DPPA2

Chr 3

developmental pluripotency associated 2

Also known as: CT100, ECAT15-2, PESCRG1

NCBI Gene: 151871 ENSG00000163530 UniProt: Q7Z7J5 OMIM: 614445

DPPA2 encodes a chromatin-binding protein that binds to target gene promoters and maintains active epigenetic status of genes involved in development. The gene is highly constrained against loss-of-function variants (pLI ~0, LOEUF 1.36), but no definitive human disease associations have been established in the provided data. Current evidence suggests involvement in developmental processes and stem cell regulation, but clinical phenotypes from DPPA2 mutations require further characterization.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable chromatin binding activity. Predicted to be involved in system development. Predicted to act upstream of or within several processes, including epigenetic regulation of gene expression; lung-associated mesenchyme development; and positive regulation of stem cell proliferation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Active trials

—

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.35

LOEUF

—

Mechanism

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.35LOEUF

pLI 0.000

Z-score 0.50

OE 0.87 (0.57–1.35)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.16Z-score

OE missense 0.96 (0.85–1.10)

162 obs / 168.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.87 (0.57–1.35)

0≤0.351.4

Missense OE?0.96 (0.85–1.10)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 14 / 16.1Missense obs/exp: 162 / 168.0Syn Z: 0.22

Background carrier burden — how many people carry a rare variant somewhere in DPPA2?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 180

385 rare PASS variants

Rare truncating (LoF)

1 in 2,500

53 rare PASS variants

Rare synonymous (reference)

1 in 360

122 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for DPPA2. 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 170	1 in 2,200
South Asian	~43k	1 in 130	1 in 4,300
Remaining (unassigned)	~30k	1 in 210	1 in 3,400
European (Finnish)	~27k	1 in 920	≈ 1 in 27,000
Admixed American	~22k	1 in 150	1 in 1,700
African / African American	~21k	1 in 180	1 in 2,900
East Asian	~20k	1 in 200	≈ 1 in 5,000
Ashkenazi Jewish	~13k	1 in 380	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 220	≈ 1 in 2,900

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.

Exome coverage (gnomAD): All 7 coding exons well covered in gnomAD exomes and genomes.? see exons ↓