PDCD1LG2

programmed cell death 1 ligand 2, the group of CD molecules|Receptor ligands|B7 family|Immunoglobulin like domain containing

Basic information

Region (hg38): 9:5510531-5571282

Links

ENSG00000197646 ∙ NCBI:80380 ∙ OMIM:605723 ∙ HGNC:18731 ∙ Uniprot:Q9BQ51 ∙ 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 PDCD1LG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDCD1LG2 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						0
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in PDCD1LG2

This is a list of pathogenic ClinVar variants found in the PDCD1LG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-5522551-T-A		not specified	Uncertain significance (Oct 12, 2024)
9-5522598-G-C		not specified	Uncertain significance (Feb 09, 2023)
9-5522599-C-T		not specified	Uncertain significance (Mar 07, 2024)
9-5534852-A-C		not specified	Likely benign (Dec 02, 2022)
9-5534853-T-C		not specified	Uncertain significance (Mar 03, 2022)
9-5534900-G-A		not specified	Uncertain significance (Jan 30, 2024)
9-5534960-C-G		not specified	Uncertain significance (Dec 27, 2023)
9-5534988-A-C		not specified	Uncertain significance (Aug 14, 2024)
9-5549351-A-G		not specified	Uncertain significance (Aug 02, 2022)
9-5549362-T-C		not specified	Uncertain significance (Aug 10, 2024)
9-5549363-C-G		not specified	Uncertain significance (Dec 17, 2023)
9-5549413-G-A		not specified	Uncertain significance (Jan 04, 2024)
9-5549415-T-A		not specified	Uncertain significance (Jun 28, 2022)
9-5549421-C-G		not specified	Uncertain significance (Dec 21, 2022)
9-5549527-C-T		not specified	Uncertain significance (Dec 27, 2023)
9-5549568-G-A		not specified	Likely benign (Dec 01, 2022)
9-5557629-C-T		not specified	Uncertain significance (Aug 21, 2023)
9-5557726-T-A		not specified	Uncertain significance (Apr 07, 2022)
9-5563170-A-G		not specified	Uncertain significance (Nov 13, 2024)
9-5563171-A-C		not specified	Uncertain significance (Sep 27, 2021)
9-5569954-A-G		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDCD1LG2	protein_coding	protein_coding	ENST00000397747	6	60738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000120	0.615	125730	0	9	125739	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.667	168	145	1.16	0.00000703	1781
Missense in Polyphen		41	37.861	1.0829		539
Synonymous	-0.788	64	56.5	1.13	0.00000297	540
Loss of Function	0.859	9	12.2	0.735	5.20e-7	147

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000623	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the costimulatory signal, essential for T- cell proliferation and IFNG production in a PDCD1-independent manner. Interaction with PDCD1 inhibits T-cell proliferation by blocking cell cycle progression and cytokine production (By similarity). {ECO:0000250}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);PD-1 signaling;Costimulation by the CD28 family;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.162

Intolerance Scores

• loftool: 0.812
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.0576
• hipred: N
• hipred_score: 0.310
• ghis: 0.472

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.890

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdcd1lg2
• Phenotype: 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; immune system phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: immune response;signal transduction;cell surface receptor signaling pathway;T cell costimulation;negative regulation of interferon-gamma production;negative regulation of interleukin-10 production;positive regulation of T cell proliferation;negative regulation of T cell proliferation;negative regulation of activated T cell proliferation;cellular response to lipopolysaccharide
• Cellular component: extracellular region;plasma membrane;external side of plasma membrane;cell surface;endomembrane system;integral component of membrane
• Molecular function: molecular_function;protein binding