Seroatlas · Human Serome Atlas

EDC3

Enhancer of mRNA-decapping protein 3

Also known as: EDC3_HUMAN, FLJ21128, hYjeF_N2-15q23, LSM16, YJDC, YJEFN2

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q96F86
Gene
EDC3
Ensembl
ENSG00000179151
Chromosome
15
Canonical length
508 aa
Protein class
Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location
Cytoplasmic bodies
Quaternary structure
Homodimer

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

508 residues, UniProt reviewed canonical sequence.

>Q96F86|EDC3
     1  MATDWLGSIV SINCGDSLGV YQGRVSAVDQ VSQTISLTRP FHNGVKCLVP EVTFRAGDIT
    61  ELKILEIPGP GDNQHFGDLH QTELGPSGAG CQVGINQNGT GKFVKKPASS SSAPQNIPKR
   121  TDVKSQDVAV SPQQQQCSKS YVDRHMESLS QSKSFRRRHN SWSSSSRHPN QATPKKSGLK
   181  NGQMKNKDDE CFGDDIEEIP DTDFDFEGNL ALFDKAAVFE EIDTYERRSG TRSRGIPNER
   241  PTRYRHDENI LESEPIVYRR IIVPHNVSKE FCTDSGLVVP SISYELHKKL LSVAEKHGLT
   301  LERRLEMTGV CASQMALTLL GGPNRLNPKN VHQRPTVALL CGPHVKGAQG ISCGRHLANH
   361  DVQVILFLPN FVKMLESITN ELSLFSKTQG QQVSSLKDLP TSPVDLVINC LDCPENVFLR
   421  DQPWYKAAVA WANQNRAPVL SIDPPVHEVE QGIDAKWSLA LGLPLPLGEH AGRIYLCDIG
   481  IPQQVFQEVG INYHSPFGCK FVIPLHSA

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against EDC3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.43
Highest tissue expression
32 nTPM

Expression across tissuesHPA

Tissue

  • testis: 32 nTPM
  • thymus: 17 nTPM
  • tonsil: 17 nTPM
  • ovary: 17 nTPM
  • smooth muscle: 16 nTPM
  • cerebellum: 16 nTPM

Single-cell type

  • late spermatids: 308 nCPM
  • early spermatids: 149 nCPM
  • late primary spermatocytes: 62 nCPM
  • myonuclei: 59 nCPM
  • renal collecting duct intercalated cells: 53 nCPM
  • epicardial cells: 52 nCPM

Immune cell

  • NK-cell: 14 nTPM
  • MAIT T-cell: 10 nTPM
  • gdT-cell: 9.6 nTPM
  • T-reg: 8.5 nTPM
  • memory B-cell: 8.3 nTPM
  • memory CD8 T-cell: 7.9 nTPM

Brain region

  • cerebellum: 36 nTPM
  • white matter: 36 nTPM
  • choroid plexus: 31 nTPM
  • basal ganglia: 30 nTPM
  • medulla oblongata: 30 nTPM
  • hypothalamus: 30 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about EDC3.

Disease | AllUniProt

Conditions EDC3 is implicated in, by any mechanism.

  • Intellectual developmental disorder, autosomal recessive 50 (MRT50) MIM:616460

Disease | GeneticClinVar

2 pathogenic / likely-pathogenic of 69 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

  • Intellectual disability, autosomal recessive 50

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.65
gnomAD pLI
0.03
gnomAD missense Z
2.05
DepMap mean gene effect
-0.04
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of EDC3 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads EDC3 as an antibody target. Whether an autoantibody or antibody against EDC3 could matter depends on whether native EDC3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

EDC3 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label EDC3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/EDC3. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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