EIF3CL

gene
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Summary

EIF3CL (eukaryotic translation initiation factor 3 subunit C like, HGNC:26347) is a protein-coding gene on chromosome 16p12.1, encoding Eukaryotic translation initiation factor 3 subunit C-like protein (B5ME19). Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis.

The protein encoded by this gene is a core subunit of the eukaryotic translation initiation factor 3 (eIF3) complex. The encoded protein is nearly identical to another protein, eIF3c, from a related gene. The eIF3 complex binds the 40S ribosome and mRNAs to enable translation initiation. Several transcript variants encoding the same protein have been found for this gene.

Source: NCBI Gene 728689 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 12 total
  • MANE Select transcript: NM_001317857

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26347
Approved symbolEIF3CL
Nameeukaryotic translation initiation factor 3 subunit C like
Location16p12.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000205609
Ensembl biotypeprotein_coding
Entrez728689

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000380876, ENST00000398944, ENST00000864343, ENST00000918077, ENST00000918078, ENST00000962381, ENST00000962382, ENST00000962383

RefSeq mRNA: 3 — MANE Select: NM_001317857 NM_001099661, NM_001317856, NM_001317857

CCDS: CCDS42136

Canonical transcript exons

ENST00000380876 — 21 exons

ExonStartEnd
ENSE000016028762839198028392142
ENSE000016221832840061528400669
ENSE000016310402838850828388698
ENSE000016369262838029228380379
ENSE000016669062840153928401604
ENSE000016795912838805828388282
ENSE000016973072838311828383481
ENSE000017098812839175228391855
ENSE000017121082838046828380533
ENSE000017186952840037728400486
ENSE000017222682837997628380138
ENSE000017353712839987128399998
ENSE000017366222840120728401396
ENSE000017554652839084028390981
ENSE000017598972838063228380791
ENSE000017611112839052028390645
ENSE000017767652840085928400984
ENSE000017900582839029128390384
ENSE000018492182840378728403841
ENSE000019407312837971528379880
ENSE000023670012840351828403648

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 92.94.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 24.6456 / max 201.7010, expressed in 1810 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
15338624.64561810

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209892.94gold quality
lower esophagus mucosaUBERON:003583487.00gold quality
heart left ventricleUBERON:000208485.92gold quality
mucosa of transverse colonUBERON:000499184.90gold quality
colonic epitheliumUBERON:000039784.08gold quality
right atrium auricular regionUBERON:000663184.07gold quality
heartUBERON:000094883.67gold quality
skeletal muscle tissueUBERON:000113483.27gold quality
gastrocnemiusUBERON:000138883.00gold quality
anterior cingulate cortexUBERON:000983582.91gold quality
Ammon’s hornUBERON:000195482.65gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.43gold quality
right frontal lobeUBERON:000281082.36gold quality
putamenUBERON:000187481.94gold quality
dorsolateral prefrontal cortexUBERON:000983481.90gold quality
amygdalaUBERON:000187681.63gold quality
muscle of legUBERON:000138381.56gold quality
stromal cell of endometriumCL:000225581.53gold quality
temporal lobeUBERON:000187181.52gold quality
right hemisphere of cerebellumUBERON:001489080.96gold quality
nucleus accumbensUBERON:000188280.68gold quality
Brodmann (1909) area 9UBERON:001354080.68gold quality
cerebellar hemisphereUBERON:000224580.58gold quality
cerebral cortexUBERON:000095680.48gold quality
primary visual cortexUBERON:000243680.46gold quality
right lobe of liverUBERON:000111480.34gold quality
muscle tissueUBERON:000238580.33gold quality
substantia nigraUBERON:000203880.32gold quality
brainUBERON:000095580.30gold quality
hypothalamusUBERON:000189880.18gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes18.24
E-MTAB-8060no554.92
E-CURD-53no511.71
E-MTAB-7008no81.12

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting EIF3CL, 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-3617-3P99.9867.86918
HSA-MIR-545-3P99.9570.742783
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-443799.5265.291266
HSA-MIR-122B-5P99.4670.811457
HSA-MIR-3606-5P99.3169.671168
HSA-MIR-877-3P99.0968.101637
HSA-MIR-1228-3P99.0066.53857
HSA-MIR-873-5P98.8466.901348
HSA-MIR-1199-5P98.4466.51829
HSA-MIR-6751-3P98.4466.35835
HSA-MIR-466097.7967.441328
HSA-MIR-475997.3965.86608
HSA-MIR-134-5P97.1166.52976
HSA-MIR-311897.1166.58984
HSA-MIR-92197.0966.45562
HSA-MIR-215-3P97.0268.011209
HSA-MIR-6759-3P96.9468.31823
HSA-MIR-34A-3P96.8067.70805
HSA-MIR-6854-5P96.7765.96848
HSA-MIR-6857-3P96.7065.43915
HSA-MIR-3117-3P95.9667.82473
HSA-MIR-808395.9367.55694

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioeif3cENSDARG00000016443
mus_musculusEif3cENSMUSG00000030738
rattus_norvegicusEif3cENSRNOG00000018761
drosophila_melanogastereIF3cFBGN0034258
caenorhabditis_eleganseif-3.CWBGENE00001226

Paralogs (1): EIF3C (ENSG00000184110)

Protein

Protein identifiers

Eukaryotic translation initiation factor 3 subunit C-like proteinB5ME19 (reviewed: B5ME19)

All UniProt accessions (1): B5ME19

UniProt curated annotations — full annotation on UniProt →

Function. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is required for several steps in the initiation of protein synthesis. The eIF-3 complex associates with the 40S ribosome and facilitates the recruitment of eIF-1, eIF-1A, eIF-2:GTP:methionyl-tRNAi and eIF-5 to form the 43S pre-initiation complex (43S PIC). The eIF-3 complex stimulates mRNA recruitment to the 43S PIC and scanning of the mRNA for AUG recognition. The eIF-3 complex is also required for disassembly and recycling of post-termination ribosomal complexes and subsequently prevents premature joining of the 40S and 60S ribosomal subunits prior to initiation. The eIF-3 complex specifically targets and initiates translation of a subset of mRNAs involved in cell proliferation, including cell cycling, differentiation and apoptosis, and uses different modes of RNA stem-loop binding to exert either translational activation or repression.

Subunit / interactions. Component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is composed of 13 subunits: EIF3A, EIF3B, EIF3C, EIF3D, EIF3E, EIF3F, EIF3G, EIF3H, EIF3I, EIF3J, EIF3K, EIF3L and EIF3M. The eIF-3 complex appears to include 3 stable modules: module A is composed of EIF3A, EIF3B, EIF3G and EIF3I; module B is composed of EIF3F, EIF3H, and EIF3M; and module C is composed of EIF3C, EIF3D, EIF3E, EIF3K and EIF3L. EIF3C of module C binds EIF3B of module A and EIF3H of module B, thereby linking the three modules. EIF3J is a labile subunit that binds to the eIF-3 complex via EIF3B. The eIF-3 complex interacts with RPS6KB1 under conditions of nutrient depletion. Mitogenic stimulation leads to binding and activation of a complex composed of MTOR and RPTOR, leading to phosphorylation and release of RPS6KB1 and binding of EIF4B to eIF-3.

Subcellular location. Cytoplasm.

Post-translational modifications. Phosphorylated. Phosphorylation is enhanced upon serum stimulation.

Similarity. Belongs to the eIF-3 subunit C family.

RefSeq proteins (3): NP_001093131, NP_001304785, NP_001304786* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000717PCI_domDomain
IPR008905EIF3C_N_domDomain
IPR027516EIF3CFamily
IPR036388WH-like_DNA-bd_sfHomologous_superfamily
IPR036390WH_DNA-bd_sfHomologous_superfamily
IPR058999EIF3CL_CDomain

Pfam: PF01399, PF05470, PF26569

UniProt features (29 total): modified residue 15, compositionally biased region 8, region of interest 4, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-B5ME19-F174.110.27

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 (15): 9, 11, 13, 15, 16, 18, 39, 99, 166, 178, 181, 182, 525, 644, 910

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 29 (showing top): GOBP_CYTOPLASMIC_TRANSLATION, GOBP_TRANSLATIONAL_INITIATION, GOCC_EUKARYOTIC_TRANSLATION_INITIATION_FACTOR_3_COMPLEX, GOMF_TRANSLATION_INITIATION_FACTOR_ACTIVITY, GOBP_TRANSLATION, GOBP_CYTOPLASMIC_TRANSLATIONAL_INITIATION, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, LINDVALL_IMMORTALIZED_BY_TERT_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, chr16p12, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOCC_CYTOSOLIC_TRANSLATION_PREINITIATION_COMPLEX, GOMF_TRANSLATION_INITIATION_FACTOR_BINDING, E2F3_UP.V1_DN, SRC_UP.V1_DN

GO Biological Process (4): formation of cytoplasmic translation initiation complex (GO:0001732), translational initiation (GO:0006413), cytoplasmic translational initiation (GO:0002183), translation (GO:0006412)

GO Molecular Function (4): RNA binding (GO:0003723), translation initiation factor activity (GO:0003743), translation initiation factor binding (GO:0031369), protein binding (GO:0005515)

GO Cellular Component (4): eukaryotic translation initiation factor 3 complex (GO:0005852), eukaryotic 43S preinitiation complex (GO:0016282), eukaryotic 48S preinitiation complex (GO:0033290), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
translational initiation3
cytosolic small ribosomal subunit2
cytosolic translation preinitiation complex2
cytoplasmic translational initiation1
protein-RNA complex assembly1
formation of translation initiation ternary complex1
translation1
metabolic process1
cytoplasmic translation1
peptidyltransferase activity1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
nucleic acid binding1
translation factor activity1
protein binding1
binding1
cytoplasm1
protein-containing complex1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

1577 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EIF3CLSOWAHDA6NJG2518
EIF3CLEIF3DO15371507
EIF3CLTUFMP49411497
EIF3CLRABEP2Q9H5N1496
EIF3CLEIF3FO00303490
EIF3CLEIF3KQ9UBQ5458
EIF3CLEIF2S2P20042458
EIF3CLEIF3MQ7L2H7458
EIF3CLEIF3LQ9Y262457
EIF3CLEIF3GO75821454
EIF3CLNPIPB9F8W1W9451
EIF3CLLRRC47Q8N1G4449
EIF3CLEIF3IQ13347447
EIF3CLEIF3JO75822443
EIF3CLEIF3AQ14152443

IntAct

66 interactions, top by confidence:

ABTypeScore
EIF3CLEIF3Hpsi-mi:“MI:0915”(physical association)0.670
EIF3HEIF3CLpsi-mi:“MI:0914”(association)0.670
EIF3FEIF3CLpsi-mi:“MI:0914”(association)0.640
EIF3IEIF3CLpsi-mi:“MI:0914”(association)0.640
EIF3MEIF3CLpsi-mi:“MI:0914”(association)0.640
EIF3EEIF3CLpsi-mi:“MI:0914”(association)0.530
EIF3LEIF3CLpsi-mi:“MI:0914”(association)0.530
EIF3CLH1-5psi-mi:“MI:0915”(physical association)0.400
STK4EIF3CLpsi-mi:“MI:0914”(association)0.350
OCRLEIF3CLpsi-mi:“MI:0914”(association)0.350
LRRK2psi-mi:“MI:0914”(association)0.350
RAB5AEIF3CLpsi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
BMI1HMGB1P1psi-mi:“MI:0914”(association)0.350
BMI1MEIS3P1psi-mi:“MI:0914”(association)0.350
RAF1EIF3CLpsi-mi:“MI:0914”(association)0.350

BioGRID (156): EIF3CL (Affinity Capture-MS), EIF3CL (Affinity Capture-MS), EIF3CL (Affinity Capture-MS), EIF3CL (Affinity Capture-MS), EIF3B (Co-fractionation), EIF3CL (Co-fractionation), EIF3CL (Co-fractionation), EIF3CL (Co-fractionation), EIF3CL (Co-fractionation), EIF3CL (Co-fractionation), EIF3CL (Co-fractionation), EIF3CL (Co-fractionation), EIF3D (Co-fractionation), EIF3G (Co-fractionation), EIF3CL (Affinity Capture-MS)

ESM2 similar proteins: A0A8I3P7X4, A7S641, A8WG88, A9ULY7, B0R034, B0W6N3, B5DFC8, B5ME19, D6WIX5, E7EXT2, F7AEX0, O60308, O95202, P0C204, P45433, P53569, Q03701, Q0VA06, Q173M7, Q1L987, Q28HX4, Q3SYW6, Q3ZC50, Q4QR58, Q5RAT8, Q5RCI4, Q5U2X6, Q5XGZ8, Q5XIN6, Q5ZK33, Q66I12, Q6AZI2, Q6IVW0, Q6P1V4, Q6PFQ2, Q6PGY6, Q7PGE8, Q7SYB2, Q8BZN6, Q8R1B4

Diamond homologs: A1C987, A1D9P1, A1ZAX1, A3GGB4, A4QSX4, A5DPQ5, A5E3Q2, A6S043, A6ZN26, A7E471, A7TML4, A8WWU0, B0W0S3, B0YEH1, B3MIF1, B3NML0, B4GIB1, B4HMY3, B4J789, B4KN00, B4LNA1, B4MRZ8, B4P562, B5DFC8, B5ME19, O02328, O14164, O49160, P0CN46, P0CN47, P32497, Q0CVT0, Q0V1H5, Q0ZB76, Q17Q06, Q1DP77, Q28Z41, Q2H731, Q2U0Q9, Q3SYW6

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 55 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
Formation of the ternary complex, and subsequently, the 43S complex1156.4×3e-15
Ribosomal scanning and start codon recognition1254.4×3e-16
Translation initiation complex formation1149.9×6e-15
GTP hydrolysis and joining of the 60S ribosomal subunit1331.0×6e-15
Formation of a pool of free 40S subunits1129.3×2e-12
L13a-mediated translational silencing of Ceruloplasmin expression1228.9×2e-13

GO biological processes:

GO termPartnersFoldFDR
formation of cytoplasmic translation initiation complex11247.2×3e-23
translational initiation1178.9×2e-16
regulation of translational initiation656.2×1e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance12
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2521 predictions. Top by Δscore:

VariantEffectΔscore
16:28379881:C:CCacceptor_gain1.0000
16:28379883:G:Cacceptor_gain1.0000
16:28379894:A:ACacceptor_gain1.0000
16:28379894:A:Cacceptor_gain1.0000
16:28379972:TCA:Tdonor_loss1.0000
16:28379973:CACC:Cdonor_loss1.0000
16:28379974:A:ACdonor_gain1.0000
16:28379974:AC:Adonor_gain1.0000
16:28379974:ACCT:Adonor_gain1.0000
16:28379975:C:CAdonor_gain1.0000
16:28379975:CC:Cdonor_gain1.0000
16:28379975:CCT:Cdonor_gain1.0000
16:28379975:CCTC:Cdonor_gain1.0000
16:28379975:CCTCG:Cdonor_gain1.0000
16:28380134:GAGGC:Gacceptor_gain1.0000
16:28380135:AGGC:Aacceptor_gain1.0000
16:28380136:GGC:Gacceptor_gain1.0000
16:28380137:GC:Gacceptor_gain1.0000
16:28380138:CC:Cacceptor_gain1.0000
16:28380139:C:CAacceptor_loss1.0000
16:28380139:C:CCacceptor_gain1.0000
16:28380139:C:Tacceptor_gain1.0000
16:28380140:T:Aacceptor_loss1.0000
16:28380144:A:Tacceptor_gain1.0000
16:28380147:C:CTacceptor_gain1.0000
16:28380150:C:CTacceptor_gain1.0000
16:28380150:C:Tacceptor_gain1.0000
16:28380151:A:Tacceptor_gain1.0000
16:28380155:C:CTacceptor_gain1.0000
16:28380156:A:Tacceptor_gain1.0000

AlphaMissense

6072 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
16:28380501:A:GL793P1.000
16:28380513:A:GL789P1.000
16:28380676:C:AW767C1.000
16:28380676:C:GW767C1.000
16:28380677:C:GW767S1.000
16:28380678:A:GW767R1.000
16:28380678:A:TW767R1.000
16:28380718:A:CC753W1.000
16:28380719:C:TC753Y1.000
16:28380729:A:GW750R1.000
16:28380729:A:TW750R1.000
16:28380753:A:GS742P1.000
16:28380755:G:TA741D1.000
16:28380756:C:GA741P1.000
16:28383147:A:GL719P1.000
16:28383158:G:CF715L1.000
16:28383158:G:TF715L1.000
16:28383159:A:CF715C1.000
16:28383159:A:GF715S1.000
16:28383160:A:GF715L1.000
16:28383164:C:AK713N1.000
16:28383164:C:GK713N1.000
16:28383166:T:CK713E1.000
16:28383167:G:CS712R1.000
16:28383167:G:TS712R1.000
16:28383169:T:GS712R1.000
16:28383220:C:TE695K1.000
16:28383225:A:GL693P1.000
16:28383231:G:TA691D1.000
16:28383232:C:GA691P1.000

dbSNP variants (sampled 300 via entrez): RS1000148590 (16:28382489 CCA>C), RS1000410100 (16:28428286 G>A,C), RS1000560068 (16:28412119 G>A), RS1000592727 (16:28411315 T>A), RS1000840889 (16:28427512 T>G), RS1001908574 (16:28427172 C>T), RS1001925069 (16:28426801 G>A), RS1002105067 (16:28410910 G>A), RS1002268117 (16:28410580 G>A), RS1002867940 (16:28396872 C>G), RS1002900237 (16:28423134 C>G,T), RS1002928103 (16:28422570 A>C), RS1003494382 (16:28402451 G>A,T), RS1004361407 (16:28413085 T>C), RS1004969234 (16:28379082 C>G,T)

Disease associations

OMIM: gene `` | 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
GCST002598_62Educational attainment1.000000e-06
GCST004131_83Inflammatory bowel disease2.000000e-12
GCST004132_69Crohn’s disease3.000000e-10
GCST010133_15Lamb consumption3.000000e-08
GCST010703_152Brain morphology (MOSTest)3.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004784self reported educational attainment
EFO:0008111diet measurement
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
Diethylhexyl Phthalateaffects cotreatment, affects expression, increases expression2
bisphenol Adecreases expression1
lead acetatedecreases expression1
pyrogallol 1,3-dimethyl etheraffects localization, increases expression, affects cotreatment, decreases expression1
tetrachlorodianincreases expression1
abrineincreases expression1
theaflavin-3,3’-digallateaffects expression1
Benztropineaffects cotreatment, decreases expression1
Cuprizoneaffects cotreatment, decreases expression1
Dimethyl Sulfoxideincreases expression1
Doxorubicinincreases expression1
Colforsinaffects cotreatment, affects expression1
Furaldehydeaffects cotreatment, decreases expression, affects localization, increases expression1
Smokedecreases expression1
Sodium Chlorideaffects cotreatment, decreases expression, affects localization, increases expression1
Tetrachlorodibenzodioxindecreases expression1
Tobacco Smoke Pollutionaffects expression1
Valproic Aciddecreases expression1
Cyclosporineincreases methylation1
Aflatoxin M1increases 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.