U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from MedGen

    • Showing Current items.

    PTPN23 protein tyrosine phosphatase non-receptor type 23 [ Homo sapiens (human) ]

    Gene ID: 25930, updated on 7-Jan-2024

    Summary

    Official Symbol
    PTPN23provided by HGNC
    Official Full Name
    protein tyrosine phosphatase non-receptor type 23provided by HGNC
    Primary source
    HGNC:HGNC:14406
    See related
    Ensembl:ENSG00000076201 MIM:606584; AllianceGenome:HGNC:14406
    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
    HDPTP; HD-PTP; NEDBASS; PTP-TD14
    Summary
    This gene encodes a member of the non-receptor type protein-tyrosine phosphatase family. The encoded protein may be involved in the regulation of small nuclear ribonucleo protein assembly and pre-mRNA splicing by modifying the survival motor neuron (SMN) complex. The encoded protein additionally plays a role in ciliogenesis and is part of endosomal sorting complex required for transport (ESCRT) pathways. This gene may serve a tumor suppressor function. [provided by RefSeq, Jul 2016]
    Expression
    Ubiquitous expression in spleen (RPKM 10.2), brain (RPKM 9.8) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PTPN23 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (47381021..47413435)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (47397442..47429855)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (47422511..47454925)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene kinesin family member 9 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:47301362-47302268 Neighboring gene small nucleolar RNA, C/D box 13 pseudogene 3 Neighboring gene small nucleolar RNA, C/D box 13J Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:47323613-47324812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19812 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14308 Neighboring gene kelch like family member 18 Neighboring gene Sharpr-MPRA regulatory region 13740 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:47403837-47405036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:47421897-47422574 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:47422575-47423250 Neighboring gene PTPN23 divergent transcript Neighboring gene ReSE screen-validated silencer GRCh37_chr3:47440022-47440203 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47446437-47446936 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47447130-47447995 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47457269-47457770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:47457771-47458270 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19815 Neighboring gene SREBF chaperone Neighboring gene small nucleolar RNA U13 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:47508426-47508527 Neighboring gene SPMIP3 pseudogene 1

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag The isolated Bro1 domains of HD-PTP and rhophilin both bind to HIV-1 NC and share the capacity to stimulate VLP production by a minimal HIV-1 Gag molecule PubMed
    Tat tat HIV-1 Tat upregulates the tyrosine phosphatase HD-PTP mRNA in a human endothelial cell line, however Tat-induction of HD-PTP mRNA parallels only with a slight increase of the protein PubMed
    nucleocapsid gag The isolated Bro1 domains of HD-PTP and rhophilin both bind to HIV-1 NC and share the capacity to stimulate VLP production by a minimal HIV-1 Gag molecule PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA1471, DKFZp564F0923

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein tyrosine phosphatase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in early endosome to late endosome transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in early endosome to late endosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endocytic recycling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of epithelial cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of Wnt protein secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of adherens junction organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of early endosome to late endosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of homophilic cell adhesion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    tyrosine-protein phosphatase non-receptor type 23
    Names
    his domain-containing protein tyrosine phosphatase
    protein tyrosine phosphatase TD14
    NP_001291411.1
    NP_056281.1
    XP_005265088.2
    XP_054202077.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_051056.1 RefSeqGene

      Range
      5040..37454
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001304482.2NP_001291411.1  tyrosine-protein phosphatase non-receptor type 23 isoform 2

      See identical proteins and their annotated locations for NP_001291411.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in its 5' UTR and uses a downstream start codon compared to variant 1. It encodes isoform 2 which has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AF290614, AK299906, BU173747
      UniProtKB/TrEMBL
      B4DST5
      Conserved Domains (5) summary
      cd09234
      Location:236574
      V_HD-PTP_like; Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
      cd00047
      Location:10941323
      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:10941324
      Y_phosphatase; Protein-tyrosine phosphatase
      pfam13949
      Location:291575
      ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV
      cl14649
      Location:1231
      BRO1_Alix_like; Protein-interacting Bro1-like domain of mammalian Alix and related domains
    2. NM_015466.4NP_056281.1  tyrosine-protein phosphatase non-receptor type 23 isoform 1

      See identical proteins and their annotated locations for NP_056281.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB040904, AF290614, BU173747
      Consensus CDS
      CCDS2754.1
      UniProtKB/Swiss-Prot
      A8K0D7, Q7KZF8, Q8N6Z5, Q9BSR5, Q9H3S7, Q9P257, Q9UG03, Q9UMZ4
      Related
      ENSP00000265562.4, ENST00000265562.5
      Conserved Domains (5) summary
      cd09234
      Location:362700
      V_HD-PTP_like; Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
      cd09239
      Location:2357
      BRO1_HD-PTP_like; Protein-interacting, N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
      cd00047
      Location:12201449
      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:12201450
      Y_phosphatase; Protein-tyrosine phosphatase
      pfam13949
      Location:417701
      ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      47381021..47413435
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005265031.3XP_005265088.2  tyrosine-protein phosphatase non-receptor type 23 isoform X1

      Conserved Domains (5) summary
      cd09234
      Location:352690
      V_HD-PTP_like; Protein-interacting V-domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
      cd09239
      Location:2347
      BRO1_HD-PTP_like; Protein-interacting, N-terminal, Bro1-like domain of mammalian His-Domain type N23 protein tyrosine phosphatase and related domains
      cd00047
      Location:12101439
      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:12101440
      Y_phosphatase; Protein-tyrosine phosphatase
      pfam13949
      Location:407691
      ALIX_LYPXL_bnd; ALIX V-shaped domain binding to HIV

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      47397442..47429855
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346102.1XP_054202077.1  tyrosine-protein phosphatase non-receptor type 23 isoform X1