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    PTPN12 protein tyrosine phosphatase non-receptor type 12 [ Homo sapiens (human) ]

    Gene ID: 5782, updated on 27-Nov-2024

    Summary

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    Official Symbol
    PTPN12provided by HGNC
    Official Full Name
    protein tyrosine phosphatase non-receptor type 12provided by HGNC
    Primary source
    HGNC:HGNC:9645
    See related
    Ensembl:ENSG00000127947 MIM:600079; AllianceGenome:HGNC:9645
    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
    PTPG1; PTP-PEST
    Summary
    The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains a C-terminal PEST motif, which serves as a protein-protein interaction domain, and may regulate protein intracellular half-life. This PTP was found to bind and dephosphorylate the product of the oncogene c-ABL and thus may play a role in oncogenesis. This PTP was also shown to interact with, and dephosphorylate, various products related to cytoskeletal structure and cell adhesion, such as p130 (Cas), CAKbeta/PTK2B, PSTPIP1, and paxillin. This suggests it has a regulatory role in controlling cell shape and mobility. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Oct 2008]
    Expression
    Ubiquitous expression in lung (RPKM 36.1), placenta (RPKM 29.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PTPN12 in Genome Data Viewer
    Location:
    7q11.23
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (77537295..77640069)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (78789201..78891996)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (77166612..77269386)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18323 Neighboring gene MPRA-validated peak6615 silencer Neighboring gene glucosaminyl (N-acetyl) transferase 1 pseudogene 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:77138003-77138978 Neighboring gene uncharacterized LOC124901681 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77154891-77155392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77155393-77155892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26205 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26206 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18324 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18325 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:77169285-77169866 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:77185513-77186127 Neighboring gene uncharacterized LOC105375363 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:77305655-77305829 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77321385-77321884 Neighboring gene Alu-mediated CDKN1A/p21 transcriptional regulator Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:77324871-77325766 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:77325767-77326662 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18329 Neighboring gene round spermatid basic protein 1 like Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:77393580-77394080

    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. Tyrosine-protein phosphatase nonreceptor type 12 is a novel prognostic biomarker for esophageal squamous cell carcinoma. Cao X, et al. Ann Thorac Surg, 2012 May. PMID 22429674
    2. PTPN12/PTP-PEST Regulates Phosphorylation-Dependent Ubiquitination and Stability of Focal Adhesion Substrates in Invasive Glioblastoma Cells. Chen Z, et al. Cancer Res, 2018 Jul 15. PMID 29743287, Free PMC Article
    3. A missense variant in PTPN12 associated with the risk of colorectal cancer by modifying Ras/MEK/ERK signaling. Shen N, et al. Cancer Epidemiol, 2019 Apr. PMID 30731403
    4. Important roles of protein tyrosine phosphatase PTPN12 in tumor progression. Lee C, et al. Pharmacol Res, 2019 Jun. PMID 30959160
    5. Structure and Molecular Dynamics Simulations of Protein Tyrosine Phosphatase Non-Receptor 12 Provide Insights into the Catalytic Mechanism of the Enzyme. Dong H, et al. Int J Mol Sci, 2017 Dec 26. PMID 29278368, Free PMC Article

    See all (137) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Identification of PTPN12 Phosphatase as a Novel Negative Regulator of Hippo Pathway Effectors YAP/TAZ in Breast Cancer.
      Title: Identification of PTPN12 Phosphatase as a Novel Negative Regulator of Hippo Pathway Effectors YAP/TAZ in Breast Cancer.
    2. Protein tyrosine phosphatase non-receptor type 12 suppresses tumor progression in osteosarcoma cells.
      Title: Protein tyrosine phosphatase non-receptor type 12 suppresses tumor progression in osteosarcoma cells.
    3. LncRNA GATA2-AS1 suppresses esophageal squamous cell carcinoma progression via the mir-940/PTPN12 axis.
      Title: LncRNA GATA2-AS1 suppresses esophageal squamous cell carcinoma progression via the mir-940/PTPN12 axis.
    4. PTP-PEST Regulated Membranous/Cytoplasmic Translocation of p120ctn in the Lung Cancer Resistance to Tyrosine Kinase Inhibitor.
      Title: PTP-PEST Regulated Membranous/Cytoplasmic Translocation of p120ctn in the Lung Cancer Resistance to Tyrosine Kinase Inhibitor.
    5. Protein tyrosine phosphatase non-receptor type 12 (PTPN12), negatively regulated by miR-106a-5p, suppresses the progression of hepatocellular carcinoma.
      Title: Protein tyrosine phosphatase non-receptor type 12 (PTPN12), negatively regulated by miR-106a-5p, suppresses the progression of hepatocellular carcinoma.
    6. The protein tyrosine phosphatase PTP-PEST mediates hypoxia-induced endothelial autophagy and angiogenesis via AMPK activation.
      Title: The protein tyrosine phosphatase PTP-PEST mediates hypoxia-induced endothelial autophagy and angiogenesis via AMPK activation.
    7. Expression and clinical significance of PTPN12 in clear cell renal cell carcinoma.
      Title: Expression and clinical significance of PTPN12 in clear cell renal cell carcinoma.
    8. tumor suppressing gene [review]
      Title: Progress in the correlation between PTPN12 gene expression and human tumors.
    9. This review provides an overview of PTPN12 and discusses the critical roles of PTPN12 in tumor progression. [review]
      Title: Important roles of protein tyrosine phosphatase PTPN12 in tumor progression.
    10. This study identifies PTPN12 expression measurement as a valuable prognostic marker in prostate cancer.
      Title: High-level expression of protein tyrosine phosphatase non-receptor 12 is a strong and independent predictor of poor prognosis in prostate cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (43)

    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

    Associated conditions

    Description Tests
    Colorectal cancer
    MedGen: C0346629 OMIM: 114500 GeneReviews: Lynch Syndrome
    		Compare labs

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables SH3 domain binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 phosphoprotein phosphatase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein tyrosine phosphatase activity EXP
    Inferred from Experiment
    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 cellular response to epidermal growth factor stimulus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of ERBB signaling pathway TAS
    Traceable Author Statement
    more info
    		  
    involved_in negative regulation of platelet-derived growth factor receptor-beta signaling pathway TAS
    Traceable Author Statement
    more info
    		  
    involved_in peptidyl-tyrosine dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of epidermal growth factor receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of epidermal growth factor receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tissue regeneration IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in focal adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in podosome IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    tyrosine-protein phosphatase non-receptor type 12
    Names
    protein-tyrosine phosphatase G1
    NP_001124480.1
    NP_001124481.1
    NP_002826.3
    XP_006716136.1
    XP_016867963.1
    XP_047276629.1
    XP_047276630.1
    XP_047276631.1
    XP_047276632.1
    XP_047276633.1
    XP_054214705.1
    XP_054214706.1
    XP_054214707.1
    XP_054214708.1
    XP_054214709.1
    XP_054214710.1
    XP_054214711.1

    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_008394.1 RefSeqGene

      Range
      4840..107614
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001131008.2 → NP_001124480.1  tyrosine-protein phosphatase non-receptor type 12 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (2) has a shorter N-terminus with an incomplete PTPc domain when compared to isoform 1.
      Source sequence(s)
      AK303602, BC050008
      Consensus CDS
      CCDS47619.1
      UniProtKB/TrEMBL
      B4E105
      Related
      ENSP00000392429.2, ENST00000415482.6
      Conserved Domains (2) summary
      cd00047
      Location:1 → 173
      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 ...
      pfam00102
      Location:1 → 173
      Y_phosphatase; Protein-tyrosine phosphatase

    2. NM_001131009.2 → NP_001124481.1  tyrosine-protein phosphatase non-receptor type 12 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains a distinct 5' UTR, skips an internal exon, and lacks an in-frame portion of the 5' coding region, compared to variant 1. The resulting isoform (3) has a shorter N-terminus with an incomplete PTPc domain when compared to isoform 1.
      Source sequence(s)
      AK296764, AK303602, BC050008
      Consensus CDS
      CCDS47620.1
      UniProtKB/TrEMBL
      B4E105
      Related
      ENSP00000397991.2, ENST00000435495.6
      Conserved Domains (2) summary
      cd00047
      Location:1 → 162
      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 ...
      pfam00102
      Location:1 → 162
      Y_phosphatase; Protein-tyrosine phosphatase

    3. NM_002835.4 → NP_002826.3  tyrosine-protein phosphatase non-receptor type 12 isoform 1

      See identical proteins and their annotated locations for NP_002826.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB209524, AC006451, BC050008, CN395133
      Consensus CDS
      CCDS5592.1
      UniProtKB/Swiss-Prot
      A4D1C5, B4DKY2, E9PBR5, E9PEH9, Q05209, Q16130, Q59FD6, Q75MN8, Q86XU4
      Related
      ENSP00000248594.6, ENST00000248594.11
      Conserved Domains (2) summary
      smart00194
      Location:28 → 292
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:60 → 292
      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 ...

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      77537295..77640069
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006716073.5 → XP_006716136.1  tyrosine-protein phosphatase non-receptor type 12 isoform X3

      Conserved Domains (2) summary
      smart00194
      Location:28 → 260
      PTPc; Protein tyrosine phosphatase, catalytic domain
      cd00047
      Location:60 → 260
      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. XM_017012474.3 → XP_016867963.1  tyrosine-protein phosphatase non-receptor type 12 isoform X4

      UniProtKB/TrEMBL
      B4E105
      Conserved Domains (2) summary
      cd00047
      Location:11 → 177
      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 ...
      pfam00102
      Location:11 → 177
      Y_phosphatase; Protein-tyrosine phosphatase

    3. XM_047420673.1 → XP_047276629.1  tyrosine-protein phosphatase non-receptor type 12 isoform X1

    4. XM_047420674.1 → XP_047276630.1  tyrosine-protein phosphatase non-receptor type 12 isoform X2

    5. XM_047420675.1 → XP_047276631.1  tyrosine-protein phosphatase non-receptor type 12 isoform X4

    6. XM_047420676.1 → XP_047276632.1  tyrosine-protein phosphatase non-receptor type 12 isoform X5

    7. XM_047420677.1 → XP_047276633.1  tyrosine-protein phosphatase non-receptor type 12 isoform X6

    RNA

    1. XR_007060120.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      78789201..78891996
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358732.1 → XP_054214707.1  tyrosine-protein phosphatase non-receptor type 12 isoform X3

    2. XM_054358733.1 → XP_054214708.1  tyrosine-protein phosphatase non-receptor type 12 isoform X4

    3. XM_054358730.1 → XP_054214705.1  tyrosine-protein phosphatase non-receptor type 12 isoform X1

    4. XM_054358731.1 → XP_054214706.1  tyrosine-protein phosphatase non-receptor type 12 isoform X2

    5. XM_054358734.1 → XP_054214709.1  tyrosine-protein phosphatase non-receptor type 12 isoform X4

    6. XM_054358735.1 → XP_054214710.1  tyrosine-protein phosphatase non-receptor type 12 isoform X5

    7. XM_054358736.1 → XP_054214711.1  tyrosine-protein phosphatase non-receptor type 12 isoform X6

    RNA

    1. XR_008487716.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q05209.3 GenPept UniProtKB/Swiss-Prot:Q05209

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