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_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (241849884..241858894, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (242351431..242360440, complement)
105.20220307	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
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?

PD-1 signaling negatively regulates the common cytokine receptor gamma chain via MARCH5-mediated ubiquitination and degradation to suppress anti-tumor immunity.
Title: PD-1 signaling negatively regulates the common cytokine receptor γ chain via MARCH5-mediated ubiquitination and degradation to suppress anti-tumor immunity.
The clinical association of programmed death-1/PD-L1 axis, myeloid derived suppressor cells subsets and regulatory T cells in peripheral blood of stable COPD patients.
Title: The clinical association of programmed death-1/PD-L1 axis, myeloid derived suppressor cells subsets and regulatory T cells in peripheral blood of stable COPD patients.
HOXC9 characterizes a suppressive tumor immune microenvironment and integration with multiple immune biomarkers predicts response to PD-1 blockade plus chemotherapy in lung adenocarcinoma.
Title: HOXC9 characterizes a suppressive tumor immune microenvironment and integration with multiple immune biomarkers predicts response to PD-1 blockade plus chemotherapy in lung adenocarcinoma.
IFN-gamma decreases PD-1 in T lymphocytes from convalescent COVID-19 patients via the AKT/GSK3beta signaling pathway.
Title: IFN-γ decreases PD-1 in T lymphocytes from convalescent COVID-19 patients via the AKT/GSK3β signaling pathway.
The prognostic significance of programmed cell death protein 1 and its ligand on lymphoma cells and tumor-immune cells in diffuse large B-cell lymphoma, not otherwise specified.
Title: The prognostic significance of programmed cell death protein 1 and its ligand on lymphoma cells and tumor-immune cells in diffuse large B-cell lymphoma, not otherwise specified.
IFIT3 accelerates the progression of head and neck squamous cell carcinoma by targeting PD-L1 to activate PI3K/AKT signaling pathway.
Title: IFIT3 accelerates the progression of head and neck squamous cell carcinoma by targeting PD-L1 to activate PI3K/AKT signaling pathway.
Frequent expression of CD45RO memory T cell marker as well as low to high expression of PD-1 and PD-L1 inhibitory molecules in seminoma and dysgerminoma.
Title: Frequent expression of CD45RO memory T cell marker as well as low to high expression of PD-1 and PD-L1 inhibitory molecules in seminoma and dysgerminoma.
PD-1 Blockade Induces Reactivation of Nonproductive T-Cell Responses Characterized by NF-kappaB Signaling in Patients with Pancreatic Cancer.
Title: PD-1 Blockade Induces Reactivation of Nonproductive T-Cell Responses Characterized by NF-κB Signaling in Patients with Pancreatic Cancer.
Elevated programmed cell death-1 protein/ligand (PD-1/PD-L1) and variants are associated with susceptibility to multiple myeloma: a case-control study in the Chinese cohort.
Title: Elevated programmed cell death-1 protein/ligand (PD-1/PD-L1) and variants are associated with susceptibility to multiple myeloma: a case-control study in the Chinese cohort.
Tumor cell-intrinsic PD-1 promotes Merkel cell carcinoma growth by activating downstream mTOR-mitochondrial ROS signaling.
Title: Tumor cell-intrinsic PD-1 promotes Merkel cell carcinoma growth by activating downstream mTOR-mitochondrial ROS signaling.

Submit: New GeneRIF Correction See all GeneRIFs (1178)

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

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 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 positive regulation of T cell apoptotic process	IDA Inferred from Direct Assay more info	PubMed
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
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.