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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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EDC3
enhancer of mRNA decapping 3
Chromosome 15 Β· 15q24.1
NCBI Gene: 80153Ensembl: ENSG00000179151.14HGNC: HGNC:26114UniProt: Q96F86
121PubMed Papers
21Diseases
0Drugs
2Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cytoplasmic ribonucleoprotein granuleprotein bindingidentical protein bindingmembraneautosomal recessive non-syndromic intellectual disabilityneurodegenerative diseasejoint diseaseThrombocytopenia
✦AI Summary

EDC3 (enhancer of mRNA decapping 3) is a conserved RNA-binding protein that functions as a scaffold in post-transcriptional gene regulation. Structurally, EDC3 possesses an N-terminal Lsm domain, central FDF domain, and C-terminal YjeF-N domain that forms functionally critical dimers 1. The protein operates through multiple mechanisms: it enhances 5' cap removal by recruiting the Dcp1/2 decapping enzyme 2, promotes P-body assembly by aggregating mRNA ribonucleoproteins 1, and acts redundantly with Scd6 to target transcripts for degradation while coordinating translational repression 3. EDC3 function is modulated by direct binding to NADH, suggesting coupling of cellular energy status to mRNA decay 4. P-body dynamics are regulated through EDC3 interaction with Sbp1, which competes with Edc3-Edc3 interactions to promote disassembly 5. EDC3 participates in metabolic adaptation by suppressing mRNAs encoding respiratory and alternative carbon source utilization proteins during glucose limitation 3. Clinical relevance includes association with autosomal recessive intellectual developmental disorder 50, and smoking-induced epigenetic changes affecting EDC3 methylation in lung epithelial cells 6.

Sources cited
1
EDC3 serves as a scaffold for P-body formation, possesses modular domain architecture (Lsm, FDF, YjeF-N domains), and dimerization is required for efficient RNA binding and P-body assembly
PMID: 18678652
2
EDC3 is a decapping coactivator enriched in cytoplasmic P-bodies that enhances Dcp1/2 activity and participates in mRNA decay and translational repression
PMID: 31231973
3
EDC3 physically interacts with Sbp1, and Sbp1-Edc3 interaction competes with Edc3-Edc3 interactions to regulate P-body disassembly
PMID: 35440550
4
Human and yeast EDC3 directly binds NADH and chemically modifies NAD in vitro, suggesting interaction with NAD-related molecules regulates mRNA translation and degradation
PMID: 24504254
5
EDC3 acts redundantly with Scd6 to recruit Dhh1 to Dcp2, regulating mRNA decapping and translational repression of starvation-response genes in nutrient-limited conditions
PMID: 41289350
6
Smoking reduces methylation levels at the EDC3 locus in bronchial basal cells, persisting beyond smoking cessation
PMID: 39980243
Disease Associationsβ“˜21
autosomal recessive non-syndromic intellectual disabilityOpen Targets
0.53Moderate
neurodegenerative diseaseOpen Targets
0.39Weak
joint diseaseOpen Targets
0.21Weak
ThrombocytopeniaOpen Targets
0.05Suggestive
autosomal dominant macrothrombocytopeniaOpen Targets
0.05Suggestive
Genetic renal or urinary tract malformationOpen Targets
0.05Suggestive
thrombocytopenia 4Open Targets
0.04Suggestive
congenital anomalies of kidney and urinary tract 1Open Targets
0.04Suggestive
platelet-type bleeding disorder 15Open Targets
0.04Suggestive
macrothrombocytopenia, isolated, 2, autosomal dominantOpen Targets
0.04Suggestive
renal hypodysplasia/aplasia 3Open Targets
0.04Suggestive
familial juvenile hyperuricemic nephropathy type 2Open Targets
0.04Suggestive
Hyperuricemia - anemia - renal failureOpen Targets
0.04Suggestive
bleeding disorder, platelet-type, 24Open Targets
0.04Suggestive
thrombocytopenia 2Open Targets
0.03Suggestive
congenital hydronephrosisOpen Targets
0.03Suggestive
focal segmental glomerulosclerosisOpen Targets
0.03Suggestive
focal segmental glomerulosclerosis 7Open Targets
0.03Suggestive
platelet-type bleeding disorder 10Open Targets
0.03Suggestive
Beta-thalassemia - X-linked thrombocytopeniaOpen Targets
0.03Suggestive
Intellectual developmental disorder, autosomal recessive 50UniProt
Pathogenic Variants2
NM_025083.5(EDC3):c.512del (p.Gln171fs)Pathogenic
Intellectual disability, autosomal recessive 50
β˜…β˜†β˜†β˜†2024β†’ Residue 171
NM_025083.5(EDC3):c.161T>C (p.Phe54Ser)Pathogenic
Intellectual disability, autosomal recessive 50
β˜†β˜†β˜†β˜†2021β†’ Residue 54
View on ClinVar β†—
Related Genes
UPF1Protein interaction100%ZFP36Protein interaction100%CNOT1Protein interaction100%LSM14AProtein interaction100%TNRC6AProtein interaction100%PNRC2Protein interaction100%
Tissue Expression6 tissues
Ovary
100%
Brain
77%
Lung
69%
Liver
68%
Heart
62%
Bone Marrow
32%
Gene Interaction Network
Click a node to explore
EDC3UPF1ZFP36CNOT1LSM14ATNRC6APNRC2
PROTEIN STRUCTURE
Preparing viewer…
PDB2VC8 Β· 1.31 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.66LoF Tolerant
pLIβ“˜
0.04Tolerant
Observed/Expected LoF0.45 [0.32–0.66]
RankingsWhere EDC3 stands among ~20K protein-coding genes
  • #3,880of 20,598
    Most Researched121 Β· top quartile
  • #4,290of 5,498
    Most Pathogenic Variants2
  • #4,787of 17,882
    Most Constrained (LOEUF)0.66
Genes detectedEDC3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Crystal structure of human Edc3 and its functional implications.
PMID: 18678652
Mol Cell Biol Β· 2008
1.00
2
Pat1 RNA-binding proteins: Multitasking shuttling proteins.
PMID: 31231973
Wiley Interdiscip Rev RNA Β· 2019
0.90
3
Low complexity RGG-motif sequence is required for Processing body (P-body) disassembly.
PMID: 35440550
Nat Commun Β· 2022
0.80
4
Edc3 function in yeast and mammals is modulated by interaction with NAD-related compounds.
PMID: 24504254
G3 (Bethesda) Β· 2014
0.70
5
Normal bronchial field basal cells show persistent methylome-wide impact of tobacco smoking, including in known cancer genes.
PMID: 39980243
Epigenetics Β· 2025
0.60