EDC3

Chr 15AR

enhancer of mRNA decapping 3

Also known as: LSM16, MRT50, YJDC, YJEFN2, hYjeF_N2-15q23

NCBI Gene: 80153 ENSG00000179151 UniProt: Q96F86 OMIM: 609842

This gene encodes a protein that is important in mRNA degradation. The encoded protein is a component of a decapping complex that promotes efficient removal of the monomethylguanosine (m7G) cap from mRNAs, as part of the 5' to 3' mRNA decay pathway. Mutations in this gene have been identified in human patients with an autosomal recessive form of intellectual disability. [provided by RefSeq, May 2017]

OMIM Research

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

?Intellectual developmental disorder, autosomal recessive 50MIM #616460

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.65

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.65LOEUF

pLI 0.026

Z-score 2.67

OE 0.33 (0.18–0.65)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

2.05Z-score

OE missense 0.66 (0.59–0.74)

191 obs / 289.0 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.33 (0.18–0.65)

0≤0.351.4

Missense OE?0.66 (0.59–0.74)

0≤0.61.4

Synonymous OE?0.89

0≤1.21.6

LoF obs/exp: 6 / 18.3Missense obs/exp: 191 / 289.0Syn Z: 0.95

Background carrier burden — how many people carry a rare variant somewhere in EDC3?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 130

512 rare PASS variants

Rare truncating (LoF)

1 in 7,500

56 rare PASS variants

Rare synonymous (reference)

1 in 190

244 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for EDC3. 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 140	1 in 6,700
South Asian	~43k	1 in 170	1 in 4,800
Remaining (unassigned)	~30k	1 in 100	≈ 1 in 7,500
European (Finnish)	~27k	1 in 550	≈ 1 in 27,000
Admixed American	~22k	1 in 140	≈ 1 in 22,000
African / African American	~21k	1 in 130	≈ 1 in 9,300
East Asian	~20k	1 in 210	≈ 1 in 9,900
Ashkenazi Jewish	~13k	1 in 650	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 240	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 6 coding exons well covered in gnomAD exomes and genomes.? see exons ↓