PDCD1LG2

protein-coding

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

Gene summary

Enables receptor ligand activity. Involved in negative regulation of T cell receptor signaling pathway; negative regulation of activated T cell proliferation; and negative regulation of cytokine production. Is active in plasma membrane. Biomarker of pulmonary tuberculosis. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_025239.4

Inheritance

—

ClinVar variants

U:43B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr9:5,510,531-5,571,282

External References & Databases

Ensembl (ENSG00000197646)

Transcript & Mutation Effects

hg38 • Region Span ~60.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PDCD1LG2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 41

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025239.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			40 clinvar	3 clinvar		43
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	43	3	0	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025239.4	RefSeq	NP_079515.2	6	MANE Select
ENST00000397747.5	Ensembl	ENSP00000380855.3	6	MANE Select
ENST00000861551.1	Ensembl	ENSP00000531610.1	5	Standard
ENST00000861551.2	Ensembl	ENSP00000531610.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Cell adhesion molecules (CAMs) - Homo sapiens (human)
PD-1 signaling
Costimulation by the CD28 family
Immune System
Adaptive Immune System

Biological Process

immune response
signal transduction
cell surface receptor signaling pathway
T cell costimulation
negative regulation of interferon-gamma production

Molecular Function

molecular_function
protein binding

Cellular Component

extracellular region
plasma membrane
external side of plasma membrane
cell surface
endomembrane system

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000397747
Coding exons: 6
Length: 60738
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125739
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.667	168	145	1.16	0.00000703	1781
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.162

Intolerance Scores

LoFtool: 0.812
RVIS EVS: 0.37
RVIS percentile EVS: 75.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.890

Gene Damage Prediction

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