U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Protein

    • Showing Current items.

    PDCD1 programmed cell death 1 [ Homo sapiens (human) ]

    Gene ID: 5133, updated on 27-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    PDCD1provided by HGNC
    Official Full Name
    programmed cell death 1provided by HGNC
    Primary source
    HGNC:HGNC:8760
    See related
    Ensembl:ENSG00000188389 MIM:600244; AllianceGenome:HGNC:8760
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PD1; PD-1; CD279; SLEB2; hPD-1; hPD-l; hSLE1; AIMTBS
    Summary
    Programmed cell death protein 1 (PDCD1) is an immune-inhibitory receptor expressed in activated T cells; it is involved in the regulation of T-cell functions, including those of effector CD8+ T cells. In addition, this protein can also promote the differentiation of CD4+ T cells into T regulatory cells. PDCD1 is expressed in many types of tumors including melanomas, and has demonstrated to play a role in anti-tumor immunity. Moreover, this protein has been shown to be involved in safeguarding against autoimmunity, however, it can also contribute to the inhibition of effective anti-tumor and anti-microbial immunity. [provided by RefSeq, Aug 2020]
    Expression
    Biased expression in lymph node (RPKM 8.8), spleen (RPKM 2.6) and 7 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See PDCD1 in Genome Data Viewer
    Location:
    2q37.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (241849884..241858894, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (242351431..242360440, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (242792036..242801046, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905349 Neighboring gene neuraminidase 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:242776389-242776889 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:242784078-242784237 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242784841-242785538 Neighboring gene uncharacterized LOC124905350 Neighboring gene uncharacterized LOC105373977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242800252-242801214 Neighboring gene uncharacterized LOC124908032 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242807941-242808722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:242813965-242814521 Neighboring gene receptor transporter protein 5 (putative)

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. PD-1 analysis on CD28(-) CD27(-) CD4 T cells allows stimulation-independent assessment of CMV viremic episodes in transplant recipients. Dirks J, et al. Am J Transplant, 2013 Dec. PMID 24148296
    2. PD-1 Tumor Suppressor Signaling in T Cell Lymphomas. Wartewig T, et al. Trends Immunol, 2019 May. PMID 30979616
    3. PD-1 (PDCD1) promoter methylation in Merkel cell carcinoma: prognostic relevance and relationship with clinico-pathological parameters. Ricci C, et al. Mod Pathol, 2019 Sep. PMID 30976104
    4. Lentiviral Vector-Based Dendritic Cell Vaccine Suppresses HIV Replication in Humanized Mice. Norton TD, et al. Mol Ther, 2019 May 8. PMID 30962161, Free PMC Article
    5. Effect and changes in PD‑1 expression of CD19 CAR‑T cells from T cells highly expressing PD‑1 combined with reduced‑dose PD‑1 inhibitor. Zhang R, et al. Oncol Rep, 2019 Jun. PMID 30942469

    See all (1000) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. High PD-1 and CTLA-4 expression correlates with host immune suppression in patients and a mouse model infected with Echinococcus multilocularis.
      Title: High PD-1 and CTLA-4 expression correlates with host immune suppression in patients and a mouse model infected with Echinococcus multilocularis.
    2. A splicing isoform of PD-1 promotes tumor progression as a potential immune checkpoint.
      Title: A splicing isoform of PD-1 promotes tumor progression as a potential immune checkpoint.
    3. Comprehensive Glycomic and Glycoproteomic Analyses of Human Programmed Cell Death Protein 1 Extracellular Domain.
      Title: Comprehensive Glycomic and Glycoproteomic Analyses of Human Programmed Cell Death Protein 1 Extracellular Domain.
    4. Association between PD-1 single nucleotide gene variants and the risk of metastatic melanoma.
      Title: Association between PD-1 single nucleotide gene variants and the risk of metastatic melanoma.
    5. PDIA3 driven STAT3/PD-1 signaling promotes M2 TAM polarization and aggravates colorectal cancer progression.
      Title: PDIA3 driven STAT3/PD-1 signaling promotes M2 TAM polarization and aggravates colorectal cancer progression.
    6. Evaluation of PD-1 and interleukin-10-receptor expression by T lymphocytes in malignant and benign pleural effusions.
      Title: Evaluation of PD-1 and interleukin-10-receptor expression by T lymphocytes in malignant and benign pleural effusions.
    7. Regulation of the PD-1/PD-L1 Axis and NK Cell Dysfunction by Exosomal miR-552-5p in Gastric Cancer.
      Title: Regulation of the PD-1/PD-L1 Axis and NK Cell Dysfunction by Exosomal miR-552-5p in Gastric Cancer.
    8. Tumor cells inhibit the activation of ILC2s through up-regulating PD-1 expression.
      Title: Tumor cells inhibit the activation of ILC2s through up-regulating PD-1 expression.
    9. Relationship Between Cytotoxic T-Lymphocyte-associated Antigen-4: Programmed Death-1 Genes Polymorphisms and Susceptibility to Pediatric B-Cell Acute Lymphoblastic Leukemia.
      Title: Relationship Between Cytotoxic T-Lymphocyte-associated Antigen-4: Programmed Death-1 Genes Polymorphisms and Susceptibility to Pediatric B-Cell Acute Lymphoblastic Leukemia.
    10. TIGIT expression in renal cell carcinoma infiltrating T cells is variable and inversely correlated with PD-1 and LAG3.
      Title: TIGIT expression in renal cell carcinoma infiltrating T cells is variable and inversely correlated with PD-1 and LAG3.
    Submit: New GeneRIF Correction See all GeneRIFs (1198)

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Multiple sclerosis, susceptibility to
    MedGen: C1868685 OMIM: 126200 GeneReviews: Not available
    		Compare labs
    Systemic lupus erythematosus, susceptibility to, 2
    MedGen: C1854577 OMIM: 605218 GeneReviews: Not available
    		Compare labs

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

    Go to the top of the page Help

    Replication interactions

    Interaction Pubs
    HIV-1 infection downregulates CXCR5 and PDCD1 (PD1) expression in primary germinal center T follicular helper cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 binds and signals through CD4, which leads to T cell activation with upregulation of the CXCR5, PD-1, Fas, and FasL expression PubMed
    Nef nef HIV-1 Nef can transcriptionally induce the expression of PD-1 during infection in vitro. Nef-induced PD-1 upregulation requires its proline-rich motif and the activation of the downstream kinase p38 PubMed
    Pr55(Gag) gag The enhancement of Tim-3 and PD-1 expression by common gamma-chain IL-2 can inhibit the function of T cells re-stimulated by HIV-1 Gag and TCR PubMed
    gag Blocking the PD-1 pathway enhances Gag-specific CD4+ T cell proliferation PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables signaling receptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in B cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in apoptotic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in humoral immune response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of B cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of T cell activation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of T cell mediated immune response to tumor cell IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of immune response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of tolerance induction IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of T cell apoptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulatory T cell apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    programmed cell death protein 1
    Names
    programmed cell death 1 protein
    protein PD-1
    systemic lupus erythematosus susceptibility 2

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012110.1 RefSeqGene

      Range
      5013..14023
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_005018.3 → NP_005009.2  programmed cell death protein 1 precursor

      Status: REVIEWED

      Source sequence(s)
      AI928135, AY238517, CR988122, U64863
      Consensus CDS
      CCDS33428.1
      UniProtKB/Swiss-Prot
      O00517, Q15116, Q8IX89
      UniProtKB/TrEMBL
      A0A0M3M0G7
      Related
      ENSP00000335062.5, ENST00000334409.10
      Conserved Domains (1) summary
      cd16088
      Location:35 → 144
      IgV_PD1; Immunoglobulin (Ig)-like domain of Programmed cell Death 1 (PD1)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      241849884..241858894 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006712573.3 → XP_006712636.1  programmed cell death protein 1 isoform X1

      Related
      ENSP00000520841.1, ENST00000718474.1
      Conserved Domains (2) summary
      smart00410
      Location:39 → 125
      IG_like; Immunoglobulin like
      pfam07686
      Location:38 → 127
      V-set; Immunoglobulin V-set domain

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_187527.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      61982..70992 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328654.1 → XP_054184629.1  programmed cell death protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      242351431..242360440 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054342460.1 → XP_054198435.1  programmed cell death protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15116.3 GenPept UniProtKB/Swiss-Prot:Q15116

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous