EBAG9

Chr 8

estrogen receptor binding site associated antigen 9

Also known as: EB9, PDAF

NCBI Gene: 9166ENSG00000147654UniProt: O00559

The EBAG9 protein may participate in suppressing cell proliferation and inducing apoptotic cell death through activation of interleukin-1-beta converting enzyme-like proteases. Currently, no established Mendelian diseases have been definitively linked to mutations in this gene in pediatric patients. This gene shows relatively low constraint against loss-of-function variants (pLI 0.08, LOEUF 0.73), suggesting it may tolerate some degree of functional variation.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
2
Pubs (1 yr)
37
P/LP submissions
0%
P/LP missense
0.73
LOEUF
DN
Mechanism· predicted
Clinical Summary— EBAG9
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.32) despite low pLI — interpret in context.
📋
ClinVar Variants
37 unique Pathogenic / Likely Pathogenic· 30 VUS of 81 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.73LOEUF
pLI 0.077
Z-score 2.24
OE 0.32 (0.16–0.73)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.97Z-score
OE missense 0.73 (0.61–0.89)
76 obs / 103.8 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.32 (0.16–0.73)
0≤0.351.4
Missense OE0.73 (0.61–0.89)
0≤0.61.4
Synonymous OE1.07
0≤1.21.6
LoF obs/exp: 4 / 12.6Missense obs/exp: 76 / 103.8Syn Z: -0.35
DN
0.6161th %ile
GOF
0.5954th %ile
LOF
0.3453th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

81 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic37
VUS30
Likely Benign2
Benign1
37
Pathogenic
30
VUS
2
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
37
0
37
Likely Pathogenic
0
0
0
0
0
VUS
0
27
3
0
30
Likely Benign
0
0
1
1
2
Benign
0
0
1
0
1
Total02742170

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

View in ClinVar →

Protein Context — Lollipop Plot

EBAG9 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 3 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients