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.

not_specified (39 variants)

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. These statistics are base on transcript: NM_000025239.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			36 clinvar	3 clinvar		39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	36	3	0

Loading clinvar variants...

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