PDCD1

programmed cell death 1, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 2:241849884-241858894

Previous symbols: [ "SLEB2" ]

Links

ENSG00000188389 ∙ NCBI:5133 ∙ OMIM:600244 ∙ HGNC:8760 ∙ Uniprot:Q15116 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDCD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			6		1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1	14	15
Total	0	0	6	3	16

Variants in PDCD1

This is a list of pathogenic ClinVar variants found in the PDCD1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-241850169-C-T			Benign (Oct 29, 2020)
2-241851121-A-C		PDCD1-related disorder	Likely benign (Dec 01, 2023)
2-241851121-A-G		not specified • PDCD1-related disorder	Benign (Jan 24, 2024)
2-241851281-G-A		not specified	Benign (Jan 24, 2024)
2-241851292-C-A		not specified	Uncertain significance (Dec 20, 2023)
2-241851407-T-C		not specified	Benign (Jan 24, 2024)
2-241851697-G-A			Benign (Nov 12, 2018)
2-241851760-C-G		RECLASSIFIED - PDCD1 POLYMORPHISM	Benign (Jul 01, 2005)
2-241851760-C-T			Benign (Jun 19, 2021)
2-241852038-T-TG			Benign (Jun 20, 2021)
2-241852039-G-C			Benign (Jun 19, 2021)
2-241852209-C-T		not specified	Uncertain significance (Sep 16, 2021)
2-241852310-G-C		PDCD1-related disorder	Likely benign (Nov 04, 2019)
2-241852361-G-A		PDCD1-related disorder	Likely benign (Jun 05, 2019)
2-241852468-C-T		not specified	Benign (Jan 24, 2024)
2-241852611-G-A		PDCD1-related disorder	Likely benign (Jun 28, 2019)
2-241852641-C-T		not specified	Uncertain significance (May 28, 2024)
2-241852710-T-A		not specified	Uncertain significance (Dec 06, 2022)
2-241852713-C-T		not specified	Uncertain significance (Mar 29, 2023)
2-241853160-C-G			Benign (Nov 12, 2018)
2-241853198-A-G			Benign (Nov 12, 2018)
2-241853266-GT-G			Benign (Nov 12, 2018)
2-241858521-G-GCTGCCCAAACTTTGGGCAGTCAC			Benign (Jun 20, 2021)
2-241858637-C-G			Benign (Jun 20, 2021)
2-241858748-G-A		not specified	Benign (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCD1	protein_coding	protein_coding	ENST00000334409	5	9028

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.417	0.576	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	139	189	0.735	0.0000127	1823
Missense in Polyphen		25	52.205	0.47889		581
Synonymous	0.670	75	82.8	0.906	0.00000592	619
Loss of Function	2.26	2	9.51	0.210	4.10e-7	92

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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. {ECO:0000269|PubMed:21276005}.
• Disease: DISEASE: 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.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);T-Cell Receptor and Co-stimulatory Signaling;T-Cell antigen Receptor (TCR) pathway during Staphylococcus aureus infection;PD-1 signaling;Costimulation by the CD28 family;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.278

Intolerance Scores

• loftool: 0.458
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.461
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.456

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pdcd1
• Phenotype: respiratory system phenotype; liver/biliary system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; cellular phenotype; renal/urinary system phenotype; skeleton phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; muscle phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of tolerance induction;apoptotic process;humoral immune response;multicellular organism development;T cell costimulation;negative regulation of apoptotic process;positive regulation of T cell apoptotic process
• Cellular component: plasma membrane;external side of plasma membrane;integral component of membrane
• Molecular function: protein binding