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PTPN7 protein tyrosine phosphatase non-receptor type 7 [ Homo sapiens (human) ]

Gene ID: 5778, updated on 14-Nov-2024

Summary

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Official Symbol
PTPN7provided by HGNC
Official Full Name
protein tyrosine phosphatase non-receptor type 7provided by HGNC
Primary source
HGNC:HGNC:9659
See related
Ensembl:ENSG00000143851 MIM:176889; AllianceGenome:HGNC:9659
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
LPTP; HEPTP; PTPNI; BPTP-4; LC-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 gene is preferentially expressed in a variety of hematopoietic cells, and is an early response gene in lymphokine stimulated cells. The non-catalytic N-terminus of this PTP can interact with MAP kinases and suppress the MAP kinase activities. This PTP was shown to be involved in the regulation of T cell antigen receptor (TCR) signaling, which was thought to function through dephosphorylating the molecules related to MAP kinase pathway. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2010]
Expression
Biased expression in bone marrow (RPKM 19.6), lymph node (RPKM 18.1) and 11 other tissues See more
Orthologs
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Genomic context

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See PTPN7 in Genome Data Viewer
Location:
1q32.1
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (202147013..202161588, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (201404580..201419169, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202116141..202130716, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371683 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202099011-202099794 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202099795-202100578 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:202104477-202104684 Neighboring gene G protein-coupled receptor 37 like 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1698 Neighboring gene ARF like GTPase 8A Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1699 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2327 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2329 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202132551-202133219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202133799-202134299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202134943-202135522 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202152613-202153112 Neighboring gene protein tyrosine phosphatase receptor type V, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202153807-202154336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202154337-202154866 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:202161513-202162316 Neighboring gene small nucleolar RNA U13 Neighboring gene leucine rich repeat containing G protein-coupled receptor 6

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 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. Structure of the hematopoietic tyrosine phosphatase (HePTP) catalytic domain: structure of a KIM phosphatase with phosphate bound at the active site. Mustelin T, et al. J Mol Biol, 2005 Nov 18. PMID 16226275
  2. Molecular cloning and chromosomal mapping of a human protein-tyrosine phosphatase LC-PTP. Adachi M, et al. Biochem Biophys Res Commun, 1992 Aug 14. PMID 1510684
  3. Cloning and expression of an inducible lymphoid-specific, protein tyrosine phosphatase (HePTPase). Zanke B, et al. Eur J Immunol, 1992 Jan. PMID 1530918
  4. A hematopoietic protein tyrosine phosphatase (HePTP) gene that is amplified and overexpressed in myeloid malignancies maps to chromosome 1q32.1. Zanke B, et al. Leukemia, 1994 Feb. PMID 8309248
  5. Negative regulation of T cell antigen receptor signal transduction by hematopoietic tyrosine phosphatase (HePTP). Saxena M, et al. J Biol Chem, 1998 Jun 19. PMID 9624114

See all (42) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PTPN7 regulates platelet functional responses downstream of GPCR agonists, but not GPVI agonists, through inhibition of ERK activation and thromboxane generation.
    Title: The protein tyrosine phosphatase PTPN7 is a negative regulator of ERK activation and thromboxane generation in platelets.
  2. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants that affect length/height in infancy/early childhood in Vietnamese-Korean families.
  3. Interactions at the active site between KIM (kinase interaction motif)-phosphatases and their substrates are predominantly nonspecific, with the majority of the KIM-phosphatase residues coordinating the peptide backbone rather than residue side chains.
    Title: Structural basis of substrate recognition by hematopoietic tyrosine phosphatase.
  4. structure of the protein tyrosine phosphatase catalytic domain of HePTP, residues 44-339
    Title: Structure of the hematopoietic tyrosine phosphatase (HePTP) catalytic domain: structure of a KIM phosphatase with phosphate bound at the active site.
  5. determined high-resolution structures of all of the human family members of Mitogen-Activated Protein Kinase-specific protein tyrosine phosphatases
    Title: Crystal structures and inhibitor identification for PTPN5, PTPRR and PTPN7: a family of human MAPK-specific protein tyrosine phosphatases.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association studies identify four ER negative-specific breast cancer risk loci.
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)

Pathways from PubChem

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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

Homology

Clone Names

  • FLJ18703

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 TAS
Traceable Author Statement
more info
  
enables protein 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, metal-dependent IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in MAPK cascade TAS
Traceable Author Statement
more info
  
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in protein dephosphorylation TAS
Traceable Author Statement
more info
 PubMed 
involved_in signal transduction IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in microtubule cytoskeleton IDA
Inferred from Direct Assay
more info
  
located_in mitotic spindle IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
tyrosine-protein phosphatase non-receptor type 7
Names
dual specificity phosphatase 1
hematopoietic protein-tyrosine phosphatase
protein-tyrosine phosphatase LC-PTP
protein-tyrosine phosphatase, nonreceptor-type, stress induced
NP_001186726.1
NP_001351806.1
NP_001351807.1
NP_002823.4
NP_542155.1
XP_011508121.1
XP_011508122.1
XP_011508125.1
XP_047282252.1
XP_047282253.1
XP_047282262.1
XP_054193897.1
XP_054193898.1
XP_054193899.1
XP_054193900.1
XP_054193901.1
XP_054193902.1

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.

mRNA and Protein(s)

  1. NM_001199797.2 → NP_001186726.1  tyrosine-protein phosphatase non-receptor type 7 isoform 3

    See identical proteins and their annotated locations for NP_001186726.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks a segment in the 5' region, resulting in an upstream AUG start codon, as compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AK302869, AL592300, DC399028
    UniProtKB/TrEMBL
    B4DZD9, J3KR55
    Conserved Domains (2) summary
    smart00194
    Location:170 → 422
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:196 → 422
    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 ...

  2. NM_001364877.2 → NP_001351806.1  tyrosine-protein phosphatase non-receptor type 7 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL592300
    UniProtKB/TrEMBL
    B4DVF0
    Conserved Domains (1) summary
    cd00047
    Location:121 → 347
    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 ...

  3. NM_001364878.1 → NP_001351807.1  tyrosine-protein phosphatase non-receptor type 7 isoform 1

    Status: REVIEWED

    Source sequence(s)
    AL592300, BT009848, DC399028
    Consensus CDS
    CCDS1423.3
    UniProtKB/Swiss-Prot
    B3KXE1, P35236, Q53XK4, Q5SXQ0, Q5SXQ1, Q9BV05
    UniProtKB/TrEMBL
    B4DVF0
    Related
    ENSP00000418416.2, ENST00000477554.6
    Conserved Domains (1) summary
    cd14612
    Location:105 → 350
    PTPc-N7; catalytic domain of tyrosine-protein phosphatase non-receptor type 7

  4. NM_002832.4 → NP_002823.4  tyrosine-protein phosphatase non-receptor type 7 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL592300
    Consensus CDS
    CCDS1423.3
    UniProtKB/Swiss-Prot
    B3KXE1, P35236, Q53XK4, Q5SXQ0, Q5SXQ1, Q9BV05
    UniProtKB/TrEMBL
    B4DVF0
    Related
    ENSP00000509436.1, ENST00000691036.1
    Conserved Domains (1) summary
    cd14612
    Location:105 → 350
    PTPc-N7; catalytic domain of tyrosine-protein phosphatase non-receptor type 7

  5. NM_080588.3 → NP_542155.1  tyrosine-protein phosphatase non-receptor type 7 isoform 2

    See identical proteins and their annotated locations for NP_542155.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon from the 5' end and contains an alternate 5' segment which includes an AUG start codon, as compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AL592300, BC001746
    Consensus CDS
    CCDS1422.1
    UniProtKB/TrEMBL
    J3KR55
    Related
    ENSP00000356248.4, ENST00000367279.8
    Conserved Domains (2) summary
    smart00194
    Location:135 → 387
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:161 → 387
    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 ...

RNA

  1. NR_037663.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an internal segment in the CDS, resulting in frame-shift and a premature stop codon, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay candidate, and probably does not make a functional protein.
    Source sequence(s)
    AK301051, AL592300

  2. NR_037664.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an exon in the CDS, resulting in frame-shift and a premature stop codon, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay candidate, and probably does not make a functional protein.
    Source sequence(s)
    AK293186, AL592300

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

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    202147013..202161588 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426297.1 → XP_047282253.1  tyrosine-protein phosphatase non-receptor type 7 isoform X4

  2. XM_047426296.1 → XP_047282252.1  tyrosine-protein phosphatase non-receptor type 7 isoform X3

  3. XM_011509820.3 → XP_011508122.1  tyrosine-protein phosphatase non-receptor type 7 isoform X2

    Conserved Domains (2) summary
    smart00194
    Location:90 → 388
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:116 → 388
    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 ...

  4. XM_011509819.2 → XP_011508121.1  tyrosine-protein phosphatase non-receptor type 7 isoform X1

    Related
    ENSP00000309116.5, ENST00000309017.9
    Conserved Domains (2) summary
    smart00194
    Location:201 → 499
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cd00047
    Location:227 → 499
    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_047426306.1 → XP_047282262.1  tyrosine-protein phosphatase non-receptor type 7 isoform X6

  6. XM_011509823.2 → XP_011508125.1  tyrosine-protein phosphatase non-receptor type 7 isoform X5

    Conserved Domains (2) summary
    smart00194
    Location:201 → 307
    PTPc; Protein tyrosine phosphatase, catalytic domain
    cl21483
    Location:227 → 307
    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 ...

RNA

  1. XR_007062439.1 RNA Sequence

  2. XR_921906.2 RNA Sequence

  3. XR_007062440.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    201404580..201419169 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337924.1 → XP_054193899.1  tyrosine-protein phosphatase non-receptor type 7 isoform X3

  2. XM_054337923.1 → XP_054193898.1  tyrosine-protein phosphatase non-receptor type 7 isoform X2

  3. XM_054337922.1 → XP_054193897.1  tyrosine-protein phosphatase non-receptor type 7 isoform X1

  4. XM_054337927.1 → XP_054193902.1  tyrosine-protein phosphatase non-receptor type 7 isoform X6

  5. XM_054337925.1 → XP_054193900.1  tyrosine-protein phosphatase non-receptor type 7 isoform X4

  6. XM_054337926.1 → XP_054193901.1  tyrosine-protein phosphatase non-receptor type 7 isoform X5

RNA

  1. XR_008486131.1 RNA Sequence

  2. XR_008486130.1 RNA Sequence

  3. XR_008486132.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_080589.1: Suppressed sequence

    Description
    NM_080589.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P35236.3 GenPept UniProtKB/Swiss-Prot:P35236

Gene LinkOut

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