EDIL3

Chr 5

EGF like and discoidin domains 3

Also known as: DEL1

NCBI Gene: 10085 ENSG00000164176 UniProt: O43854

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.

ResearchSummary from RefSeq, UniProt

The protein encoded by this gene is an integrin ligand. It plays an important role in mediating angiogenesis and may be important in vessel wall remodeling and development. It also influences endothelial cell behavior. [provided by RefSeq, Jul 2008]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.63

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

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 OE?0.39 (0.25–0.63)

0≤0.351.4

Missense OE?0.80 (0.71–0.89)

0≤0.61.4

Synonymous OE?0.94

0≤1.21.6

LoF obs/exp: 12 / 30.8Missense obs/exp: 206 / 258.7Syn Z: 0.48

Background carrier burden — how many people carry a rare variant somewhere in EDIL3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 150

568 rare PASS variants

Rare truncating (LoF)

1 in 3,800

71 rare PASS variants

Rare synonymous (reference)

1 in 220

204 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for EDIL3. 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 240	1 in 3,300
South Asian	~43k	1 in 160	1 in 6,100
Remaining (unassigned)	~30k	1 in 91	≈ 1 in 7,500
European (Finnish)	~27k	1 in 370	≈ 1 in 27,000
Admixed American	~22k	1 in 120	1 in 3,800
African / African American	~21k	1 in 79	≈ 1 in 8,300
East Asian	~20k	1 in 120	1 in 990
Ashkenazi Jewish	~13k	1 in 680	1 in 2,600
Middle Eastern	~2,884	1 in 100	none seen

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 11 coding exons well covered in gnomAD exomes and genomes.? see exons ↓