PDCD1LG2

Chr 9

programmed cell death 1 ligand 2

Also known as: B7DC, Btdc, CD273, PD-L2, PDCD1L2, PDL2, bA574F11.2

NCBI Gene: 80380ENSG00000197646UniProt: Q9BQ51

Involved in negative regulation of activated T cell proliferation; negative regulation of interleukin-10 production; and negative regulation of type II interferon production. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. Biomarker of pulmonary tuberculosis. [provided by Alliance of Genome Resources, Jul 2025]

218
ClinVar variants
160
Pathogenic / LP
0.00
pLI score
2
Active trials
Clinical Summary— PDCD1LG2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
160 Pathogenic / Likely Pathogenic· 47 VUS of 218 total submissions
💊
Clinical Trials
2 active or recruiting trials — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.28LOEUF
pLI 0.000
Z-score 0.86
OE 0.73 (0.44–1.28)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.67Z-score
OE missense 1.16 (1.02–1.31)
168 obs / 145.4 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.73 (0.44–1.28)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.16 (1.02–1.31)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.13
0≤1.21.6
LoF obs/exp: 9 / 12.2Missense obs/exp: 168 / 145.4Syn Z: -0.79

ClinVar Variant Classifications

218 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic153
Likely Pathogenic7
VUS47
Likely Benign3
Benign1
153
Pathogenic
7
Likely Pathogenic
47
VUS
3
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
153
0
153
Likely Pathogenic
0
0
7
0
7
VUS
0
38
9
0
47
Likely Benign
0
3
0
0
3
Benign
0
0
1
0
1
Total0411700211

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

PDCD1LG2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Comprehensive molecular characterization of gastric adenocarcinoma.
Cancer Genome Atlas Research Network·Nature
2014
Proteome-wide Mendelian randomization identified potential drug targets for migraine.
Xiong Z et al.·J Headache Pain
2024
Shared molecular biomarkers and therapeutic targets in rheumatoid arthritis and osteoarthritis: Focus on EIF3B, KHSRP, NCL, PDCD1LG2, and SLC25A37.
Li H et al.·Cytokine
2025
Tumor PDCD1LG2 (PD-L2) Expression and the Lymphocytic Reaction to Colorectal Cancer.
Masugi Y et al.·Cancer Immunol Res
2017
Identifying the prognostic significance of mitophagy-associated genes in multiple myeloma: a novel risk model construction.
Min R et al.·Clin Exp Med
2024Functional
Genomic alterations underlying immune privilege in malignant lymphomas.
Mottok A et al.·Curr Opin Hematol
2015Review
Identification and characterization of mitochondrial autophagy-related genes in osteosarcoma and predicting clinical prognosis.
Zhang H et al.·Sci Rep
2025
Ferroptosis-related LINC02535/has-miR-30c-5p/EIF2S1 axis as a novel prognostic biomarker involved in immune infiltration and progression of PDAC.
Huang Z et al.·Cell Signal
2024
Genomic assays for Epstein-Barr virus-positive gastric adenocarcinoma.
Gulley ML·Exp Mol Med
2015Review
Liquid biopsy-based circulating tumour (ct)DNA analysis of a spectrum of myeloid and lymphoid malignancies yields clinically actionable results.
Mata DA et al.·Histopathology
2024
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
Breast NeoplasmsTriple Negative Breast NeoplasmsHR Low-Positive/HER2-Negative Breast Neoplasms

A Clinical Study of Sacituzumab Tirumotecan (Sac-TMT, MK-2870) in People With Breast Cancer (MK-2870-032)

RECRUITING
NCT06966700Phase PHASE3Merck Sharp & Dohme LLCStarted 2025-06-30
Sacituzumab tirumotecanPembrolizumabRescue Medication
Malignant Neoplasm

KEYMAKER-U01 Substudy 01J: A Study of Pembrolizumab Plus MK-1084 in Participants With Non-Small Cell Lung Cancer (NSCLC) With Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) G12C Mutations (MK-3475-01J/KEYMAKER-U01J)

RECRUITING
NCT07252739Phase PHASE2Merck Sharp & Dohme LLCStarted 2025-12-19
MK-1084PembrolizumabCetuximab

External Resources

Links to major genomics databases and tools