EDIL3

Chr 5

EGF like and discoidin domains 3

Also known as: DEL1

NCBI Gene: 10085ENSG00000164176UniProt: O43854OMIM: 606018

The protein promotes endothelial cell adhesion through interaction with the alpha-v/beta-3 integrin receptor and regulates vascular morphogenesis during embryonic development. Mutations cause developmental and epileptic encephalopathy with microcephaly and simplified gyral pattern, inherited in an autosomal recessive pattern. This gene is highly constrained against loss-of-function variants, suggesting such mutations have severe consequences.

OMIMResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 0.63
Clinical Summary— EDIL3
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
8 unique Pathogenic / Likely Pathogenic· 78 VUS of 109 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
0.63LOEUF
pLI 0.000
Z-score 3.14
OE 0.39 (0.25–0.63)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.16Z-score
OE missense 0.80 (0.71–0.89)
206 obs / 258.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.39 (0.25–0.63)
0≤0.351.4
Missense OE0.80 (0.71–0.89)
0≤0.61.4
Synonymous OE0.94
0≤1.21.6
LoF obs/exp: 12 / 30.8Missense obs/exp: 206 / 258.7Syn Z: 0.48
DN
0.75top 25%
GOF
0.72top 25%
LOF
0.2680th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction 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

109 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic7
Likely Pathogenic1
VUS78
Likely Benign5
Benign2
7
Pathogenic
1
Likely Pathogenic
78
VUS
5
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
7
0
7
Likely Pathogenic
0
0
1
0
1
VUS
0
70
8
0
78
Likely Benign
0
4
1
0
5
Benign
0
1
1
0
2
Total07518093

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

View in ClinVar →

Protein Context — Lollipop Plot

EDIL3 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

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
Overexpressed EDIL3 predicts poor prognosis and promotes anchorage-independent tumor growth in human pancreatic cancer.
Jiang SH et al.·Oncotarget
2016
Highly sensitive fluorescent detection of EDIL3 overexpressed exosomes for the diagnosis of triple-negative breast cancer.
Wei YX et al.·Nanotechnology
2022
Targeted plasma proteomics reveals organ damage signatures of AIDS- and noncommunicable disease-related deaths in people with HIV.
Lin H et al.·Nat Commun
2025
EDIL3 induced by GLIS2 suppresses the anti-tumor activity of CD8(+) T cells and expedites epithelial-mesenchymal transition in thyroid cancer.
Qian X et al.·J Mol Histol
2025
The expression and biological information analysis of miR-375-3p in head and neck squamous cell carcinoma based on 1825 samples from GEO, TCGA, and peer-reviewed publications.
Cen WN et al.·Pathol Res Pract
2018Meta-analysis
Top 5 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