PDCD1LG2

Chr 9

programmed cell death 1 ligand 2

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

NCBI Gene: 80380 ENSG00000197646 UniProt: Q9BQ51 OMIM: 605723

The protein encoded by this gene acts as a ligand for the inhibitory receptor PD-1 and plays a critical role in maintaining immune tolerance by inhibiting T-cell proliferation and cytokine production. The gene shows very low constraint against loss-of-function variants (pLI near 0, LOEUF > 1), suggesting that complete loss of function is well-tolerated in humans. No Mendelian diseases have been definitively associated with pathogenic variants in this gene based on the available data.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.28

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

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?

-0.67Z-score

OE missense 1.16 (1.02–1.31)

168 obs / 145.4 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.73 (0.44–1.28)

0≤0.351.4

Missense OE?1.16 (1.02–1.31)

0≤0.61.4

Synonymous OE?1.13

0≤1.21.6

LoF obs/exp: 9 / 12.2Missense obs/exp: 168 / 145.4Syn Z: -0.79

Background carrier burden — how many people carry a rare variant somewhere in PDCD1LG2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 160

411 rare PASS variants

Rare truncating (LoF)

1 in 1,200

64 rare PASS variants

Rare synonymous (reference)

1 in 490

129 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for PDCD1LG2. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 250	1 in 2,500
South Asian	~43k	1 in 120	1 in 3,300
Remaining (unassigned)	~30k	1 in 130	1 in 1,700
European (Finnish)	~27k	1 in 860	1 in 2,100
Admixed American	~22k	1 in 180	1 in 1,500
African / African American	~21k	1 in 140	1 in 920
East Asian	~20k	1 in 130	1 in 510
Ashkenazi Jewish	~13k	1 in 200	≈ 1 in 3,300
Middle Eastern	~2,884	1 in 110	1 in 320

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.