PDCD2

Chr 6

programmed cell death 2

Also known as: RP8, ZMYND7

NCBI Gene: 5134ENSG00000071994UniProt: Q16342

This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that BCL6 regulates apoptosis by its effects on this protein. Alternative splicing results in multiple transcript variants and pseudogenes have been identified on chromosomes 9 and 12. [provided by RefSeq, Dec 2010]

159
ClinVar variants
82
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— PDCD2
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
82 Pathogenic / Likely Pathogenic· 74 VUS of 159 total submissions

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.
1.37LOEUF
pLI 0.000
Z-score 0.57
OE 0.83 (0.52–1.37)
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.
0.05Z-score
OE missense 0.99 (0.86–1.13)
149 obs / 150.8 exp
Tolerant

Mild missense constraint

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.0.83 (0.52–1.37)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.99 (0.86–1.13)
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.1.01
0≤1.21.6
LoF obs/exp: 11 / 13.3Missense obs/exp: 149 / 150.8Syn Z: -0.04

ClinVar Variant Classifications

159 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic75
Likely Pathogenic7
VUS74
Benign3
75
Pathogenic
7
Likely Pathogenic
74
VUS
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
75
0
75
Likely Pathogenic
0
0
7
0
7
VUS
0
63
11
0
74
Likely Benign
0
0
0
0
0
Benign
0
1
1
1
3
Total064941159

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

View in ClinVar →

Protein Context — Lollipop Plot

PDCD2 · 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
Biallelic variants in the conserved ribosomal protein chaperone gene PDCD2 are associated with hydrops fetalis and early pregnancy loss.
Landry-Voyer AM et al.·Proc Natl Acad Sci U S A
2025
Zfrp8/PDCD2 is required in ovarian stem cells and interacts with the piRNA pathway machinery.
Minakhina S et al.·Development
2014
PDCD2 functions in cancer cell proliferation and predicts relapsed leukemia.
Barboza N et al.·Cancer Biol Ther
2013
Significance of liquid-liquid phase separation (LLPS)-related genes in breast cancer: a multi-omics analysis.
Xie J et al.·Aging (Albany NY)
2023
Microbial infections in eight genomic subtypes of chronic fatigue syndrome/myalgic encephalomyelitis.
Zhang L et al.·J Clin Pathol
2010
A microarray based expression profiling of paclitaxel and vincristine resistant MCF-7 cells.
Kars MD et al.·Eur J Pharmacol
2011
Transcriptional repressor BCL-6 immortalizes germinal center-like B cells in the absence of p53 function.
Kusam S et al.·Oncogene
2004
Expression patterns of cell cycle and apoptosis-related genes in a multidrug-resistant human colon carcinoma cell line.
Fan CW et al.·Scand J Gastroenterol
2004
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

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools