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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
  • 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 NF-kappaB Signaling and Immune System. 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 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PDCD1 on UCSC Golden Path with GeneCards custom track

Promoters for PDCD1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs 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

Proteomics data for PDCD1 Gene at MOPED

Post-translational modifications for PDCD1 Gene

  • Glycosylation at Asn 49, Asn 58, Asn 74, and Asn 116
  • Modification sites at PhosphoSitePlus

Other Protein References for PDCD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PDCD1 (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

Q15116

UniProtKB/Swiss-Prot:

PDCD1_HUMAN :
  • Contains 1 Ig-like V-type (immunoglobulin-like) domain.
Domain:
  • Contains 1 Ig-like V-type (immunoglobulin-like) domain.
genes like me logo Genes that share domains with PDCD1: view

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.
genes like me logo Genes that share phenotypes with PDCD1: view

Animal Models for PDCD1 Gene

MGI Knock Outs for PDCD1:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
Jensen Localization Image for PDCD1 Gene COMPARTMENTS Subcellular localization image for PDCD1 gene
Compartment Confidence
plasma membrane 5
cytosol 2
endoplasmic reticulum 1
extracellular 1
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PDCD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009897 external side of plasma 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

Pathways by source for PDCD1 Gene

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 --
GO:0007165 signal transduction TAS 1396582
GO:0043065 positive regulation of apoptotic process IEA --
GO:0043066 negative regulation of apoptotic process IEA --
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 218
Pembrolizumab Approved Pharma Target, antagonist, antibody 315
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:

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 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



SOURCE GeneReport for Unigene cluster for PDCD1 Gene Hs.158297

genes like me logo Genes that share expression patterns with PDCD1: view

Protein tissue co-expression partners for PDCD1 Gene

Primer Products

No data available for mRNA Expression by UniProt/SwissProt 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
cow
(Bos Taurus)
Mammalia PDCD1 35
  • 75 (n)
  • 65.36 (a)
PDCD1 36
  • 66 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDCD1 35
  • 75.53 (n)
  • 66.67 (a)
PDCD1 36
  • 66 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdcd1 35
  • 70.16 (n)
  • 59.09 (a)
Pdcd1 16
Pdcd1 36
  • 60 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PDCD1 35
  • 98.37 (n)
  • 96.95 (a)
rat
(Rattus norvegicus)
Mammalia LOC102550808 35
  • 70.57 (n)
  • 60.64 (a)
oppossum
(Monodelphis domestica)
Mammalia PDCD1 36
  • 18 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDCD1 36
  • 30 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDCD1 35
  • 50.78 (n)
  • 34.47 (a)
PDCD1 36
  • 29 (a)
OneToOne
Species with no ortholog for PDCD1:
  • 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
VAR_031685 -
rs6749527 -- 241,850,859(-) ACAGT(A/G)AGCCC utr-variant-3-prime
rs5839828 -- 241,859,601(-) CCCCC(-/C)GTCAG upstream-variant-2KB
rs13023138 -- 241,857,486(-) CTGAG(C/G)GAGGC intron-variant
rs6605259 -- 241,850,699(-) GCGCC(A/G)TGGCC utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
nsv876226 CNV Loss 21882294
dgv4493n71 CNV Loss 21882294
dgv4495n71 CNV Loss 21882294
dgv165e55 CNV Loss 17911159
nsv876255 CNV Loss 21882294
dgv4499n71 CNV Gain 21882294
nsv470533 CNV Loss 18288195
dgv4500n71 CNV Loss 21882294
dgv4501n71 CNV Loss 21882294
nsv821942 CNV Gain 20364138

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

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

Disorders for PDCD1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
systemic lupus erythematosus 2
  • systemic lupus erythematosus, susceptibility to, 2
multiple sclerosis, disease progression, modifier of
  • multiple sclerosis 1
systemic lupus erythematosus
  • lupus nephritis
autoimmune neuropathy
lupus erythematosus
  • systemic lupus erythematosus
- 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 23 48 67
  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 23
  3. Enhanced PD-1 expression by T cells in cerebrospinal fluid does not reflect functional exhaustion during chronic human immunodeficiency virus type 1 infection. (PMID: 19828602) Sadagopal S. … Haas D.W. (J. Virol. 2010) 3 23
  4. PD-1 expression in T-cell lymphomas and reactive lymphoid entities: potential overlap in staining patterns between lymphoma and viral lymphadenitis. (PMID: 20087161) Krishnan C. … Natkunam Y. (Am. J. Surg. Pathol. 2010) 3 23
  5. 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 23

Products for PDCD1 Gene

Sources for PDCD1 Gene

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