The protein encoded by this gene contains a characteristic motif of protein tyrosine phosphatases (PTPs). PTPs regulate activities of phosphoproteins through dephosphorylation. They are signaling molecules involved in the regulation of a wide variety of biological processes. The specific function of this protein has not yet been determined. Alternatively spliced transcript vari... See more...

Aliases for PTPDC1 Gene

Aliases for PTPDC1 Gene

  • Protein Tyrosine Phosphatase Domain Containing 1 2 3 5
  • PTP9Q22 2 3 4
  • Protein Tyrosine Phosphatase Domain-Containing Protein 1 3 4
  • Protein Tyrosine Phosphatase PTP9Q22 2 3
  • EC 3.1.3.67 51
  • EC 3.1.3.- 4
  • FLJ37312 2
  • EC 3.1.3 51
  • PTPDC1 5

External Ids for PTPDC1 Gene

Previous GeneCards Identifiers for PTPDC1 Gene

  • GC09P092135
  • GC09P093872
  • GC09P095832
  • GC09P096793
  • GC09P066469

Summaries for PTPDC1 Gene

Entrez Gene Summary for PTPDC1 Gene

  • The protein encoded by this gene contains a characteristic motif of protein tyrosine phosphatases (PTPs). PTPs regulate activities of phosphoproteins through dephosphorylation. They are signaling molecules involved in the regulation of a wide variety of biological processes. The specific function of this protein has not yet been determined. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]

GeneCards Summary for PTPDC1 Gene

PTPDC1 (Protein Tyrosine Phosphatase Domain Containing 1) is a Protein Coding gene. Among its related pathways are PAK Pathway. Gene Ontology (GO) annotations related to this gene include phosphatase activity and protein tyrosine/serine/threonine phosphatase activity. An important paralog of this gene is CDC14A.

UniProtKB/Swiss-Prot Summary for PTPDC1 Gene

Additional gene information for PTPDC1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PTPDC1 Gene

Genomics for PTPDC1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PTPDC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH09J094029 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 608.1 +2.0 1976 2.8 SP1 CREB1 GATAD2A HNRNPL PRDM10 ZNF629 TFE3 LEF1 ZNF692 POLR2A PTPDC1 HSALNG0072877 PHF2 ENSG00000232063 BARX1 CYCSP24 LOC107987099
GH09J093954 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 604.5 -73.4 -73432 2 ZNF629 EZH2 ZNF341 KLF9 ZBTB20 SP2 ZEB1 POLR2A ZBTB17 WT1 BARX1-DT PTPDC1 BARX1 HSALNG0072874
GH09J094083 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 605.2 +55.9 55933 2.1 PRDM10 RFX1 JUND PRDM1 ZIC2 POLR2A FOXJ2 ZBTB44 RFX3 GTF2E2 PTPDC1 MIRLET7D MIRLET7A1 MIRLET7F1 piR-55361-579 piR-57133-625 LOC107987099
GH09J094037 Promoter 0.3 EPDnew 600.4 +8.9 8914 0.1 CYCSP24 lnc-ZNF169-3 PTPDC1 HSALNG0072877 LOC107987099
GH09J093949 Promoter/Enhancer 1.2 Ensembl ENCODE dbSUPER 8 -78.5 -78522 2.6 IKZF1 JUND ZNF24 EZH2 GABPA HMBOX1 EGR1 ZNF444 JUN ESRRA PTPDC1 BARX1-DT BARX1 HSALNG0072868 PHF2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PTPDC1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PTPDC1

Top Transcription factor binding sites by QIAGEN in the PTPDC1 gene promoter:
  • COMP1
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4
  • NF-kappaB1
  • POU2F1
  • RelA
  • XBP-1

Genomic Locations for PTPDC1 Gene

Genomic Locations for PTPDC1 Gene
chr9:94,029,031-94,109,856
(GRCh38/hg38)
Size:
80,826 bases
Orientation:
Plus strand
chr9:96,793,076-96,872,138
(GRCh37/hg19)
Size:
79,063 bases
Orientation:
Plus strand

Genomic View for PTPDC1 Gene

Genes around PTPDC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PTPDC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PTPDC1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PTPDC1 Gene

Proteins for PTPDC1 Gene

  • Protein details for PTPDC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A2A3K4-PTPC1_HUMAN
    Recommended name:
    Protein tyrosine phosphatase domain-containing protein 1
    Protein Accession:
    A2A3K4
    Secondary Accessions:
    • Q5T3M4
    • Q6NXE8
    • Q8IWM1
    • Q8N1X4
    • Q8N9F5

    Protein attributes for PTPDC1 Gene

    Size:
    754 amino acids
    Molecular mass:
    84457 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC04391.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAC04421.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PTPDC1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PTPDC1 Gene

Selected DME Specific Peptides for PTPDC1 Gene

A2A3K4:
  • EQLKEPVITK
  • FVRAKRPNSIQTRGQLLCVREF
  • KYTKVGE
  • RQRHLLHGYEAR
  • TDNILAM

Post-translational modifications for PTPDC1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for PTPDC1 Gene

Gene Families for PTPDC1 Gene

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

Suggested Antigen Peptide Sequences for PTPDC1 Gene

GenScript: Design optimal peptide antigens:
  • Protein tyrosine phosphatase domain-containing protein 1 (PTPC1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A2A3K4

UniProtKB/Swiss-Prot:

PTPC1_HUMAN :
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class PTPDC1 subfamily.
Family:
  • Belongs to the protein-tyrosine phosphatase family. Non-receptor class PTPDC1 subfamily.
genes like me logo Genes that share domains with PTPDC1: view

Function for PTPDC1 Gene

Molecular function for PTPDC1 Gene

UniProtKB/Swiss-Prot Function:
May play roles in cilia formation and/or maintenance.

Enzyme Numbers (IUBMB) for PTPDC1 Gene

Phenotypes From GWAS Catalog for PTPDC1 Gene

Gene Ontology (GO) - Molecular Function for PTPDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004725 protein tyrosine phosphatase activity IEA,IBA 21873635
GO:0008138 protein tyrosine/serine/threonine phosphatase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0016791 phosphatase activity IEA --
genes like me logo Genes that share ontologies with PTPDC1: view
genes like me logo Genes that share phenotypes with PTPDC1: view

Animal Models for PTPDC1 Gene

MGI Knock Outs for PTPDC1:

Animal Model Products

  • Taconic Biosciences Mouse Models for PTPDC1

CRISPR Products

miRNA for PTPDC1 Gene

miRTarBase miRNAs that target PTPDC1

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTPDC1

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PTPDC1 Gene

Localization for PTPDC1 Gene

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 PTPDC1 gene
Compartment Confidence
nucleus 5
mitochondrion 2
cytoskeleton 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PTPDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IBA 21873635
genes like me logo Genes that share ontologies with PTPDC1: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PTPDC1 Gene

Pathways & Interactions for PTPDC1 Gene

PathCards logo

SuperPathways for PTPDC1 Gene

SuperPathway Contained pathways
1 PAK Pathway
.36
genes like me logo Genes that share pathways with PTPDC1: view

Pathways by source for PTPDC1 Gene

1 Qiagen pathway for PTPDC1 Gene
  • Epithelial Adherens Junctions

Gene Ontology (GO) - Biological Process for PTPDC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA --
GO:0007224 smoothened signaling pathway IEA --
GO:0016311 dephosphorylation IEA --
GO:0030030 cell projection organization IEA --
GO:0035335 peptidyl-tyrosine dephosphorylation IEA --
genes like me logo Genes that share ontologies with PTPDC1: view

No data available for SIGNOR curated interactions for PTPDC1 Gene

Drugs & Compounds for PTPDC1 Gene

(2) Drugs for PTPDC1 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0

(1) Additional Compounds for PTPDC1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
14066-19-4, 14265-44-2
genes like me logo Genes that share compounds with PTPDC1: view

Transcripts for PTPDC1 Gene

mRNA/cDNA for PTPDC1 Gene

4 REFSEQ mRNAs :
14 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PTPDC1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PTPDC1 Gene

No ASD Table

Relevant External Links for PTPDC1 Gene

GeneLoc Exon Structure for
PTPDC1

Expression for PTPDC1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PTPDC1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

mRNA differential expression in normal tissues according to GTEx for PTPDC1 Gene

This gene is overexpressed in Nerve - Tibial (x4.3).

Protein differential expression in normal tissues from HIPED for PTPDC1 Gene

This gene is overexpressed in Heart (52.3) and Testis (11.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PTPDC1 Gene



Protein tissue co-expression partners for PTPDC1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PTPDC1

SOURCE GeneReport for Unigene cluster for PTPDC1 Gene:

Hs.437943

Evidence on tissue expression from TISSUES for PTPDC1 Gene

  • Nervous system(4.6)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with PTPDC1: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PTPDC1 Gene

Orthologs for PTPDC1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PTPDC1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PTPDC1 30 31
  • 99.5 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PTPDC1 30 31
  • 84.59 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Ptpdc1 30 17 31
  • 82.45 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PTPDC1 30 31
  • 82.25 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ptpdc1 30
  • 81.26 (n)
Oppossum
(Monodelphis domestica)
Mammalia PTPDC1 31
  • 74 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PTPDC1 31
  • 72 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PTPDC1 30 31
  • 69.42 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PTPDC1 31
  • 59 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia LOC100490857 30
  • 62.72 (n)
Zebrafish
(Danio rerio)
Actinopterygii ptpdc1 30 31
  • 58.21 (n)
OneToMany
PTPDC1 (2 of 3) 31
  • 48 (a)
OneToMany
PTPDC1 (1 of 3) 31
  • 34 (a)
OneToMany
Dr.12870 30
Worm
(Caenorhabditis elegans)
Secernentea T12B3.1 31
  • 28 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 62 (a)
OneToOne
Species where no ortholog for PTPDC1 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)
  • Baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • 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)
  • 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 PTPDC1 Gene

ENSEMBL:
Gene Tree for PTPDC1 (if available)
TreeFam:
Gene Tree for PTPDC1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PTPDC1: view image

Paralogs for PTPDC1 Gene

Paralogs for PTPDC1 Gene

genes like me logo Genes that share paralogs with PTPDC1: view

Variants for PTPDC1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PTPDC1 Gene

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs16909677 - p.Leu571Gln

Additional dbSNP identifiers (rs#s) for PTPDC1 Gene

Structural Variations from Database of Genomic Variants (DGV) for PTPDC1 Gene

Variant ID Type Subtype PubMed ID
esv2761543 CNV gain 21179565
esv3621110 CNV gain 21293372
esv3621111 CNV gain 21293372
nsv476461 CNV novel sequence insertion 20440878
nsv507521 OTHER sequence alteration 20534489
nsv831655 CNV gain 17160897
nsv982322 CNV duplication 23825009

Variation tolerance for PTPDC1 Gene

Residual Variation Intolerance Score: 76.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.76; 47.02% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PTPDC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PTPDC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PTPDC1 Gene

Disorders for PTPDC1 Gene

No disorders were found for PTPDC1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PTPDC1 Gene

Publications for PTPDC1 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 2 3 4
  2. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  3. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. (PMID: 28611215) Fei T … Brown M (Proceedings of the National Academy of Sciences of the United States of America 2017) 3
  4. A Human Tyrosine Phosphatase Interactome Mapped by Proteomic Profiling. (PMID: 28675297) Kumar P … Maddika S (Journal of proteome research 2017) 3
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3

Products for PTPDC1 Gene

  • Signalway ELISA kits for PTPDC1

Sources for PTPDC1 Gene