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PDCD1 Gene(Protein Coding)

Programmed Cell Death 1

GCID:
GC02M241849
GIFtS:
55
Genes Participants
UDN Logo

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. Among its related pathways are T-Cell Receptor and Co-stimulatory Signaling and Innate Immune System. Gene Ontology (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

Additional gene information 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

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for PDCD1 Gene

Promoters and enhancers for PDCD1 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
GH02I241858 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 550.8 -0.8 -836 3.1 HDGF PKNOX1 ZNF473 BATF KLF5 IRF4 ZNF48 GLIS2 EGR1 HSF1 PDCD1 ENSG00000224272 D2HGDH NEU4 ENSG00000234793 ENSG00000215023 ATG4B LOC285095 LINC01237 ENSG00000235151
GH02I241863 Enhancer 0.8 FANTOM5 dbSUPER 3.7 -4.9 -4888 0.1 ZNF687 BACH1 MAX EBF1 DPF2 RELA IKZF1 NFATC1 ZNF143 RUNX3 ENSG00000234793 D2HGDH NEU4 ENSG00000215023 PDCD1 GAL3ST2 ATG4B ING5 RTP5
GH02I241762 Enhancer 1 FANTOM5 ENCODE 2 +95.6 95642 2.1 PKNOX1 NFIB ZNF207 ATF7 RCOR1 IKZF2 RUNX3 JUNB ELF1 ZNF217 PIR37451 D2HGDH GAL3ST2 ENSG00000224272 ATG4B PDCD1 LOC105373976 GC02P241747
GH02I241759 Enhancer 0.6 FANTOM5 2.5 +99.7 99668 0.2 PKNOX1 GATA3 CREB1 CUX1 MAFK EMSY D2HGDH PDCD1 ATG4B THAP4 ENSG00000234793 PIR37451 GC02P241747
GH02I241864 Enhancer 0.8 ENCODE dbSUPER 0.8 -4.8 -4756 0.1 ZNF687 BACH1 MAX DPF2 RELA IKZF1 NFATC1 ZNF143 IKZF2 ENSG00000234793 D2HGDH NEU4 ENSG00000215023 PDCD1 RTP5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PDCD1 on UCSC Golden Path with GeneCards custom track

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

Genomic Locations for PDCD1 Gene

Genomic Locations for PDCD1 Gene
chr2:241,849,881-241,858,908
(GRCh38/hg38)
Size:
9,028 bases
Orientation:
Minus strand
chr2:242,792,033-242,801,060
(GRCh37/hg19)

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 Structure • Gene Density

RefSeq DNA sequence for PDCD1 Gene

Proteins for PDCD1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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

Protein Expression for PDCD1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PDCD1 Gene

  • Glycosylation at Asn49, Asn58, Asn74, and isoforms=116
  • Modification sites at PhosphoSitePlus

Other Protein References for PDCD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for PDCD1

No data available for DME Specific Peptides for PDCD1 Gene

Domains & Families for PDCD1 Gene

Gene Families for PDCD1 Gene

HGNC:
Human Protein Atlas (HPA):
  • CD markers
  • Disease related genes
  • FDA approved drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for PDCD1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PDCD1 Gene

GenScript: Design optimal peptide antigens:

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

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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.

Phenotypes From GWAS Catalog for PDCD1 Gene

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 15240681
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

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
nucleus 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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDCD1 Gene

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 IEA,TAS --
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

Products:

  1. Drug

(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 Target, antibody, immunotherapy, inhibitor Therapeutic Antibodies, Immunotherapies 604
Pembrolizumab Approved Pharma Target, antagonist, antibody 709
Keytruda Approved September 2014 Pharma 0
Opdivo Approved March 2015/ Approved December 2014 Pharma 0
CT-011 Investigational Pharma Target, Antibody 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

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

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:

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

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for PDCD1 Gene
mRNA expression by BioGPS for PDCD1 GenemRNA expression by GTEx 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(2.8)
  • Lymph node(2.6)
  • Intestine(2.5)
  • Lung(2)
  • Spleen(2)
genes like me logo Genes that share expression patterns with PDCD1: view

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 33
  • 98.37 (n)
dog
(Canis familiaris)
 Mammalia PDCD1 33 34
  • 75.53 (n)
cow
(Bos Taurus)
 Mammalia PDCD1 33 34
  • 75 (n)
rat
(Rattus norvegicus)
 Mammalia LOC102550808 33
  • 70.57 (n)
mouse
(Mus musculus)
 Mammalia Pdcd1 33 16 34
  • 70.16 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia PDCD1 34
  • 30 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia PDCD1 34
  • 18 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PDCD1 33 34
  • 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

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for PDCD1 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs11568821 risk-factor, Systemic lupus erythematosus, association wit 2, Multiple sclerosis modifier of disease progression 241,851,760(-) C/G/T downstream_transcript_variant, genic_downstream_transcript_variant, intron_variant
rs1000249974 -- 241,852,874(-) C/A/T coding_sequence_variant, missense_variant, synonymous_variant
rs1000309869 -- 241,857,398(-) T/G intron_variant
rs1000350301 -- 241,857,216(-) C/T intron_variant
rs1000554864 -- 241,856,991(-) A/G 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)

Additional Variant Information for PDCD1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for PDCD1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
systemic lupus erythematosus 2
  • systemic lupus erythematosus, susceptibility to, 2
multiple sclerosis
  • multiple sclerosis, susceptibility to
igg4-related disease
  • hyper-igg4 disease
systemic lupus erythematosus
  • sle
nodular lymphocyte predominant hodgkin lymphoma
  • nlphl
- 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.

Additional Disease Information for PDCD1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 … Alarcón-Riquelme ME (Nature genetics 2002) 2 3 4 22 44 58
  2. Programmed death-1 (PD-1) gene polymorphisms lodged in the genetic predispositions of Kawasaki Disease. (PMID: 19468750) Chun JK … Kim DS (European journal of pediatrics 2010) 3 22 44 58
  3. Genetic, immunologic, and immunohistochemical analysis of the programmed death 1/programmed death ligand 1 pathway in human systemic lupus erythematosus. (PMID: 19116915) Bertsias GK … Boumpas DT (Arthritis and rheumatism 2009) 3 22 44 58
  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 JL … Zhang XJ (Journal of the European Academy of Dermatology and Venereology : JEADV 2009) 3 22 44 58
  5. PDCD1, CTLA-4 and p53 gene polymorphism and susceptibility to gestational trophoblastic diseases. (PMID: 19263877) Dehaghani AS … Ghaderi A (The Journal of reproductive medicine 2009) 3 22 44 58

Products for PDCD1 Gene

Sources for PDCD1 Gene

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