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

Summary

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
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
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Genomic context

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_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
Human Immunodeficiency Virus-Human Pegivirus Coinfected Individuals Display Functional Mucosal-Associated Invariant T Cells and Follicular T Cells Irrespective of PD-1 Expression.
Title: Human Immunodeficiency Virus-Human Pegivirus Coinfected Individuals Display Functional Mucosal-Associated Invariant T Cells and Follicular T Cells Irrespective of PD-1 Expression.

Submit: New GeneRIF Correction See all GeneRIFs (1197)

Phenotypes

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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

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PDCD1_1679 (e-PCR)
- UniSTS:462388

NoName (e-PCR)
- UniSTS:481888

D2S162 (e-PCR), detects polymorphism
- UniSTS:86625

D2S325 (e-PCR), detects polymorphism
- UniSTS:14192

D2S301 (e-PCR), detects polymorphism
- UniSTS:27539

D2S151 (e-PCR), detects polymorphism
- UniSTS:3225

NoName (e-PCR)
- UniSTS:480687

D2S1391 (e-PCR), detects polymorphism
- UniSTS:36563

NoName (e-PCR)
- UniSTS:482776

RH71365 (e-PCR)
- UniSTS:48877

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

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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)

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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.