EIF4E3

gene
On this page

Also known as MGC39820

Summary

EIF4E3 (eukaryotic translation initiation factor 4E family member 3, HGNC:31837) is a protein-coding gene on chromosome 3p13, encoding Eukaryotic translation initiation factor 4E type 3 (Q8N5X7). Recognizes and binds the 7-methylguanosine-containing mRNA cap during an early step in the initiation of protein synthesis.

EIF4E3 belongs to the EIF4E family of translational initiation factors that interact with the 5-prime cap structure of mRNA and recruit mRNA to the ribosome (Joshi et al., 2004 [PubMed 15153109]).

Source: NCBI Gene 317649 — RefSeq curated summary.

At a glance

  • GWAS associations: 16
  • Clinical variants (ClinVar): 86 total — 2 pathogenic
  • MANE Select transcript: NM_001134651

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:31837
Approved symbolEIF4E3
Nameeukaryotic translation initiation factor 4E family member 3
Location3p13
Locus typegene with protein product
StatusApproved
AliasesMGC39820
Ensembl geneENSG00000163412
Ensembl biotypeprotein_coding
OMIM609896
Entrez317649

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000295612, ENST00000389826, ENST00000421769, ENST00000425534, ENST00000448225, ENST00000468147, ENST00000469524, ENST00000481525, ENST00000496214, ENST00000497838, ENST00000859497, ENST00000948192

RefSeq mRNA: 5 — MANE Select: NM_001134651 NM_001134649, NM_001134650, NM_001134651, NM_001282886, NM_173359

CCDS: CCDS33786, CCDS46867

Canonical transcript exons

ENST00000425534 — 7 exons

ExonStartEnd
ENSE000012524407169646071696520
ENSE000017462097172519271725402
ENSE000018588497167541471684728
ENSE000035351207171041271710484
ENSE000035777867169961471699708
ENSE000036856467169001071690165
ENSE000037855547169387571693941

Expression profiles

Bgee: expression breadth ubiquitous, 259 present calls, max score 96.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.1634 / max 475.9939, expressed in 1496 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
430959.02121471
431010.4708261
431000.237093
430970.117861
431020.106860
430980.106160
431030.075941
430960.027819

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233696.74gold quality
tibialis anteriorUBERON:000138596.08gold quality
deltoidUBERON:000147695.39gold quality
ileal mucosaUBERON:000033195.17gold quality
monocyteCL:000057694.81gold quality
leukocyteCL:000073894.59gold quality
left ventricle myocardiumUBERON:000656694.44gold quality
skeletal muscle tissueUBERON:000113493.54gold quality
quadriceps femorisUBERON:000137793.54gold quality
skeletal muscle organUBERON:001489293.23gold quality
muscle of legUBERON:000138393.17gold quality
gastrocnemiusUBERON:000138893.17gold quality
vastus lateralisUBERON:000137993.10gold quality
biceps brachiiUBERON:000150792.69gold quality
muscle tissueUBERON:000238592.55gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450292.55gold quality
cardiac muscle of right atriumUBERON:000337992.51gold quality
secondary oocyteCL:000065592.50gold quality
bloodUBERON:000017892.23gold quality
hindlimb stylopod muscleUBERON:000425292.12gold quality
myocardiumUBERON:000234991.27gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451191.24gold quality
bone marrowUBERON:000237190.12gold quality
bone marrow cellCL:000209290.09gold quality
prefrontal cortexUBERON:000045189.75gold quality
colonic epitheliumUBERON:000039789.66gold quality
epithelial cell of pancreasCL:000008389.49gold quality
parotid glandUBERON:000183189.40gold quality
calcaneal tendonUBERON:000370189.05gold quality
islet of LangerhansUBERON:000000688.97gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

210 targeting EIF4E3, 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-656-3P100.0072.152788
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-9-5P100.0072.282361
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-3925-3P100.0069.951237
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-4692100.0067.322066
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-3163100.0077.238605
HSA-MIR-5692A100.0074.406850
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-453199.9969.703181
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-186-5P99.9970.833707
HSA-MIR-451499.9967.101870
HSA-MIR-477599.9875.006394
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-616-5P99.9875.584775
HSA-MIR-373-5P99.9875.364753
HSA-MIR-569699.9872.364487
HSA-MIR-1213699.9872.815713
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-590-3P99.9674.346478
HSA-MIR-570-3P99.9672.414910
HSA-MIR-548AA99.9670.643753

Literature-anchored findings (GeneRIF, showing 6)

  • eIF4E3 impedes oncogenic transformation and its expression is lost in some cancers. (PMID:23587918)
  • MNK1 and MNK2 inhibition ablates eIF4E1 phosphorylation and concurrently enhances eIF4E3 expression in diffuse large B-cell lymphoma. (PMID:25403230)
  • Following heat shock, eIF4E2 is found in both processing bodies and stress granules, whereas eIF4E3_A relocates only to stress granules. (PMID:27578149)
  • We performed bioinformatics analyses of ESTs and the 3’UTRs of the main transcript splice variants of the translational initiation factor eIF4E1 and its family members, eIF4E2 and eIF4E3. We propose to elucidate the minor splice variants of eIF4E2 and eIF4E3 in great detail because they might produce proteins with modified features that fulfill different cellular roles from their major counterparts. (PMID:28942592)
  • eIF4E3 forms an active eIF4F complex during stresses (eIF4FS) targeting mTOR and re-programs the translatome. (PMID:33893802)
  • m7G-related genes-NCBP2 and EIF4E3 determine immune contexture in head and neck squamous cell carcinoma by regulating CCL4/CCL5 expression. (PMID:37067401)

Cross-species orthologs

13 orthologs

OrganismSymbolGene ID
danio_rerioeif4e3ENSDARG00000005078
mus_musculusEif4e3ENSMUSG00000093661
rattus_norvegicusEif4e3ENSRNOG00000010301
drosophila_melanogastereIF4E1FBGN0015218
drosophila_melanogastereIF4E4FBGN0035709
drosophila_melanogastereIF4E5FBGN0035823
drosophila_melanogastereIF4E6FBGN0039622
drosophila_melanogastereIF4E7FBGN0040368
drosophila_melanogastereIF4EHPFBGN0053100
drosophila_melanogastereIF4E3FBGN0265089
caenorhabditis_elegansWBGENE00002059
caenorhabditis_elegansWBGENE00002062
caenorhabditis_elegansWBGENE00002063

Paralogs (3): EIF4E2 (ENSG00000135930), EIF4E (ENSG00000151247), EIF4E1B (ENSG00000175766)

Protein

Protein identifiers

Eukaryotic translation initiation factor 4E type 3Q8N5X7 (reviewed: Q8N5X7)

All UniProt accessions (4): C9J6E5, C9J7Z6, C9JUY2, Q8N5X7

UniProt curated annotations — full annotation on UniProt →

Function. Recognizes and binds the 7-methylguanosine-containing mRNA cap during an early step in the initiation of protein synthesis. May act as an inhibitor of EIF4E1 activity.

Subunit / interactions. eIF4F is a multi-subunit complex, the composition of which varies with external and internal environmental conditions. It is composed of at least eIF4A, eIF4E and eIF4G. EIF4E3 interacts with EIF4G1, but not with EIF4EBP1, EIF4EBP2 and EIF4EBP3.

Similarity. Belongs to the eukaryotic initiation factor 4E family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N5X7-11yes
Q8N5X7-22

RefSeq proteins (5): NP_001128121, NP_001128122, NP_001128123, NP_001269815, NP_775495 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001040TIF_eIF_4EFamily
IPR023398TIF_eIF4e-likeHomologous_superfamily

Pfam: PF01652

UniProt features (6 total): binding site 2, chain 1, region of interest 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N5X7-F180.020.41

Functional residue map

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

Ligand- & substrate-binding residues (2): 115–116; 169–174

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-1169408ISG15 antiviral mechanism
R-HSA-9918487Dengue Virus Genome Translation and Replication

MSigDB gene sets: 188 (showing top): BENPORATH_ES_WITH_H3K27ME3, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_TRANSLATIONAL_INITIATION, GOMF_TRANSLATION_INITIATION_FACTOR_ACTIVITY, BEIER_GLIOMA_STEM_CELL_DN, GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GGGCATT_MIR365, chr3p13, ATTCTTT_MIR186, ATGCTGG_MIR338, ACTTTAT_MIR1425P, DOUGLAS_BMI1_TARGETS_UP

GO Biological Process (3): translational initiation (GO:0006413), regulation of translation (GO:0006417), translation (GO:0006412)

GO Molecular Function (4): RNA 7-methylguanosine cap binding (GO:0000340), translation initiation factor activity (GO:0003743), RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (2): cytosol (GO:0005829), eukaryotic translation initiation factor 4F complex (GO:0016281)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Antimicrobial mechanism of IFN-stimulated genes1
Dengue Virus Infection1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
translation2
translational initiation2
cytoplasm2
formation of translation initiation ternary complex1
metabolic process1
post-transcriptional regulation of gene expression1
regulation of protein metabolic process1
peptidyltransferase activity1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
RNA cap binding1
translation factor activity1
nucleic acid binding1
binding1
cellular anatomical structure1
RNA cap binding complex1

Protein interactions and networks

STRING

2076 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EIF4E3EIF4G1Q04637915
EIF4E3EIF4A1P04765830
EIF4E3EIF4G3O43432785
EIF4E3EIF4EBP1Q13541721
EIF4E3YTHDF1Q9BYJ9685
EIF4E3EIF3DO15371660
EIF4E3EIF5BO60841603
EIF4E3GPR27Q9NS67580
EIF4E3PABPN1Q86U42574
EIF4E3EIF4EBP2Q13542535
EIF4E3MAGOHP50606517
EIF4E3MAGOHBQ96A72513
EIF4E3EIF4E2O60573502
EIF4E3CASC3O15234473
EIF4E3EIF4G2P78344463

IntAct

8 interactions, top by confidence:

ABTypeScore
DCCNTN1psi-mi:“MI:0914”(association)0.700
EIF4A1EIF3Dpsi-mi:“MI:0914”(association)0.530
BMP2KEIF4E3psi-mi:“MI:0915”(physical association)0.490
CFTREIF4E3psi-mi:“MI:0915”(physical association)0.370
EIF4E3TBC1D4psi-mi:“MI:0914”(association)0.350
EIF4E3fliPpsi-mi:“MI:0915”(physical association)0.000

BioGRID (17): TBC1D4 (Affinity Capture-MS), THEMIS2 (Affinity Capture-MS), EIF4E3 (Synthetic Lethality), THEMIS2 (Affinity Capture-MS), TBC1D4 (Affinity Capture-MS), EIF4E3 (Affinity Capture-MS), EIF4E3 (Two-hybrid), EIF4E3 (Affinity Capture-MS), THEMIS2 (Affinity Capture-MS), TBC1D4 (Affinity Capture-MS), EIF4E3 (PCA), CTNNB1 (Affinity Capture-RNA), EIF4E3 (Affinity Capture-Western), EIF4E3 (Affinity Capture-Western), EIF4E3 (Affinity Capture-Western)

ESM2 similar proteins: A0JN27, A0PJN4, A1L167, A1L3K1, A2ADY9, B5DFI8, C1C3R6, D3Z7P3, G3MWR8, O43741, O88508, O94925, P13264, Q07G17, Q12800, Q13888, Q16763, Q1LZ53, Q1RML1, Q28D01, Q28F89, Q2KJ29, Q2TBV5, Q3MHJ2, Q4R9A8, Q4W5Z4, Q5NVP9, Q5R532, Q5RBN9, Q5SP67, Q5TDH0, Q66H54, Q6AYU1, Q6P1K8, Q6PAM0, Q76EZ2, Q7L5Y9, Q7RTP6, Q86TJ2, Q8AVU2

Diamond homologs: A0A075QQ08, A0A1D8EJF9, A0A1U8F5V2, A0A1U8GR65, A0A2J6L8Y7, A0A3Q7FGP1, A0A3Q7I7R4, A0A445AGS0, A3RCV9, A6NMX2, A7KWF8, C6ZJZ3, C7SG33, D3UW26, K0P2S0, M1J8U6, M1JJT8, O04663, O23252, O45551, O60573, O61955, O74743, O77210, O81481, O81482, P06730, P07260, P0DXI0, P0DXI5, P29338, P29557, P48597, P48598, P48599, P48600, P56570, P63073, P63074, P78954

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance70
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
148629GRCh38/hg38 3p13(chr3:70943620-71861889)x1Pathogenic
3062672GRCh37/hg19 3p13(chr3:70583776-72793789)x1Pathogenic

SpliceAI

1204 predictions. Top by Δscore:

VariantEffectΔscore
3:71690003:CACTT:Cdonor_loss1.0000
3:71690004:ACTTA:Adonor_loss1.0000
3:71690005:CTTA:Cdonor_loss1.0000
3:71690006:TTA:Tdonor_loss1.0000
3:71690007:T:TCdonor_loss1.0000
3:71690008:A:ACdonor_gain1.0000
3:71690008:ACGTT:Adonor_loss1.0000
3:71690009:C:Adonor_loss1.0000
3:71690009:C:CGdonor_gain1.0000
3:71690009:CG:Cdonor_gain1.0000
3:71690009:CGT:Cdonor_gain1.0000
3:71690009:CGTT:Cdonor_gain1.0000
3:71690009:CGTTT:Cdonor_gain1.0000
3:71690162:TCAT:Tacceptor_gain1.0000
3:71690163:CAT:Cacceptor_gain1.0000
3:71690163:CATC:Cacceptor_gain1.0000
3:71690164:AT:Aacceptor_gain1.0000
3:71690165:TC:Tacceptor_loss1.0000
3:71690166:C:CCacceptor_gain1.0000
3:71690166:CT:Cacceptor_loss1.0000
3:71710501:A:Tacceptor_gain1.0000
3:71690161:ATCAT:Aacceptor_gain0.9900
3:71690178:C:CTacceptor_gain0.9900
3:71690179:A:Tacceptor_gain0.9900
3:71691706:A:Cacceptor_gain0.9900
3:71691708:T:Cacceptor_gain0.9900
3:71693947:A:Cacceptor_gain0.9900
3:71710500:C:CTacceptor_gain0.9900
3:71710505:C:CTacceptor_gain0.9900
3:71725186:CCTCA:Cdonor_loss0.9900

AlphaMissense

1437 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:71690106:A:GW178R0.999
3:71690106:A:TW178R0.999
3:71690143:A:CS165R0.999
3:71690143:A:TS165R0.999
3:71690145:T:GS165R0.999
3:71693932:A:GW139R0.999
3:71693932:A:TW139R0.999
3:71684706:A:CF217L0.998
3:71684706:A:TF217L0.998
3:71684708:A:GF217L0.998
3:71690114:A:TV175D0.998
3:71690141:A:TV166D0.998
3:71690150:C:TG163E0.998
3:71696489:A:GW126R0.998
3:71696489:A:TW126R0.998
3:71696520:C:AW115C0.998
3:71696520:C:GW115C0.998
3:71699648:A:CY104D0.998
3:71699702:A:GW86R0.998
3:71699702:A:TW86R0.998
3:71690011:T:AK209N0.997
3:71690011:T:GK209N0.997
3:71690016:A:CY208D0.997
3:71690017:A:CF207L0.997
3:71690017:A:TF207L0.997
3:71690019:A:GF207L0.997
3:71690104:C:AW178C0.997
3:71690104:C:GW178C0.997
3:71690108:A:TV177D0.997
3:71690137:A:CS167R0.997

dbSNP variants (sampled 300 via entrez): RS1000025866 (3:71728605 G>C), RS1000123616 (3:71696861 G>A), RS1000135104 (3:71720463 G>A), RS1000166597 (3:71721575 T>C), RS1000190302 (3:71712012 C>T), RS1000208414 (3:71725680 T>C), RS1000236470 (3:71755752 G>A), RS1000239523 (3:71726018 G>A), RS1000327646 (3:71723500 A>G), RS1000345851 (3:71739029 A>G), RS1000361277 (3:71674570 G>A), RS1000373700 (3:71678731 T>C), RS1000377169 (3:71717437 C>A,T), RS1000383922 (3:71698935 T>C), RS1000401981 (3:71720356 C>T)

Disease associations

OMIM: gene MIM:609896 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

16 associations (top):

StudyTraitp-value
GCST003999_1Nose size8.000000e-26
GCST004608_77Granulocyte percentage of myeloid white cells1.000000e-11
GCST004609_113Monocyte percentage of white cells2.000000e-14
GCST007576_379Chronotype1.000000e-08
GCST007576_69Chronotype6.000000e-12
GCST008114_21Type 2 diabetes5.000000e-06
GCST009066_5Mosaic loss of chromosome Y (Y chromosome dosage)2.000000e-09
GCST009067_7Mosaic loss of chromosome Y (Y chromosome dosage)1.000000e-24
GCST009391_1118Metabolite levels1.000000e-06
GCST009391_150Metabolite levels3.000000e-06
GCST009391_983Metabolite levels9.000000e-06
GCST010148_5Cutaneous squamous cell carcinoma2.000000e-09
GCST010241_367Apolipoprotein A1 levels8.000000e-11
GCST010242_46HDL cholesterol levels8.000000e-15
GCST90002393_240Monocyte count3.000000e-16
GCST90002394_246Monocyte percentage of white cells9.000000e-24

EFO canonical traits (11, from GWAS)

EFO IDTrait name
EFO:0007997granulocyte percentage of myeloid white cells
EFO:0007989monocyte percentage of leukocytes
EFO:0008328chronotype measurement
EFO:0007783mosaic loss of chromosome Y measurement
EFO:0010523phosphoglyceric acid measurement
EFO:0010476dimethylglycine measurement
EFO:0010538taurocholate measurement
EFO:1001927cutaneous squamous cell carcinoma
EFO:0004614apolipoprotein A 1 measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0005091monocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

36 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression, increases expression5
trichostatin Aaffects cotreatment, decreases expression3
mercuric bromidedecreases expression, affects cotreatment2
Panobinostataffects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
p-Chloromercuribenzoic Aciddecreases expression, affects cotreatment2
aristolochic acid Idecreases expression1
sotorasibaffects cotreatment, decreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases methylation, affects cotreatment1
sodium arsenateincreases abundance, decreases expression1
tris(2-butoxyethyl) phosphateaffects expression1
arseniteaffects binding, decreases reaction1
sulforaphaneincreases expression1
sodium arseniteincreases expression1
nickel chlorideaffects cotreatment, increases expression1
potassium chromate(VI)decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
dorsomorphindecreases expression, affects cotreatment1
trametinibaffects cotreatment, decreases expression1
(+)-JQ1 compounddecreases expression1
NVP-BKM120affects cotreatment, decreases expression1
Sunitinibincreases expression1
Arsenic Trioxideincreases expression1
Fulvestrantaffects cotreatment, increases methylation1
Air Pollutantsincreases abundance, decreases expression1
Arsenicdecreases expression, increases abundance1
Benzo(a)pyrenedecreases methylation, increases methylation1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_IN95HLY-1 eIF4E3Cancer cell lineSex unspecified

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.