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    PTPN9 protein tyrosine phosphatase non-receptor type 9 [ Homo sapiens (human) ]

    Gene ID: 5780, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PTPN9provided by HGNC
    Official Full Name
    protein tyrosine phosphatase non-receptor type 9provided by HGNC
    Primary source
    HGNC:HGNC:9661
    See related
    Ensembl:ENSG00000169410 MIM:600768; AllianceGenome:HGNC:9661
    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
    MEG2; PTPMEG2
    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 contains an N-terminal domain that shares a significant similarity with yeast SEC14, which is a protein that has phosphatidylinositol transfer activity and is required for protein secretion through the Golgi complex in yeast. This PTP was found to be activated by polyphosphoinositide, and is thought to be involved in signaling events regulating phagocytosis. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 22.0), small intestine (RPKM 10.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    15q24.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (75463251..75579315, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (73333337..73450019, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (75755592..75871656, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 1822 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6667 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75660721-75661253 Neighboring gene nei like DNA glycosylase 1 Neighboring gene mannosidase alpha class 2C member 1 Neighboring gene SIN3 transcription regulator family member A Neighboring gene ribosomal protein L13 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6668 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:75742449-75743368 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75744915-75745446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:75745447-75745979 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9855 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6671 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9857 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9858 Neighboring gene Sharpr-MPRA regulatory region 2587 Neighboring gene uncharacterized LOC105370902 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:75797079-75797864 Neighboring gene small nuclear ribonucleoprotein F-like Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6673 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:75871223-75871821 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9859 Neighboring gene snurportin 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6676 Neighboring gene IMP U3 small nucleolar ribonucleoprotein 3

    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. MEG2 is regulated by miR-181a-5p and functions as a tumour suppressor gene to suppress the proliferation and migration of gastric cancer cells. Liu Z, et al. Mol Cancer, 2017 Jul 26. PMID 28747184, Free PMC Article
    2. Downregulated Expression of PTPN9 Contributes to Human Hepatocellular Carcinoma Growth and Progression. Hu B, et al. Pathol Oncol Res, 2016 Jul. PMID 26715439
    3. Association of protein-tyrosine phosphatase MEG2 via its Sec14p homology domain with vesicle-trafficking proteins. Saito K, et al. J Biol Chem, 2007 May 18. PMID 17387180
    4. Homotypic secretory vesicle fusion induced by the protein tyrosine phosphatase MEG2 depends on polyphosphoinositides in T cells. Huynh H, et al. J Immunol, 2003 Dec 15. PMID 14662869
    5. PTP-MEG2 is activated in polycythemia vera erythroid progenitor cells and is required for growth and expansion of erythroid cells. Xu MJ, et al. Blood, 2003 Dec 15. PMID 12920026

    See all (60) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Signature of miR-21 and MEG-2 and their correlation with TGF-beta signaling in breast cancer.
      Title: Signature of miR-21 and MEG-2 and their correlation with TGF-β signaling in breast cancer.
    2. CircMMD_007 promotes oncogenic effects in the progression of lung adenocarcinoma through microRNA-197-3p/protein tyrosine phosphatase non-receptor type 9 axis.
      Title: CircMMD_007 promotes oncogenic effects in the progression of lung adenocarcinoma through microRNA-197-3p/protein tyrosine phosphatase non-receptor type 9 axis.
    3. PTPN9-mediated dephosphorylation of VTI1B promotes ATG16L1 precursor fusion and autophagosome formation.
      Title: PTPN9-mediated dephosphorylation of VTI1B promotes ATG16L1 precursor fusion and autophagosome formation.
    4. Effect of L3MBTL3/PTPN9 polymorphisms on risk to alcohol-induced ONFH in Chinese Han population.
      Title: Effect of L3MBTL3/PTPN9 polymorphisms on risk to alcohol-induced ONFH in Chinese Han population.
    5. The Critical Role of the miR-21-MEG2 Axis in Colorectal Cancer.
      Title: The Critical Role of the miR-21-MEG2 Axis in Colorectal Cancer.
    6. Low MEG2 expression is associated with metastasis of hepatocellular carcinoma.
      Title: MEG2 inhibits the growth and metastasis of hepatocellular carcinoma by inhibiting AKT pathway.
    7. Results from a study on gene expression variability markers in early-stage human embryos shows that PTPN9 is a putative expression variability marker for the 3-day, 8-cell embryo stage.
      Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
    8. this study highlights an important role for miR-96 in the regulation of PTPN9 in breast cancer cells and may provide insight into the molecular mechanisms of breast carcinogenesis.
      Title: miR-96 promotes cell proliferation, migration and invasion by targeting PTPN9 in breast cancer.
    9. Expression of MEG2 is reversely correlated with that of miR-181a-5p in gastric cancer.
      Title: MEG2 is regulated by miR-181a-5p and functions as a tumour suppressor gene to suppress the proliferation and migration of gastric cancer cells.
    10. PTPN9 inhibited cell proliferation in HepG2 cells.
      Title: Downregulated Expression of PTPN9 Contributes to Human Hepatocellular Carcinoma Growth and Progression.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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 in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    EBI GWAS Catalog
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel 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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Screening in Jurkat T-cells with a short-hairpin-RNA (shRNA) library identifies PTPN9/PTP-MEG2, a member of the protein tyrosine phosphatase family, is important for HIV-1 replication 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

    Potential readthrough

    Included gene: SNUPN

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables non-membrane spanning protein tyrosine phosphatase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within negative regulation of neuron projection development IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within peptidyl-tyrosine dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of protein localization to plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein dephosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein dephosphorylation TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in neuron projection terminus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    tyrosine-protein phosphatase non-receptor type 9
    Names
    PTPase-MEG2
    protein-tyrosine phosphatase MEG2
    NP_002824.1

    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_002833.4 → NP_002824.1  tyrosine-protein phosphatase non-receptor type 9

      See identical proteins and their annotated locations for NP_002824.1

      Status: REVIEWED

      Source sequence(s)
      AC105036, AC105137, BC071574, M83738
      Consensus CDS
      CCDS10280.1
      UniProtKB/Swiss-Prot
      P43378, Q53XR9
      UniProtKB/TrEMBL
      Q6IQ43
      Related
      ENSP00000482732.1, ENST00000618819.5
      Conserved Domains (3) summary
      smart00516
      Location:90 → 240
      SEC14; Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p)
      smart01100
      Location:20 → 68
      CRAL_TRIO_N; CRAL/TRIO, N-terminal domain
      cd14543
      Location:299 → 569
      PTPc-N9; catalytic domain of tyrosine-protein phosphatase non-receptor type 9

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      75463251..75579315 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      73333337..73450019 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P43378.1 GenPept UniProtKB/Swiss-Prot:P43378

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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