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Aliases for PDCD1 Gene

Aliases for PDCD1 Gene

  • Programmed Cell Death 1 2 3 5
  • Systemic Lupus Erythematosus Susceptibility 2 2 3
  • Protein PD-1 3 4
  • HPD-1 3 4
  • PD1 3 4
  • Programmed Cell Death 1 Protein 3
  • Programmed Cell Death Protein 1 3
  • CD279 Antigen 4
  • CD279 3
  • HPD-L 3
  • HSLE1 3
  • SLEB2 3
  • PD-1 3

External Ids for PDCD1 Gene

Previous HGNC Symbols for PDCD1 Gene

  • SLEB2

Previous GeneCards Identifiers for PDCD1 Gene

  • GC02U990074
  • GC02P241575
  • GC02P9D0113
  • GC02M242440
  • GC02M242792
  • GC02M234541

Summaries for PDCD1 Gene

Entrez Gene Summary for PDCD1 Gene

  • This gene encodes a cell surface membrane protein of the immunoglobulin superfamily. This protein is expressed in pro-B-cells and is thought to play a role in their differentiation. In mice, expression of this gene is induced in the thymus when anti-CD3 antibodies are injected and large numbers of thymocytes undergo apoptosis. Mice deficient for this gene bred on a BALB/c background developed dilated cardiomyopathy and died from congestive heart failure. These studies suggest that this gene product may also be important in T cell function and contribute to the prevention of autoimmune diseases. [provided by RefSeq, Jul 2008]

GeneCards Summary for PDCD1 Gene

PDCD1 (Programmed Cell Death 1) is a Protein Coding gene. Diseases associated with PDCD1 include Systemic Lupus Erythematosus 2 and Multiple Sclerosis, Disease Progression, Modifier Of. Among its related pathways are Innate Immune System and CD28 co-stimulation. GO annotations related to this gene include signal transducer activity.

UniProtKB/Swiss-Prot for PDCD1 Gene

  • Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.

Gene Wiki entry for PDCD1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDCD1 Gene

Genomics for PDCD1 Gene

Regulatory Elements for PDCD1 Gene

Enhancers for PDCD1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02G241863 1 FANTOM5 dbSUPER 3.7 -4.9 -4889 0.1 MTA2 BHLHE40 BACH1 MAX GATAD2B EBF1 DPF2 EP300 RELA ARID3A ENSG00000234793 D2HGDH NEU4 ENSG00000215023 PDCD1 GAL3ST2 ATG4B ING5 RTP5
GH02G241762 1.2 FANTOM5 ENCODE 2 +95.6 95642 2.1 PKNOX1 NFIB ZNF207 RCOR1 RELB IKZF2 JUNB GATAD2B TBX21 ZNF217 D2HGDH GAL3ST2 ENSG00000224272 ATG4B PDCD1 PIR37451 LOC105373976
GH02G241759 0.7 FANTOM5 2.5 +99.7 99669 0.2 PKNOX1 GATA3 RAD51 CREB1 CUX1 EMSY MAFK D2HGDH PDCD1 ATG4B THAP4 ENSG00000234793 PIR37451
GH02G241858 1.4 Ensembl ENCODE dbSUPER 0.7 -0.8 -836 3.1 HDGF TBP PKNOX1 TBL1XR1 ZNF473 ZNF48 GLIS2 EGR1 HSF1 ZNF207 ENSG00000224272 NEU4 ENSG00000234793 D2HGDH ENSG00000215023 LOC285095 LINC01237 ENSG00000235151 PDCD1 RTP5
GH02G241864 1 ENCODE dbSUPER 0.7 -4.8 -4756 0.1 MTA2 BHLHE40 BACH1 MAX GATAD2B EBF1 DPF2 EP300 RELA POLR2A ENSG00000234793 D2HGDH NEU4 ENSG00000215023 RTP5 PDCD1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDCD1 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the PDCD1 gene promoter:

Genomic Location for PDCD1 Gene

Chromosome:
2
Start:
241,849,881 bp from pter
End:
241,858,908 bp from pter
Size:
9,028 bases
Orientation:
Minus strand

Genomic View for PDCD1 Gene

Genes around PDCD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDCD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDCD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDCD1 Gene

Proteins for PDCD1 Gene

  • Protein details for PDCD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15116-PDCD1_HUMAN
    Recommended name:
    Programmed cell death protein 1
    Protein Accession:
    Q15116
    Secondary Accessions:
    • O00517
    • Q8IX89

    Protein attributes for PDCD1 Gene

    Size:
    288 amino acids
    Molecular mass:
    31647 Da
    Quaternary structure:
    • Monomer.

    Three dimensional structures from OCA and Proteopedia for PDCD1 Gene

neXtProt entry for PDCD1 Gene

Post-translational modifications for PDCD1 Gene

  • Glycosylation at posLast=4949, Asn58, posLast=7474, and Asn116
  • Modification sites at PhosphoSitePlus

Other Protein References for PDCD1 Gene

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PDCD1 (PDCD1)
  • Cloud-Clone Corp. Antibodies for PDCD1

Assay Products

  • Cloud-Clone Corp Assay Kits for PDCD1

No data available for DME Specific Peptides for PDCD1 Gene

Domains & Families for PDCD1 Gene

Gene Families for PDCD1 Gene

Protein Domains for PDCD1 Gene

Suggested Antigen Peptide Sequences for PDCD1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PDCD1: view

No data available for UniProtKB/Swiss-Prot for PDCD1 Gene

Function for PDCD1 Gene

Molecular function for PDCD1 Gene

GENATLAS Biochemistry:
programmed cell death (apoptosis) 1,mouse PD1 homolog
UniProtKB/Swiss-Prot Function:
Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.

Gene Ontology (GO) - Molecular Function for PDCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004871 signal transducer activity TAS 1396582
GO:0005515 protein binding IPI 17489864
genes like me logo Genes that share ontologies with PDCD1: view
genes like me logo Genes that share phenotypes with PDCD1: view

Animal Models for PDCD1 Gene

MGI Knock Outs for PDCD1:

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDCD1 Gene

Localization for PDCD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDCD1 Gene

Membrane; Single-pass type I membrane protein.

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 PDCD1 gene
Compartment Confidence
plasma membrane 5
extracellular 2
cytosol 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for PDCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0009897 external side of plasma membrane IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PDCD1: view

Pathways & Interactions for PDCD1 Gene

genes like me logo Genes that share pathways with PDCD1: view

SIGNOR curated interactions for PDCD1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for PDCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002644 negative regulation of tolerance induction IEA --
GO:0006915 apoptotic process TAS,IEA --
GO:0006959 humoral immune response TAS 9332365
GO:0007165 signal transduction IEA --
GO:0007275 multicellular organism development TAS 9332365
genes like me logo Genes that share ontologies with PDCD1: view

Drugs & Compounds for PDCD1 Gene

(11) Drugs for PDCD1 Gene - From: DrugBank, DGIdb, FDA Approved Drugs, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
nivolumab Approved Pharma antibody, immunotherapy, inhibitor, Target Therapeutic Antibodies, Immunotherapies 424
Pembrolizumab Approved Pharma Target, antagonist, antibody 507
Keytruda Approved September 2014 Pharma 0
Opdivo Approved March 2015/ Approved December 2014 Pharma 0
CT-011 Investigational Pharma Antibody, Target 0

(1) Additional Compounds for PDCD1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PDCD1: view

Transcripts for PDCD1 Gene

mRNA/cDNA for PDCD1 Gene

(3) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(9) Selected AceView cDNA sequences:
(3) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PDCD1 Gene

Programmed cell death 1:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDCD1 Gene

No ASD Table

Relevant External Links for PDCD1 Gene

GeneLoc Exon Structure for
PDCD1
ECgene alternative splicing isoforms for
PDCD1

Expression for PDCD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDCD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDCD1 Gene

This gene is overexpressed in Whole Blood (x6.8), Heart - Atrial Appendage (x5.4), and Spleen (x5.3).

Protein differential expression in normal tissues from HIPED for PDCD1 Gene

This gene is overexpressed in Vitreous humor (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PDCD1 Gene



Protein tissue co-expression partners for PDCD1 Gene

NURSA nuclear receptor signaling pathways regulating expression of PDCD1 Gene:

PDCD1

SOURCE GeneReport for Unigene cluster for PDCD1 Gene:

Hs.158297

Evidence on tissue expression from TISSUES for PDCD1 Gene

  • Blood(2.7)
  • Lymph node(2.6)
  • Intestine(2.5)
  • Spleen(2)
genes like me logo Genes that share expression patterns with PDCD1: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDCD1 Gene

Orthologs for PDCD1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDCD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDCD1 34
  • 98.37 (n)
dog
(Canis familiaris)
Mammalia PDCD1 34 35
  • 75.53 (n)
cow
(Bos Taurus)
Mammalia PDCD1 34 35
  • 75 (n)
rat
(Rattus norvegicus)
Mammalia LOC102550808 34
  • 70.57 (n)
mouse
(Mus musculus)
Mammalia Pdcd1 34 16 35
  • 70.16 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PDCD1 35
  • 30 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDCD1 35
  • 18 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDCD1 34 35
  • 50.78 (n)
Species where no ortholog for PDCD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • lizard (Anolis carolinensis)
  • 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 squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PDCD1 Gene

ENSEMBL:
Gene Tree for PDCD1 (if available)
TreeFam:
Gene Tree for PDCD1 (if available)

Paralogs for PDCD1 Gene

(1) SIMAP similar genes for PDCD1 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with PDCD1: view

No data available for Paralogs for PDCD1 Gene

Variants for PDCD1 Gene

Sequence variations from dbSNP and Humsavar for PDCD1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs11568821 other 241,851,760(-) CCTGC(A/C/G)GTCTC intron-variant, downstream-variant-500B, upstream-variant-2KB
rs1000249974 -- 241,852,874(+) AAGCT(C/T)TCCGA upstream-variant-2KB, reference, synonymous-codon
rs1000309869 -- 241,857,398(+) ATCTT(G/T)CCCGC intron-variant
rs1000350301 -- 241,857,216(+) GCGGC(C/T)GGGGT intron-variant
rs1000554864 -- 241,856,991(+) GTGGC(A/G)GCGCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDCD1 Gene

Variant ID Type Subtype PubMed ID
dgv165e55 CNV loss 17911159
dgv4200n100 CNV loss 25217958
dgv4201n100 CNV gain 25217958
esv3893582 CNV gain 25118596
nsv1002941 CNV gain 25217958
nsv470533 CNV loss 18288195
nsv584991 CNV loss 21841781
nsv821942 CNV gain 20364138
nsv955302 CNV deletion 24416366
nsv997984 CNV gain 25217958
nsv998059 CNV loss 25217958

Variation tolerance for PDCD1 Gene

Residual Variation Intolerance Score: 55.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.80; 73.69% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDCD1 Gene

Human Gene Mutation Database (HGMD)
PDCD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDCD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDCD1 Gene

Disorders for PDCD1 Gene

MalaCards: The human disease database

(10) MalaCards diseases for PDCD1 Gene - From: OMIM, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PDCD1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PDCD1_HUMAN
  • Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. {ECO:0000269 PubMed:12402038}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Relevant External Links for PDCD1

Genetic Association Database (GAD)
PDCD1
Human Genome Epidemiology (HuGE) Navigator
PDCD1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDCD1
genes like me logo Genes that share disorders with PDCD1: view

No data available for Genatlas for PDCD1 Gene

Publications for PDCD1 Gene

  1. A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans. (PMID: 12402038) Prokunina L. … Alarcon-Riquelme M.E. (Nat. Genet. 2002) 2 3 4 22 46 64
  2. Programmed death-1 (PD-1) gene polymorphisms lodged in the genetic predispositions of Kawasaki Disease. (PMID: 19468750) Chun J.K. … Kim D.S. (Eur. J. Pediatr. 2010) 3 22 46 64
  3. Genetic, immunologic, and immunohistochemical analysis of the programmed death 1/programmed death ligand 1 pathway in human systemic lupus erythematosus. (PMID: 19116915) Bertsias G.K. … Boumpas D.T. (Arthritis Rheum. 2009) 3 22 46 64
  4. Association between the PD1.3A/G polymorphism of the PDCD1 gene and systemic lupus erythematosus in European populations: a meta-analysis. (PMID: 19220647) Liu J.L. … Zhang X.J. (J Eur Acad Dermatol Venereol 2009) 3 22 46 64
  5. PDCD1, CTLA-4 and p53 gene polymorphism and susceptibility to gestational trophoblastic diseases. (PMID: 19263877) Dehaghani A.S. … Ghaderi A. (J Reprod Med 2009) 3 22 46 64

Products for PDCD1 Gene

Sources for PDCD1 Gene

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