EDC4

gene
On this page

Also known as RCD-8Ge-1HEDLS

Summary

EDC4 (enhancer of mRNA decapping 4, HGNC:17157) is a protein-coding gene on chromosome 16q22.1, encoding Enhancer of mRNA-decapping protein 4 (Q6P2E9). In the process of mRNA degradation, seems to play a role in mRNA decapping. It is a selective cancer dependency (DepMap: 29.8% of cell lines).

Predicted to be involved in deadenylation-independent decapping of nuclear-transcribed mRNA. Located in P-body and nucleoplasm.

Source: NCBI Gene 23644 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 188 total
  • Cancer dependency (DepMap): dependent in 29.8% of screened cell lines
  • MANE Select transcript: NM_014329

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17157
Approved symbolEDC4
Nameenhancer of mRNA decapping 4
Location16q22.1
Locus typegene with protein product
StatusApproved
AliasesRCD-8, Ge-1, HEDLS
Ensembl geneENSG00000038358
Ensembl biotypeprotein_coding
OMIM606030
Entrez23644

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 21 protein_coding, 9 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000358933, ENST00000536072, ENST00000572031, ENST00000572221, ENST00000572724, ENST00000573985, ENST00000573992, ENST00000574770, ENST00000575033, ENST00000575507, ENST00000575514, ENST00000576972, ENST00000577028, ENST00000577105, ENST00000851718, ENST00000851719, ENST00000851720, ENST00000851721, ENST00000851722, ENST00000851723, ENST00000851724, ENST00000851725, ENST00000851726, ENST00000851727, ENST00000851728, ENST00000936214, ENST00000936215, ENST00000936216, ENST00000969096, ENST00000969097, ENST00000969098

RefSeq mRNA: 2 — MANE Select: NM_014329 NM_001427345, NM_014329

CCDS: CCDS10849

Canonical transcript exons

ENST00000358933 — 29 exons

ExonStartEnd
ENSE000015504676788395667884499
ENSE000026690596787305267873343
ENSE000034689696787816667878275
ENSE000034827976788006367880216
ENSE000034862156788295867883177
ENSE000034979276788107667881180
ENSE000035092746788149767881533
ENSE000035102416787594567876101
ENSE000035201716787985067879971
ENSE000035230616787648867876599
ENSE000035278806787923767879309
ENSE000035284036788267967882865
ENSE000035631636788195467882109
ENSE000035634946788221267882327
ENSE000035692096787721767877406
ENSE000035715316788126567881417
ENSE000035898576787836067878443
ENSE000035951916787687367876972
ENSE000035958226787895767879137
ENSE000035975726788055767880990
ENSE000036290286787750967877656
ENSE000036442936787941267879503
ENSE000036511026788242967882594
ENSE000036618826787774167877845
ENSE000036687416787958767879774
ENSE000036691576788166867881845
ENSE000036780796787873767878839
ENSE000036823256787853667878631
ENSE000036906506788356867883731

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 96.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.5764 / max 123.9643, expressed in 1810 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
15468917.62411807
1546880.8663588
1546900.086127

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489096.65gold quality
cerebellumUBERON:000203796.54gold quality
cerebellar cortexUBERON:000212996.52gold quality
cerebellar hemisphereUBERON:000224596.50gold quality
pituitary glandUBERON:000000796.04gold quality
mucosa of transverse colonUBERON:000499195.55gold quality
adenohypophysisUBERON:000219695.49gold quality
left testisUBERON:000453395.49gold quality
granulocyteCL:000009495.47gold quality
right testisUBERON:000453495.44gold quality
left ovaryUBERON:000211995.12gold quality
right ovaryUBERON:000211894.86gold quality
apex of heartUBERON:000209894.85gold quality
ovaryUBERON:000099294.81gold quality
right lobe of thyroid glandUBERON:000111994.79gold quality
ganglionic eminenceUBERON:000402394.69gold quality
small intestine Peyer’s patchUBERON:000345494.57gold quality
testisUBERON:000047394.51gold quality
transverse colonUBERON:000115794.41gold quality
spleenUBERON:000210694.36gold quality
metanephros cortexUBERON:001053394.36gold quality
ventricular zoneUBERON:000305394.27gold quality
right uterine tubeUBERON:000130294.25gold quality
left lobe of thyroid glandUBERON:000112094.24gold quality
small intestineUBERON:000210894.23gold quality
left uterine tubeUBERON:000130394.22gold quality
prostate glandUBERON:000236794.19gold quality
stromal cell of endometriumCL:000225594.17gold quality
thyroid glandUBERON:000204694.06gold quality
body of stomachUBERON:000116194.02gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-GEOD-110499no456.05
E-GEOD-106540no455.28
E-GEOD-124858no81.99
E-ANND-3no1.88

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

24 targeting EDC4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-1213699.9872.815713
HSA-MIR-60799.9773.625593
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-335-3P99.9373.364958
HSA-MIR-130599.9171.433443
HSA-MIR-4802-3P99.7270.131273
HSA-MIR-442299.7272.072908
HSA-MIR-513C-5P99.5068.421730
HSA-MIR-514B-5P99.5068.191766
HSA-MIR-136-5P99.5067.261153
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-429299.1665.571767
HSA-MIR-939-3P98.9765.072347
HSA-MIR-4725-5P98.6765.42628
HSA-MIR-6509-3P98.3267.331343
HSA-MIR-451898.1266.821030
HSA-MIR-1212098.0568.441768
HSA-MIR-1266-5P97.7166.921052
HSA-MIR-6859-3P97.2664.69428
HSA-MIR-6773-5P97.0464.30595
HSA-MIR-4436B-5P96.7168.371346
HSA-MIR-6724-5P96.4163.11507
HSA-MIR-6777-3P95.3564.30699

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 29.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 8)

  • EDC4 might contribute to regulation of CoA biosynthesis in addition to its scaffold function in processing bodies (PMID:22982864)
  • The data indicates that DCP2 activation by DCP1 occurs preferentially on the EDC4 scaffold, which may serve to couple DCP2 activation by DCP1 with 5’-to-3’ mRNA degradation by XRN1 in human cells. (PMID:24510189)
  • LMKB is the first protein identified to date that interacts with this portion of Ge-1. LMKB was expressed in human B and T lymphocyte cell lines; depletion of LMKB increased expression of IFI44L. (PMID:24755989)
  • EDC4 is a processing body (P-body) component. (PMID:24858563)
  • The assembly of EDC4 and Dcp1a into processing bodies is critical for the translational regulation of IL-6. (PMID:25970328)
  • EDC4 plays a key role in homologous recombination by stimulating end resection at double-strand breaks. (PMID:29511213)
  • A non-canonical role for the EDC4 decapping factor in regulating MARF1-mediated mRNA decay. (PMID:32510323)
  • Enhancer of mRNA Decapping protein 4 (EDC4) interacts with replication protein a (RPA) and contributes to Cisplatin resistance in cervical Cancer by alleviating DNA damage. (PMID:33054858)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioedc4ENSDARG00000062266
mus_musculusEdc4ENSMUSG00000036270
rattus_norvegicusEdc4ENSRNOG00000024025
drosophila_melanogasterGe-1FBGN0283682
caenorhabditis_elegansedc-4WBGENE00021551

Protein

Protein identifiers

Enhancer of mRNA-decapping protein 4Q6P2E9 (reviewed: Q6P2E9)

Alternative names: Autoantigen Ge-1, Autoantigen RCD-8, Human enhancer of decapping large subunit

All UniProt accessions (4): Q6P2E9, I3L0V0, I3L2F4, I3L3M2

UniProt curated annotations — full annotation on UniProt →

Function. In the process of mRNA degradation, seems to play a role in mRNA decapping. Component of a complex containing DCP2 and DCP1A which functions in decapping of ARE-containing mRNAs. Promotes complex formation between DCP1A and DCP2. Enhances the catalytic activity of DCP2 (in vitro).

Subunit / interactions. Part of a decapping complex consisting of DCP1A, DCP2, EDC3, EDC4 and probably DDX6. Part of a complex consisting of DCP1A, EDC3, EDC4 and DDX6. Part of a complex consisting of DCP1B, EDC3, EDC4 and DDX6. Interacts with DCP2. Interacts with RC3H1. Interacts with NBDY. Interacts with TEX19. Interacts with LSM14A. Interacts with DDX6. Interacts with HELZ. (Microbial infection) Interacts with rotavirus A non-structural protein 2; this interaction probably plays a role in the sequestration of EDC4 in viral factories. Interacts with rotavirus A non-structural protein 5; this interaction probably plays a role in its sequestration in viral factories.

Subcellular location. Cytoplasm. P-body. Nucleus.

Similarity. Belongs to the WD repeat EDC4 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q6P2E9-11yes
Q6P2E9-22

RefSeq proteins (2): NP_001414274, NP_055144* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR032401EDC4_WD40Domain
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR044938EDC4_C_sfHomologous_superfamily
IPR045152EDC4-likeFamily
IPR049404EDC4_CDomain

Pfam: PF16529, PF21289

UniProt features (53 total): modified residue 26, region of interest 8, repeat 7, compositionally biased region 4, sequence conflict 4, initiator methionine 1, chain 1, coiled-coil region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6P2E9-F163.180.22

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (26): 2, 3, 6, 125, 560, 565, 583, 585, 676, 693, 708, 723, 725, 727, 729, 741, 821, 844, 871, 875 …

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-430039mRNA decay by 5’ to 3’ exoribonuclease

MSigDB gene sets: 171 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_UP, YAATNRNNNYNATT_UNKNOWN, MYOGENIN_Q6, chr16q22, GOBP_REGULATION_OF_MRNA_CATABOLIC_PROCESS, GCANCTGNY_MYOD_Q6, CMYB_01, MODULE_45, REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE, MORF_HDAC1, MORF_UBE2N, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, AREB6_01, RACCACAR_AML_Q6, MORF_HDAC2

GO Biological Process (1): deadenylation-independent decapping of nuclear-transcribed mRNA (GO:0031087)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (7): P-body (GO:0000932), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), membrane (GO:0016020), cytoplasmic ribonucleoprotein granule (GO:0036464)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Deadenylation-dependent mRNA decay1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
cytoplasm2
nuclear-transcribed mRNA catabolic process, deadenylation-independent decay1
mRNA methylguanosine-cap decapping1
binding1
cytoplasmic ribonucleoprotein granule1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
ribonucleoprotein granule1

Protein interactions and networks

STRING

1856 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EDC4DCP1AQ9NPI6999
EDC4DCP2Q8IU60998
EDC4EDC3Q96F86998
EDC4DDX6P26196994
EDC4XRN1Q8IZH2978
EDC4LSM14AQ8ND56936
EDC4LSM1O15116882
EDC4UPF1Q92900877
EDC4AGO2Q9UKV8786
EDC4DCP1BQ8IZD4780
EDC4PATL1Q86TB9728
EDC4TNRC6AQ8NDV7725
EDC4CNOT1A5YKK6723
EDC4EIF4ENIF1Q9NRA8713
EDC4LSM4Q9Y4Z0696

IntAct

219 interactions, top by confidence:

ABTypeScore
EDC3DDX6psi-mi:“MI:0914”(association)0.960
MED4MED19psi-mi:“MI:2364”(proximity)0.900
DCP2EDC4psi-mi:“MI:0915”(physical association)0.890
EDC4DCP2psi-mi:“MI:0914”(association)0.890
EDC4DCP2psi-mi:“MI:0915”(physical association)0.890
DCP1AEDC4psi-mi:“MI:0914”(association)0.880
EDC4DCP1Apsi-mi:“MI:0403”(colocalization)0.880
DCP1AEDC4psi-mi:“MI:0403”(colocalization)0.880
DCP1AEDC4psi-mi:“MI:0915”(physical association)0.880
EDC4DCP1Apsi-mi:“MI:0915”(physical association)0.880
SGF29NDC80psi-mi:“MI:0914”(association)0.840
ATXN2PABPC1psi-mi:“MI:0915”(physical association)0.820
DDX6EDC4psi-mi:“MI:0914”(association)0.820
PATL1LSM1psi-mi:“MI:0914”(association)0.770
EDC4XRN1psi-mi:“MI:0915”(physical association)0.750
XRN1EDC4psi-mi:“MI:0914”(association)0.750
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
EDC3EDC4psi-mi:“MI:0914”(association)0.640

BioGRID (327): EDC4 (Affinity Capture-RNA), EDC4 (Affinity Capture-RNA), EDC4 (Affinity Capture-RNA), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Affinity Capture-MS), EDC4 (Co-fractionation), EDC4 (Affinity Capture-MS), EDC4 (Proximity Label-MS)

ESM2 similar proteins: A0A140LI67, A0A1W2PR48, A0JP70, D3YYM4, F1LW30, O13034, O15040, O70173, Q15345, Q3SXM0, Q3UDP0, Q3UJB9, Q3ULW6, Q3V129, Q3ZAV8, Q58DC2, Q5F479, Q5JV73, Q5M9H0, Q5M9H1, Q5R6T6, Q5R9H2, Q68DX3, Q6IRN0, Q6NV72, Q6P2E9, Q6P4K6, Q6PCD5, Q6ZPG2, Q6ZW76, Q7TNH6, Q80TQ5, Q8BLD6, Q8C008, Q8C5V5, Q8CBW4, Q8CIK8, Q8IWE5, Q8JZL1, Q8K1C9

Diamond homologs: Q1LUT1, Q3UJB9, Q3ZAV8, Q6P2E9, Q7ZXT3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 193 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
mRNA decay by 5’ to 3’ exoribonuclease740.4×9e-08
Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA524.0×3e-04
SARS-CoV-1-host interactions912.0×2e-05
SARS-CoV-1 modulates host translation machinery511.7×5e-03
SARS-CoV-1 Infection88.7×6e-04
Translation initiation complex formation68.7×5e-03
SARS-CoV-2-host interactions76.3×7e-03
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)85.9×5e-03

GO biological processes:

GO termPartnersFoldFDR
P-body assembly531.5×4e-04
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay616.8×6e-04
mRNA transport711.0×8e-04
negative regulation of translation78.2×3e-03
translation95.5×4e-03
mRNA splicing, via spliceosome105.5×2e-03
mRNA processing104.7×5e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

188 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance151
Likely benign9
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

4524 predictions. Top by Δscore:

VariantEffectΔscore
16:67873339:GGGCG:Gdonor_gain1.0000
16:67873340:GGCG:Gdonor_gain1.0000
16:67873340:GGCGG:Gdonor_gain1.0000
16:67873341:GCGG:Gdonor_gain1.0000
16:67875839:T:Gdonor_gain1.0000
16:67875940:CCCA:Cacceptor_loss1.0000
16:67875942:CA:Cacceptor_loss1.0000
16:67875943:A:AGacceptor_gain1.0000
16:67875943:A:ATacceptor_loss1.0000
16:67875943:AG:Aacceptor_gain1.0000
16:67875944:G:GTacceptor_gain1.0000
16:67875944:GG:Gacceptor_gain1.0000
16:67875944:GGC:Gacceptor_gain1.0000
16:67875944:GGCC:Gacceptor_gain1.0000
16:67875944:GGCCC:Gacceptor_gain1.0000
16:67876097:GTCAT:Gdonor_gain1.0000
16:67876102:G:GGdonor_gain1.0000
16:67876485:CAG:Cacceptor_loss1.0000
16:67876486:A:AGacceptor_gain1.0000
16:67876486:AGCT:Aacceptor_gain1.0000
16:67876487:G:GGacceptor_gain1.0000
16:67876487:G:GTacceptor_loss1.0000
16:67876487:GCT:Gacceptor_gain1.0000
16:67876487:GCTG:Gacceptor_gain1.0000
16:67876487:GCTGT:Gacceptor_gain1.0000
16:67876862:T:Aacceptor_gain1.0000
16:67876863:G:Aacceptor_gain1.0000
16:67876868:CTCAG:Cacceptor_loss1.0000
16:67876870:CA:Cacceptor_loss1.0000
16:67876871:A:ACacceptor_loss1.0000

AlphaMissense

9136 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:67873308:T:CL16P1.000
16:67873320:T:CL20P1.000
16:67876903:T:AW128R1.000
16:67876903:T:CW128R1.000
16:67878206:T:CL312P1.000
16:67878209:C:AA313D1.000
16:67878239:T:CF323S1.000
16:67878412:T:CF353L1.000
16:67878413:T:CF353S1.000
16:67878414:C:AF353L1.000
16:67878414:C:GF353L1.000
16:67878419:A:TD355V1.000
16:67878546:T:AW367R1.000
16:67878546:T:CW367R1.000
16:67878552:T:CF369L1.000
16:67878554:C:AF369L1.000
16:67878554:C:GF369L1.000
16:67878556:T:CL370P1.000
16:67878594:T:AW383R1.000
16:67878594:T:CW383R1.000
16:67878609:T:AW388R1.000
16:67878609:T:CW388R1.000
16:67878611:G:CW388C1.000
16:67878611:G:TW388C1.000
16:67878814:T:CL421P1.000
16:67878961:T:CL431P1.000
16:67879291:T:CL508P1.000
16:67883170:T:CF1281S1.000
16:67883572:T:CL1285P1.000
16:67883671:T:CL1318P1.000

dbSNP variants (sampled 300 via entrez): RS1000217523 (16:67880426 G>A), RS1000491813 (16:67873193 G>A,C,T), RS1000842486 (16:67873411 A>G,T), RS1001072909 (16:67876814 G>A), RS1001232055 (16:67872067 G>T), RS1001308848 (16:67883857 C>T), RS1001516286 (16:67874270 C>A,G,T), RS1001946610 (16:67872663 T>A), RS1002011024 (16:67873800 C>T), RS1002301810 (16:67875653 A>G,T), RS1002344442 (16:67879424 T>C), RS1002605561 (16:67875657 C>G,T), RS1002632472 (16:67873644 A>T), RS1002924613 (16:67875874 G>A,T), RS1003296910 (16:67881065 T>C)

Disease associations

OMIM: gene MIM:606030 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

5 associations (top):

StudyTraitp-value
GCST000974_8HDL cholesterol8.000000e-06
GCST001436_3Metabolic syndrome2.000000e-10
GCST002539_84Schizophrenia2.000000e-08
GCST006803_42Schizophrenia4.000000e-08
GCST010002_113Refractive error2.000000e-14

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0000195metabolic syndrome

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases abundance, increases expression, decreases expression3
Smokeincreases abundance, increases expression, decreases expression2
FR900359affects phosphorylation1
bisphenol Adecreases expression1
perfluorooctanoic aciddecreases expression1
coumarinincreases phosphorylation1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
Fulvestrantincreases methylation1
Leflunomidedecreases expression1
Air Pollutantsincreases abundance, increases expression1
Arsenicdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Caffeinedecreases phosphorylation1
Clozapineincreases expression1
Diazinonincreases methylation1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Ivermectindecreases expression1
Ribonucleotidesaffects binding1
Rotenonedecreases expression1
Aflatoxin B1increases methylation1
Genisteindecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.