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

Gene ID: 5782, updated on 11-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (77537295..77640069)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (78789201..78891996)
105.20220307 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. Protein tyrosine phosphatase non-receptor type 12 suppresses tumor progression in osteosarcoma cells. Wang X, et al. J Orthop Sci, 2023 Mar. PMID 35063332
  2. PTP-PEST Regulated Membranous/Cytoplasmic Translocation of p120ctn in the Lung Cancer Resistance to Tyrosine Kinase Inhibitor. Liu WW, et al. Appl Immunohistochem Mol Morphol, 2022 Mar 1. PMID 35030104
  3. The protein tyrosine phosphatase PTP-PEST mediates hypoxia-induced endothelial autophagy and angiogenesis via AMPK activation. Chandel S, et al. J Cell Sci, 2021 Jan 11. PMID 33323505
  4. Expression and clinical significance of PTPN12 in clear cell renal cell carcinoma. Jin Y, et al. J Int Med Res, 2020 Dec. PMID 33292053, Free PMC Article
  5. Progress in the correlation between PTPN12 gene expression and human tumors. Huo YH, et al. Medicine (Baltimore), 2020 Jun 12. PMID 32541467, Free PMC Article

See all (134) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. tumor suppressing gene [review]
    Title: Progress in the correlation between PTPN12 gene expression and human tumors.
  8. 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.
  9. 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.
  10. PTPN12 rs3750050 could impair the inhibitory effect of PTPN12 on Ras/MEK/ERK signaling by impeding SHC dephosphorylation, increase the expression of cyclin D1 and ultimately lead to aberrant cell proliferation, thus contributing to colorectal cancer pathogenesis.
    Title: A missense variant in PTPN12 associated with the risk of colorectal cancer by modifying Ras/MEK/ERK signaling.
Submit: New GeneRIF Correction See all GeneRIFs (42)

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)

Genotypes

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 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
  
Process Evidence Code Pubs
involved_in cellular response to epidermal growth factor stimulus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein dephosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
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_2023_10

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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