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 ... See more...

Aliases for PTPN23 Gene

Aliases for PTPN23 Gene

  • Protein Tyrosine Phosphatase Non-Receptor Type 23 2 3 5
  • HD-PTP 2 3 4
  • His Domain-Containing Protein Tyrosine Phosphatase 3 4
  • Tyrosine-Protein Phosphatase Non-Receptor Type 23 3 4
  • Protein Tyrosine Phosphatase TD14 3 4
  • EC 3.1.3.48 4 50
  • PTP-TD14 3 4
  • KIAA1471 2 4
  • DKFZP564F0923 2
  • NEDBASS 3
  • PTPN23 5
  • HDPTP 3

External Ids for PTPN23 Gene

Previous GeneCards Identifiers for PTPN23 Gene

  • GC03P047211
  • GC03P046642
  • GC03P047383
  • GC03P047343

Summaries for PTPN23 Gene

Entrez Gene Summary for PTPN23 Gene

  • 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]

GeneCards Summary for PTPN23 Gene

PTPN23 (Protein Tyrosine Phosphatase Non-Receptor Type 23) is a Protein Coding gene. Diseases associated with PTPN23 include Neurodevelopmental Disorder And Structural Brain Anomalies With Or Without Seizures And Spasticity and Cerebral Degeneration. Among its related pathways are PAK Pathway. Gene Ontology (GO) annotations related to this gene include protein kinase binding and protein tyrosine phosphatase activity. An important paralog of this gene is PTPRS.

UniProtKB/Swiss-Prot Summary for PTPN23 Gene

  • Plays a role in sorting of endocytic ubiquitinated cargos into multivesicular bodies (MVBs) via its interaction with the ESCRT-I complex (endosomal sorting complex required for transport I), and possibly also other ESCRT complexes (PubMed:18434552, PubMed:21757351). May act as a negative regulator of Ras-mediated mitogenic activity (PubMed:18434552). Plays a role in ciliogenesis (PubMed:20393563).

Gene Wiki entry for PTPN23 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PTPN23 Gene

Genomics for PTPN23 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PTPN23 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTPN23 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTPN23

Top Transcription factor binding sites by QIAGEN in the PTPN23 gene promoter:
  • AML1a
  • C/EBPalpha
  • Chx10
  • GATA-2
  • HOXA9
  • HOXA9B
  • Meis-1
  • Meis-1b
  • POU3F1

Genomic Locations for PTPN23 Gene

Latest Assembly
chr3:47,381,001-47,413,435
(GRCh38/hg38)
Size:
32,435 bases
Orientation:
Plus strand

Previous Assembly
chr3:47,422,511-47,454,925
(GRCh37/hg19 by Entrez Gene)
Size:
32,415 bases
Orientation:
Plus strand

chr3:47,422,501-47,454,931
(GRCh37/hg19 by Ensembl)
Size:
32,431 bases
Orientation:
Plus strand

Genomic View for PTPN23 Gene

Genes around PTPN23 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTPN23 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTPN23 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTPN23 Gene

Proteins for PTPN23 Gene

  • Protein details for PTPN23 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H3S7-PTN23_HUMAN
    Recommended name:
    Tyrosine-protein phosphatase non-receptor type 23
    Protein Accession:
    Q9H3S7
    Secondary Accessions:
    • A8K0D7
    • Q7KZF8
    • Q8N6Z5
    • Q9BSR5
    • Q9P257
    • Q9UG03
    • Q9UMZ4

    Protein attributes for PTPN23 Gene

    Size:
    1636 amino acids
    Molecular mass:
    178974 Da
    Quaternary structure:
    • Interacts with GRAP2 and GRB2 (PubMed:21179510). Interacts with UBAP1 (PubMed:21757351, PubMed:27839950). Interacts with CHMP4B (PubMed:18434552).
    SequenceCaution:
    • Sequence=BAA95995.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PTPN23 Gene

neXtProt entry for PTPN23 Gene

Selected DME Specific Peptides for PTPN23 Gene

Q9H3S7:
  • PIIVHCS
  • PYDSNRV

Post-translational modifications for PTPN23 Gene

  • Ubiquitination at Lys32, Lys279, Lys285, Lys288, and Lys1635
  • Modification sites at PhosphoSitePlus

Other Protein References for PTPN23 Gene

Domains & Families for PTPN23 Gene

Gene Families for PTPN23 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for PTPN23 Gene

InterPro:
Blocks:
  • Protein tyrosine phosphatase signature
  • BRO1-like domain

Suggested Antigen Peptide Sequences for PTPN23 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ58078, highly similar to Tyrosine-protein phosphatase non-receptortype 23 (EC 3.1.3.48) (B4DST5_HUMAN)
  • Protein tyrosine phosphatase TD14 (PTN23_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9H3S7

UniProtKB/Swiss-Prot:

PTN23_HUMAN :
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily.
Family:
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class subfamily.
genes like me logo Genes that share domains with PTPN23: view

Function for PTPN23 Gene

Molecular function for PTPN23 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in sorting of endocytic ubiquitinated cargos into multivesicular bodies (MVBs) via its interaction with the ESCRT-I complex (endosomal sorting complex required for transport I), and possibly also other ESCRT complexes (PubMed:18434552, PubMed:21757351). May act as a negative regulator of Ras-mediated mitogenic activity (PubMed:18434552). Plays a role in ciliogenesis (PubMed:20393563).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + O-phospho-L-tyrosyl-[protein] = L-tyrosyl-[protein] + phosphate; Xref=Rhea:RHEA:10684, Rhea:RHEA-COMP:10136, Rhea:RHEA-COMP:10137, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474, ChEBI:CHEBI:46858, ChEBI:CHEBI:82620; EC=3.1.3.48; Evidence={ECO:0000255|PROSITE-ProRule:PRU10044};.

Enzyme Numbers (IUBMB) for PTPN23 Gene

Phenotypes From GWAS Catalog for PTPN23 Gene

Gene Ontology (GO) - Molecular Function for PTPN23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004725 protein tyrosine phosphatase activity IMP 21724833
GO:0005515 protein binding IPI 17174262
GO:0016787 hydrolase activity IEA --
GO:0016791 phosphatase activity IEA --
genes like me logo Genes that share ontologies with PTPN23: view
genes like me logo Genes that share phenotypes with PTPN23: view

Human Phenotype Ontology for PTPN23 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PTPN23 Gene

MGI Knock Outs for PTPN23:
  • Ptpn23 Ptpn23<tm1b(EUCOMM)Hmgu>

Animal Models for research

  • Taconic Biosciences Mouse Models for PTPN23

miRNA for PTPN23 Gene

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTPN23

No data available for Transcription Factor Targets and HOMER Transcription for PTPN23 Gene

Localization for PTPN23 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PTPN23 Gene

Nucleus. Cytoplasm. Cytoplasmic vesicle. Endosome. Cytoplasm, cytoskeleton, cilium basal body. Early endosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PTPN23 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
endosome 5
extracellular 4
cytosol 3
lysosome 2
plasma membrane 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1
peroxisome 0

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
  • Nucleoplasm (3)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PTPN23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 21179510
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 21179510
GO:0005768 endosome IEA,IDA 21179510
GO:0005769 early endosome IEA,IDA 21757351
genes like me logo Genes that share ontologies with PTPN23: view

Pathways & Interactions for PTPN23 Gene

PathCards logo

SuperPathways for PTPN23 Gene

SuperPathway Contained pathways
1 PAK Pathway
.36
genes like me logo Genes that share pathways with PTPN23: view

Pathways by source for PTPN23 Gene

1 Qiagen pathway for PTPN23 Gene
  • Epithelial Adherens Junctions

Gene Ontology (GO) - Biological Process for PTPN23 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA --
GO:0010633 negative regulation of epithelial cell migration IMP 21724833
GO:0015031 protein transport IEA --
GO:0016311 dephosphorylation IEA --
GO:0030030 cell projection organization IEA --
genes like me logo Genes that share ontologies with PTPN23: view

No data available for SIGNOR curated interactions for PTPN23 Gene

Drugs & Compounds for PTPN23 Gene

(2) Drugs for PTPN23 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Phosphate Experimental Pharma 0
genes like me logo Genes that share compounds with PTPN23: view

Transcripts for PTPN23 Gene

mRNA/cDNA for PTPN23 Gene

2 REFSEQ mRNAs :
17 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTPN23

Alternative Splicing Database (ASD) splice patterns (SP) for PTPN23 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21 ^
SP1: - -
SP2: -
SP3:
SP4:
SP5:

ExUns: 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27
SP1:
SP2:
SP3:
SP4:
SP5:

Relevant External Links for PTPN23 Gene

GeneLoc Exon Structure for
PTPN23

Expression for PTPN23 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PTPN23 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PTPN23 Gene

This gene is overexpressed in Lymph node (8.8) and Peripheral blood mononuclear cells (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PTPN23 Gene



Protein tissue co-expression partners for PTPN23 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTPN23

SOURCE GeneReport for Unigene cluster for PTPN23 Gene:

Hs.25524

Evidence on tissue expression from TISSUES for PTPN23 Gene

  • Nervous system(4.7)
  • Skin(4.4)
  • Liver(4.4)
  • Muscle(4.3)
genes like me logo Genes that share expression patterns with PTPN23: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTPN23 Gene

Orthologs for PTPN23 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PTPN23 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PTPN23 29 30
  • 98.82 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PTPN23 29 30
  • 86.99 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PTPN23 30
  • 86 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Ptpn23 29 16 30
  • 85.67 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ptpn23 29
  • 85.64 (n)
Oppossum
(Monodelphis domestica)
Mammalia PTPN23 30
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PTPN23 29 30
  • 80.13 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 30
  • 86 (a)
OneToMany
-- 30
  • 61 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ptpn23 29
  • 69.49 (n)
Zebrafish
(Danio rerio)
Actinopterygii ptpn23a 29 30
  • 65.98 (n)
OneToMany
ptpn23b 30
  • 49 (a)
OneToMany
Dr.13034 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG9311 31
  • 39 (a)
mop 30
  • 27 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea Y53H1C.2 31
  • 28 (a)
ego-2 30
  • 24 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RIM20 30
  • 21 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 37 (a)
OneToOne
Species where no ortholog for PTPN23 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PTPN23 Gene

ENSEMBL:
Gene Tree for PTPN23 (if available)
TreeFam:
Gene Tree for PTPN23 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PTPN23: view image
Alliance of Genome Resources:
Additional Orthologs for PTPN23

Paralogs for PTPN23 Gene

(7) SIMAP similar genes for PTPN23 Gene using alignment to 4 proteins:

  • PTN23_HUMAN
  • B4DST5_HUMAN
  • C9JD91_HUMAN
  • R4GMM7_HUMAN
genes like me logo Genes that share paralogs with PTPN23: view

Variants for PTPN23 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTPN23 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
1013474 Uncertain Significance: not provided 47,409,156(+) C/G
NM_015466.4(PTPN23):c.1643-7C>G
INTRON
843686 Uncertain Significance: not provided 47,407,334(+) C/T
NM_015466.4(PTPN23):c.890C>T (p.Ala297Val)
MISSENSE
870420 Uncertain Significance: PTPN23-related neurodevelopmental disorder 47,410,775(+) CCCCCACAATCC/TT
NM_015466.4(PTPN23):c.2977_2988delinsTT (p.Pro993fs)
FRAMESHIFT
872546 Uncertain Significance: not provided 47,410,373(+) G/C
NM_015466.4(PTPN23):c.2575G>C (p.Gly859Arg)
MISSENSE
872547 Uncertain Significance: not provided 47,410,835(+) C/T
NM_015466.4(PTPN23):c.3037C>T (p.Pro1013Ser)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PTPN23 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PTPN23 Gene

Variant ID Type Subtype PubMed ID
nsv3802 CNV deletion 18451855
nsv3803 CNV insertion 18451855
nsv3804 CNV insertion 18451855
nsv428417 CNV loss 18775914
nsv479512 CNV novel sequence insertion 20440878
nsv480723 CNV novel sequence insertion 20440878
nsv954480 CNV deletion 24416366

Variation tolerance for PTPN23 Gene

Residual Variation Intolerance Score: 2.81% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.37; 76.95% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTPN23 Gene

Human Gene Mutation Database (HGMD)
PTPN23
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTPN23
Leiden Open Variation Database (LOVD)
PTPN23

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTPN23 Gene

Disorders for PTPN23 Gene

MalaCards: The human disease database

(3) MalaCards diseases for PTPN23 Gene - From: OMI, CVR, GTR, COP, and GCD

- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PTPN23

genes like me logo Genes that share disorders with PTPN23: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PTPN23 Gene

Publications for PTPN23 Gene

  1. HD-PTP: A novel protein tyrosine phosphatase gene on human chromosome 3p21.3. (PMID: 11095967) Toyooka S … Shimizu K (Biochemical and biophysical research communications 2000) 2 3 4 22
  2. Structural Basis for Selective Interaction between the ESCRT Regulator HD-PTP and UBAP1. (PMID: 27839950) Gahloth D … Tabernero L (Structure (London, England : 1993) 2016) 3 4
  3. UBAP1 is a component of an endosome-specific ESCRT-I complex that is essential for MVB sorting. (PMID: 21757351) Stefani F … Woodman P (Current biology : CB 2011) 3 4
  4. Functional genomic screen for modulators of ciliogenesis and cilium length. (PMID: 20393563) Kim J … Gleeson JG (Nature 2010) 3 4
  5. Histidine domain-protein tyrosine phosphatase interacts with Grb2 and GrpL. (PMID: 21179510) Tanase CA (PloS one 2010) 3 4

Products for PTPN23 Gene

Sources for PTPN23 Gene