EDC3 Enhancer of mRNA Decapping 3

A key regulator of mRNA decay and P-body assembly

Gene Information Card

Symbol EDC3
Full Name Enhancer of mRNA Decapping 3
Gene Type Protein coding
Chromosomal Location 15q24.1
NCBI Gene ID 80153 ncbi.nlm.nih.gov/gene/80153
Ensembl ID ENSG00000179151
UniProt ID Q96F86
OMIM ID 609842
HGNC ID 26141
Aliases LSm16, YJEFN2, hYjeF_N2

Description

EDC3 encodes a protein that functions as an enhancer of mRNA decapping, a critical step in the 5'-to-3' mRNA decay pathway. The protein localizes to cytoplasmic processing bodies (P-bodies) and interacts with the decapping enzyme DCP2 and other decapping cofactors. EDC3 contains an LSm domain and a YjeF-N domain, which are involved in RNA binding and protein-protein interactions. It plays a role in post-transcriptional gene regulation by promoting the removal of the 5' cap from mRNAs, thereby facilitating their degradation.

Disease Associations

Disease category Pathophysiological mechanism Genomic evidence
Cancer (various types) Altered expression of EDC3 may disrupt mRNA turnover of oncogenes or tumor suppressors, contributing to tumorigenesis. COSMIC database reports somatic mutations in multiple cancer types.
Neurodevelopmental disorders Potential role in mRNA regulation in neurons; variants may affect synaptic mRNA decay. Limited evidence from rare variant studies; not yet confirmed in large cohorts.

Expression Profile

Tissue Expression
Tissue nTPM level
Testis 12.5 Medium
Lymph node 10.2 Medium
Spleen 9.8 Medium
Brain 6.3 Low
Liver 5.1 Low
Cell Line Expression
Cell Line nTPM Notes
HEK293 15.0 High expression in embryonic kidney cells
HeLa 12.3 Moderate expression in cervical cancer cells
K562 8.7 Moderate expression in leukemia cells
HepG2 6.5 Low expression in liver cancer cells
Data source:Human Protein Atlas(proteinatlas.org)

Mutations & Variants

Hotspot Mutations
Variant Type Frequency Functional Description
c.1A>G (p.Met1?) Missense <0.01% Likely loss of start codon; predicted loss of function
c.287C>T (p.Pro96Leu) Missense <0.01% Unknown significance; reported in COSMIC
c.1045G>A (p.Glu349Lys) Missense <0.01% Unknown significance; reported in COSMIC
Mutation functional classification

Loss of Function (LOF)

Loss-of-function mutations in EDC3 are predicted to impair mRNA decapping and P-body assembly, potentially leading to dysregulated gene expression.

Gain of Function (GOF)

No gain-of-function mutations have been characterized for EDC3.

Dominant Negative (DN)

No dominant-negative mutations have been reported for EDC3.

Gene Ontology (GO)

• deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290) • P-body (GO:0000932)
• RNA binding (GO:0003723) • protein binding (GO:0005515)
• deadenylation-independent decapping of nuclear-transcribed mRNA (GO:0031087)

Pathways

• mRNA decay by 5'-to-3' exoribonuclease
• Processing of capped intron-containing pre-mRNA

Protein Summary

EDC3 is a 508-amino acid protein with a molecular weight of approximately 57 kDa. It contains an N-terminal LSm domain (residues 1-70) that mediates RNA binding and interaction with the decapping complex, and a C-terminal YjeF-N domain (residues 200-400) of unknown function but conserved in bacteria and eukaryotes. The protein is predominantly cytoplasmic and localizes to P-bodies, where it enhances the activity of DCP2. EDC3 also interacts with other decapping factors such as DCP1A, DDX6, and PATL1. Post-translational modifications include phosphorylation, which may regulate its localization and activity.

Related Products

Product name Cat.No. Species Gene ID
EDC3 Knockout HEK293 Cell Line EDJ-KQ9466 Human 80153 Details Get a Quote
EDC3 Knockout HeLa Cell Line EDJ-KQ34926 Human 80153 Details Get a Quote
EDC3 Knockout A-549 Cell Line EDJ-KQ36170 Human 80153 Details Get a Quote
EDC3 Knockout HCT 116 Cell Line EDJ-KQ36171 Human 80153 Details Get a Quote
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