Location:512 → 575

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

pfam14948
Location:59 → 138

RESP18; RESP18 domain
XM_011516449.3 → XP_011514751.1 receptor-type tyrosine-protein phosphatase N2 isoform X9

UniProtKB/TrEMBL

I6L9F8

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

NC_060931.1 Alternate T2T-CHM13v2.0

Range

158727687..159797184 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054358737.1 → XP_054214712.1 receptor-type tyrosine-protein phosphatase N2 isoform X1

UniProtKB/TrEMBL

Q9Y4I9
XM_054358739.1 → XP_054214714.1 receptor-type tyrosine-protein phosphatase N2 isoform X3

UniProtKB/TrEMBL

Q9Y4I9
XM_054358738.1 → XP_054214713.1 receptor-type tyrosine-protein phosphatase N2 isoform X2

UniProtKB/TrEMBL

Q9Y4I9
XM_054358741.1 → XP_054214716.1 receptor-type tyrosine-protein phosphatase N2 isoform X5

UniProtKB/TrEMBL

Q9Y4I9
XM_054358740.1 → XP_054214715.1 receptor-type tyrosine-protein phosphatase N2 isoform X4

UniProtKB/TrEMBL

Q9Y4I9
XM_054358742.1 → XP_054214717.1 receptor-type tyrosine-protein phosphatase N2 isoform X6
XM_054358744.1 → XP_054214719.1 receptor-type tyrosine-protein phosphatase N2 isoform X8
XM_054358743.1 → XP_054214718.1 receptor-type tyrosine-protein phosphatase N2 isoform X7

UniProtKB/TrEMBL

I6L9F8
XM_054358745.1 → XP_054214720.1 receptor-type tyrosine-protein phosphatase N2 isoform X9

UniProtKB/TrEMBL

I6L9F8