ILF3

gene
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Also known as NF90MPHOSPH4MPP4NFAR-1NFAR110NFAR-2TCP110NF110DRBP76NFAR90NF110bNF90aNF90cNF90ctvMPP4110

Summary

ILF3 (interleukin enhancer binding factor 3, HGNC:6038) is a protein-coding gene on chromosome 19p13.2, encoding Interleukin enhancer-binding factor 3 (Q12906). RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. It is a common-essential gene (DepMap: required in 97.4% of cancer cell lines).

This gene encodes a double-stranded RNA (dsRNA) binding protein that complexes with other proteins, dsRNAs, small noncoding RNAs, and mRNAs to regulate gene expression and stabilize mRNAs. This protein (NF90, ILF3) forms a heterodimer with a 45 kDa transcription factor (NF45, ILF2) required for T-cell expression of interleukin 2. This complex has been shown to affect the redistribution of nuclear mRNA to the cytoplasm. Knockdown of NF45 or NF90 protein retards cell growth, possibly by inhibition of mRNA stabilization. In contrast, an isoform (NF110) of this gene that is predominantly restricted to the nucleus has only minor effects on cell growth when its levels are reduced. Alternative splicing results in multiple transcript variants encoding distinct isoforms.

Source: NCBI Gene 3609 — RefSeq curated summary.

At a glance

  • GWAS associations: 14
  • Clinical variants (ClinVar): 242 total — 2 pathogenic
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer dependency (DepMap): dependent in 97.4% of screened cell lines (common-essential)
  • MANE Select transcript: NM_017620

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6038
Approved symbolILF3
Nameinterleukin enhancer binding factor 3
Location19p13.2
Locus typegene with protein product
StatusApproved
AliasesNF90, MPHOSPH4, MPP4, NFAR-1, NFAR110, NFAR-2, TCP110, NF110, DRBP76, NFAR90, NF110b, NF90a, NF90c, NF90ctv, MPP4110
Ensembl geneENSG00000129351
Ensembl biotypeprotein_coding
OMIM603182
Entrez3609

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 25 protein_coding, 6 nonsense_mediated_decay, 3 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000250241, ENST00000407004, ENST00000585835, ENST00000586544, ENST00000587505, ENST00000587840, ENST00000587928, ENST00000587941, ENST00000588657, ENST00000589052, ENST00000589173, ENST00000589283, ENST00000589416, ENST00000589485, ENST00000589600, ENST00000589998, ENST00000590009, ENST00000590261, ENST00000590869, ENST00000591649, ENST00000592763, ENST00000593061, ENST00000593199, ENST00000899691, ENST00000899692, ENST00000899693, ENST00000938413, ENST00000938414, ENST00000938415, ENST00000938416, ENST00000938417, ENST00000938418, ENST00000938419, ENST00000938420, ENST00000970392

RefSeq mRNA: 24 — MANE Select: NM_017620 NM_001137673, NM_001394808, NM_001394809, NM_001394810, NM_001394811, NM_001394812, NM_001394813, NM_001394814, NM_001394815, NM_001394816, NM_001394817, NM_001394818, NM_001394819, NM_001394820, NM_001394821, NM_001394822, NM_001394823, NM_001394824, NM_001394826, NM_001394827, NM_004516, NM_012218, NM_017620, NM_153464

CCDS: CCDS12246, CCDS12247, CCDS45965, CCDS45966, CCDS45967

Canonical transcript exons

ENST00000588657 — 20 exons

ExonStartEnd
ENSE000008882801068199310682192
ENSE000027467351068917910692400
ENSE000028277361065434610654487
ENSE000035352031068336610683542
ENSE000035353751068121910681329
ENSE000035507711067981610679927
ENSE000035552761068101910681130
ENSE000035595831068363610683789
ENSE000035599741067051610670608
ENSE000035647911068253710682704
ENSE000035775321067716310677310
ENSE000035817831067909710679192
ENSE000035849231068034610680443
ENSE000036043201068391710683970
ENSE000036528521068312510683262
ENSE000036772281067135810671535
ENSE000036826151068734610687708
ENSE000036870821068855010688678
ENSE000036909211067861310678704
ENSE000037879571067097410671203

Expression profiles

Bgee: expression breadth ubiquitous, 303 present calls, max score 99.23.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 191.8387 / max 1731.8458, expressed in 1828 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
173834123.58891828
17383363.82511822
1738371.9545318
1738420.8074510
1738390.7361441
1738360.4440188
1738400.3396146
1738350.143070

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
ganglionic eminenceUBERON:000402399.23gold quality
ventricular zoneUBERON:000305399.21gold quality
cortical plateUBERON:000534398.92gold quality
embryoUBERON:000092298.67gold quality
sural nerveUBERON:001548898.37gold quality
left ovaryUBERON:000211998.24gold quality
right ovaryUBERON:000211898.22gold quality
right uterine tubeUBERON:000130298.19gold quality
left lobe of thyroid glandUBERON:000112098.03gold quality
adenohypophysisUBERON:000219698.01gold quality
right lobe of thyroid glandUBERON:000111997.97gold quality
pituitary glandUBERON:000000797.90gold quality
left uterine tubeUBERON:000130397.89gold quality
endocervixUBERON:000045897.81gold quality
body of uterusUBERON:000985397.78gold quality
cerebellar hemisphereUBERON:000224597.70gold quality
ectocervixUBERON:001224997.68gold quality
thyroid glandUBERON:000204697.67gold quality
cerebellar cortexUBERON:000212997.67gold quality
skin of abdomenUBERON:000141697.62gold quality
right hemisphere of cerebellumUBERON:001489097.62gold quality
right testisUBERON:000453497.59gold quality
lymph nodeUBERON:000002997.58gold quality
left testisUBERON:000453397.55gold quality
granulocyteCL:000009497.51gold quality
metanephros cortexUBERON:001053397.47gold quality
skin of legUBERON:000151197.46gold quality
spleenUBERON:000210697.36gold quality
secondary oocyteCL:000065597.30gold quality
paraflocculusUBERON:000535197.30gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes11.28
E-GEOD-125970no3.48
E-HCAD-31no2.59

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

7 targets.

TargetRegulation
ACRV1Activation
BIRC5Activation
HLA-DQA1Unknown
HLA-DRARepression
HLA-DRB1Unknown
IL2Activation
PLAUActivation

Upstream regulators (CollecTRI, top): GLI2, ILF2, NR5A2, THRA

miRNA regulators (miRDB)

43 targeting ILF3, 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-118499.9968.191458
HSA-MIR-548AW99.9972.573559
HSA-MIR-1213699.9872.815713
HSA-MIR-806899.9873.852376
HSA-MIR-1468-3P99.9672.743797
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-548E-5P99.8972.734486
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-442099.8270.081624
HSA-MIR-181B-2-3P99.8170.061646
HSA-MIR-181B-3P99.8170.061646
HSA-MIR-10394-5P99.6566.831852
HSA-MIR-120599.6566.761826
HSA-MIR-58799.6470.862611
HSA-MIR-766-5P99.4767.912225
HSA-MIR-6839-3P99.3968.861301
HSA-MIR-6507-3P99.3567.321059
HSA-MIR-3191-5P99.2466.521722
HSA-MIR-427999.1966.702437
HSA-MIR-146A-3P99.1368.991881
HSA-MIR-371A-5P99.0866.511914
HSA-MIR-4717-3P99.0666.341072
HSA-MIR-1213598.9970.261814
HSA-MIR-887-5P98.8265.901347
HSA-MIR-1537-5P98.7068.33999
HSA-MIR-518C-5P98.5369.201640
HSA-MIR-6831-5P98.2667.20990
HSA-MIR-444398.0266.251928
HSA-MIR-427597.9668.421549
HSA-MIR-10526-3P97.8664.971342

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 97.4% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 40)

  • plays important role in protein priming of HBV polymerase (PMID:11958450)
  • Nuclear export of this protein is required for interleukin-2 mRNA stabilization. (PMID:12504009)
  • Results describe the expression of four isoforms of nuclear factor 90, including NF110, by cDNA cloning and mass spectrometric analysis of proteins isolated from human cells (PMID:12946349)
  • nuclear export of ILF3 is mediated by exportin-5 and minihelix-containing RNA (PMID:14570900)
  • the multiple cellular functions, i.e., translation control, interleukin-2 enhancer binding, or cell division, of ILF3 are fulfilled by alternatively spliced isoforms. (PMID:14654356)
  • NF90 and NF110 engage RNA differentially and translocate from the nucleus to the cytoplasm in mitosis (PMID:15811368)
  • ADAR1 has the potential both to change information content through editing of mRNA and to regulate gene expression through interacting with NF90 (PMID:16055709)
  • The human Nuclear Factor 90 c-terminal variant protein encoded by ILF3 interacts with Rev to inhibit Rev-mediated RNA transport. (PMID:17125513)
  • Our results show that perturbation Tat/TAR RNA interaction by the dsRNA binding nuclear factor 90 protein is sufficient to inhibit transcriptional activation of HIV-1. (PMID:17565699)
  • DRBP76/NF90 isoform facilitates VEGF expression by promoting VEGF mRNA loading onto polysomes (PMID:18039850)
  • CD28 costimulation activates AKT to phosphorylate NF90 at Ser647 and phosphorylation triggers NF90 to relocate to the cytoplasm and stabilize IL-2 mRNA. (PMID:18097023)
  • NFARs exert influence on mRNA trafficking and the modulation of translation rates and may constitute an innate immune translational surveillance mechanism important in host defense countermeasures against virus infection (PMID:18337511)
  • Cell growth is retarded and giant multinucleated cells accumulate when the expression of NF45 or NF90, but not NF110, is reduced in HeLa cells. (PMID:18458058)
  • MKP-1 upregulation by oxidative stress is potently influenced by increased mRNA stability and translation, mediated at least in part by the RNA-binding proteins HuR and NF90. (PMID:18490444)
  • ILF-3, which has been known to regulate IL-2 expression in T cells, up-regulates synoviolin expression with GABPalpha in rheumatoid synovial cells (PMID:19116932)
  • Results suggest that the association of the NF90-NF45 complex with pri-miRNAs impairs access of the Microprocessor complex to the pri-miRNAs, resulting in a reduction of mature miRNA production. (PMID:19398578)
  • NF90 inhibits influenza virus replication during the early phase of infection through direct interaction with viral NP. (PMID:19494010)
  • our results identify NF45 and NF90 as novel regulators of HS4-dependent human IL13 transcription in response to T cell activation (PMID:20051514)
  • Data suggest that physiologic DRBP76 expression, isoform distribution and subcellular localization are profoundly altered upon malignant transformation. (PMID:20668518)
  • associations of rs2569512 of ILF3 to myocardial infarction among individuals stratified by the absence or presence of hypertension, diabetes mellitus and chronic kidney disease (PMID:21347509)
  • Production of HIV particles is regulated by altering sub-cellular localization and dynamics of Rev induced by double-strand RNA binding protein. (PMID:21364984)
  • NF90 binds the dengue virus RNA 3’ terminus and is a positive regulator of dengue virus. (PMID:21386893)
  • The relationship between rs6929846 of BTN2A1 or rs2569512 of ILF3 and myocardial infarction is influenced by the serum concentrations of high density lipoprotein cholesterol and low density lipoprotein cholesterol, respectively. (PMID:21468600)
  • The protein polymorphism of Ilf3/NF90 and the various subcellular localizations of their isoforms may partially explain the various functions previously reported for these proteins. (PMID:21811582)
  • The NF90/NF45 complex participates in DNA break repair via nonhomologous end joining (PMID:21969602)
  • high expression of ERCC1, XPB and ILF3 was observed in human epithelial ovarian cancer (PMID:21971700)
  • These data suggest that DRBP76, via its association with VP35, exerts an anti-Ebola virus function. (PMID:21987769)
  • The unique C-terminal region of ILF3/NF110 is important for promoting survivin expression and for high affinity binding to YM155. (PMID:22442257)
  • Data indicate that knockdown of interleukin enhancer-binding factor 3 (ILF3) leads to the increased levels of mature urokinase-type plasminogen activator (uPA) mRNA-targeting miRNAs miR-193a, miR-193b and miR-181a. (PMID:22986534)
  • contributes to maintaining low levels of senescence-associated secretory phenotype factors in non-senescent cells (PMID:23117626)
  • The function of NF90 in posttranscriptional gene regulation and microRNA biogenesis. [Review] (PMID:23965975)
  • NF90 exerts antiviral activity through regulation of PKR phosphorylation and stress granules in infected cells. (PMID:24623135)
  • These results suggest a novel molecular mechanism for the modulation of RNA granule assembly and disassembly by NFAR2, NF45, and phosphorylation at double-stranded RNA-activated kinase PKR sites. (PMID:24920670)
  • Suppression of NF90 caused a decrease in the half-life of cyclin E1 mRNA (PMID:25399696)
  • the role of the human NF90 protein isoforms in DNA and RNA virus replication (PMID:25447144)
  • Data indicate the role of cyclin-dependent kinase inhibitor 1A (p21) and interleukin enhancer binding factor 3 (ILF3) pathway in mediating the anti-leukemic activity of sodium dichloroacetate (DCA) in oncoprotein p53null leukemic cells. (PMID:25544776)
  • NF45 and NF90 are novel higher-eukaryote-specific factors required for the maturation of 60S ribosomal subunits. (PMID:26240280)
  • Taken together, our discovery of the function of TCP80 and RHA in regulating p53 IRES and p53 induction following DNA damage provides a better understanding of the mechanisms that regulate IRES-mediated p53 translation in response to genotoxic stress. (PMID:26273641)
  • The RNA binding complexes NF45-NF90 and NF45-NF110 associate dynamically with the c-fos gene and function as transcriptional coactivators. (PMID:26381409)
  • data suggest that lncRNA SALNR modulates cellular senescence at least partly through changing NF90 activity (PMID:26491010)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_rerioilf3bENSDARG00000105177
mus_musculusIlf3ENSMUSG00000032178
rattus_norvegicusIlf3ENSRNOG00000022741
drosophila_melanogasterloqsFBGN0032515
drosophila_melanogasterCG12493FBGN0035571
drosophila_melanogasterblanksFBGN0035608
drosophila_melanogasterZn72DFBGN0263603
caenorhabditis_eleganszfr-1WBGENE00022388

Paralogs (14): STAU2 (ENSG00000040341), ZFR (ENSG00000056097), ADAT1 (ENSG00000065457), ZFR2 (ENSG00000105278), STAU1 (ENSG00000124214), TARBP2 (ENSG00000139546), ADAD2 (ENSG00000140955), ILF2 (ENSG00000143621), ADAR (ENSG00000160710), ADAD1 (ENSG00000164113), STRBP (ENSG00000165209), PRKRA (ENSG00000180228), ADARB2 (ENSG00000185736), ADARB1 (ENSG00000197381)

Protein

Protein identifiers

Interleukin enhancer-binding factor 3Q12906 (reviewed: Q12906)

Alternative names: Double-stranded RNA-binding protein 76, M-phase phosphoprotein 4, Nuclear factor associated with dsRNA, Nuclear factor of activated T-cells 90 kDa, Translational control protein 80

All UniProt accessions (13): Q12906, K7EJ09, K7EKJ9, K7EKY0, K7ELV3, K7EM82, K7EMZ8, K7ENK6, K7EPG3, K7EQ75, K7EQR9, K7ER69, K7ERM6

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Within the nucleus, promotes circRNAs processing by stabilizing the regulatory elements residing in the flanking introns of the circularized exons. Plays thereby a role in the back-splicing of a subset of circRNAs. As a consequence, participates in a wide range of transcriptional and post-transcriptional processes. Binds to poly-U elements and AU-rich elements (AREs) in the 3’-UTR of target mRNAs. Upon viral infection, ILF3 accumulates in the cytoplasm and participates in the innate antiviral response. Mechanistically, ILF3 becomes phosphorylated and activated by the double-stranded RNA-activated protein kinase/PKR which releases ILF3 from cellular mature circRNAs. In turn, unbound ILF3 molecules are able to interact with and thus inhibit viral mRNAs. (Microbial infection) Plays a positive role in HIV-1 virus production by binding to and thereby stabilizing HIV-1 RNA, together with ILF3.

Subunit / interactions. Identified in a IGF2BP1-dependent mRNP granule complex containing untranslated mRNAs. Interacts with FUS and SMN. Interacts (via C-terminus) with PRMT1. Forms a complex with ILF2. Can also bind to PRKDC/XRCC7: this may stabilize the interaction of PRKDC/XRCC7 and the heterodimeric complex of XRCC6/KU70 and XRCC5/KU80. Forms a heteromeric complex with ZNF346 and ILF3. Found in a nuclear export complex with XPO5, ILF3, Ran and double-stranded RNA or double-stranded minihelix VA1 RNA. Found in a nuclear export complex with XPO5, RAN, ILF3, ZNF346 and double-stranded RNA. Interacts with XPO5 and ZNF346. Forms a complex with ILF2, YLPM1, KHDRBS1, RBMX, NCOA5 and PPP1CA. Interacts with AGO1 and AGO2. Interacts with DHX36; this interaction occurs in a RNA-dependent manner. Interacts with ELAVL1; this interaction occurs in a RNA-dependent manner. Interacts with HAVCR2; this interaction promotes ILF3 ubiquitination and subsequent degradation.

Subcellular location. Nucleus. Nucleolus. Cytoplasm.

Tissue specificity. Ubiquitous.

Post-translational modifications. Phosphorylated at Thr-188 and Thr-315 by PKR in response to certain RNA viruses. This phosphorylation results in the dissociation of ILF2 from the ILF2-ILF3 complex resulting in a cytoplasmic sequestration of ILF3 where it can bind to viral RNAs and impede viral replication. Methylated by protein arginine N-methyltransferase 1. Ubiquitinated at Lys-297 in a TRIM47-dependent manner; this ‘Lys-48’-linked ubiquitination promotes ILF3 degradation.

Miscellaneous. Dubious isoform produced through aberrant splice sites.

Isoforms (7)

UniProt IDNamesCanonical?
Q12906-11, NFAR-2, ILF3-Eyes
Q12906-22, NFAR-1, DRBP76
Q12906-33
Q12906-44, DRBP76 Alpha, ILF3-A
Q12906-55, DRBP76 Delta, Gamma, ILF3-C
Q12906-66
Q12906-77

RefSeq proteins (24): NP_001131145, NP_001381737, NP_001381738, NP_001381739, NP_001381740, NP_001381741, NP_001381742, NP_001381743, NP_001381744, NP_001381745, NP_001381746, NP_001381747, NP_001381748, NP_001381749, NP_001381750, NP_001381751, NP_001381752, NP_001381753, NP_001381755, NP_001381756, NP_004507, NP_036350, NP_060090, NP_703194 (=MANE)

Domains & families (InterPro)

IDNameType
IPR006561DZF_domDomain
IPR014720dsRBD_domDomain
IPR033099DSRM1_ILF3Domain
IPR043519NT_sfHomologous_superfamily
IPR049401DZF_dom_NDomain
IPR049402DZF_dom_CDomain

Pfam: PF00035, PF07528, PF20965

UniProt features (71 total): modified residue 19, compositionally biased region 12, splice variant 9, sequence conflict 8, region of interest 6, cross-link 4, domain 3, helix 3, strand 3, sequence variant 2, chain 1, short sequence motif 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
7RJQX-RAY DIFFRACTION1.72
3P1XX-RAY DIFFRACTION1.9
7RJMX-RAY DIFFRACTION2.1
2L33SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q12906-F167.740.43

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 (23): 62, 100, 188, 190, 315, 382, 384, 460, 476, 477, 482, 592, 792, 810, 812, 816, 297, 348, 396, 489 …

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-9762293Regulation of CDH11 gene transcription
R-HSA-9833482PKR-mediated signaling

MSigDB gene sets: 409 (showing top): E2F_Q4, MODULE_52, HORIUCHI_WTAP_TARGETS_DN, E2F4DP1_01, REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM, PAL_PRMT5_TARGETS_UP, HOFMANN_CELL_LYMPHOMA_UP, MORF_UBE2I, GOBP_NEGATIVE_REGULATION_OF_VIRAL_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, MORF_HDAC1, MORF_UBE2N

GO Biological Process (8): protein phosphorylation (GO:0006468), negative regulation of translation (GO:0017148), negative regulation of viral genome replication (GO:0045071), negative regulation of DNA-templated transcription (GO:0045892), positive regulation of DNA-templated transcription (GO:0045893), defense response to virus (GO:0051607), spliceosome-depend formation of circular RNA (GO:0160091), symbiont entry into host cell (GO:0046718)

GO Molecular Function (7): virus receptor activity (GO:0001618), DNA binding (GO:0003677), RNA binding (GO:0003723), double-stranded RNA binding (GO:0003725), single-stranded RNA binding (GO:0003727), mRNA 3’-UTR AU-rich region binding (GO:0035925), protein binding (GO:0005515)

GO Cellular Component (9): extracellular region (GO:0005576), nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), mitochondrion (GO:0005739), cytosol (GO:0005829), membrane (GO:0016020), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Regulation of CDH11 Expression and Function1
Antimicrobial mechanism of IFN-stimulated genes1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure5
DNA-templated transcription2
regulation of DNA-templated transcription2
nucleic acid binding2
RNA binding2
intracellular membrane-bounded organelle2
nuclear lumen2
cytoplasm2
phosphorylation1
protein modification process1
translation1
regulation of translation1
negative regulation of gene expression1
negative regulation of protein metabolic process1
viral genome replication1
regulation of viral genome replication1
negative regulation of viral process1
negative regulation of RNA biosynthetic process1
positive regulation of RNA biosynthetic process1
defense response1
response to virus1
mRNA splicing, via spliceosome1
viral life cycle1
symbiont entry into host1
symbiont entry into host cell1
exogenous protein binding1
mRNA 3’-UTR binding1
binding1
intracellular membraneless organelle1
intracellular anatomical structure1
protein-containing complex1

Protein interactions and networks

STRING

3148 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ILF3ILF2Q12905988
ILF3HNRNPLP14866972
ILF3HNRNPA2B1P22626940
ILF3FUSP35637927
ILF3HNRNPH1P31943906
ILF3XPO5Q9HAV4869
ILF3HNRNPMP52272869
ILF3EIF2AK2P19525865
ILF3HNRNPCP07910854
ILF3HNRNPH2P55795832
ILF3NONOP30807765
ILF3MATR3P43243765
ILF3DHX9Q08211754
ILF3DICER1Q9UPY3709
ILF3HNRNPDP07029697

IntAct

325 interactions, top by confidence:

ABTypeScore
PTPN3YWHAQpsi-mi:“MI:2364”(proximity)0.850
IFIT2IFIT3psi-mi:“MI:0914”(association)0.780
CFTRESYT2psi-mi:“MI:0914”(association)0.710
PTPN3MCCpsi-mi:“MI:0914”(association)0.660
IGF2BP1IGF2BP3psi-mi:“MI:0914”(association)0.640
NCBP1KPNA3psi-mi:“MI:0914”(association)0.640
NCBP2KPNA3psi-mi:“MI:0914”(association)0.640
HNRNPLHNRNPA2B1psi-mi:“MI:0914”(association)0.630
HNRNPLHNRNPA2B1psi-mi:“MI:0914”(association)0.620
ILF3HNRNPA2B1psi-mi:“MI:0915”(physical association)0.560
ILF3NSpsi-mi:“MI:0915”(physical association)0.550
ILKHAX1psi-mi:“MI:0914”(association)0.530
ILF2IGF2BP3psi-mi:“MI:0914”(association)0.530
CBX6IGF2BP3psi-mi:“MI:0914”(association)0.530
SYNGAP1IGF2BP3psi-mi:“MI:0914”(association)0.530
MILF3psi-mi:“MI:0915”(physical association)0.500
ILF3Mpsi-mi:“MI:0914”(association)0.500
HNRNPLILF3psi-mi:“MI:0915”(physical association)0.500
CFTRPLEKHG3psi-mi:“MI:0914”(association)0.480
RBM45HNRNPDLpsi-mi:“MI:0914”(association)0.460
FUSDDX3Xpsi-mi:“MI:0914”(association)0.430
CUEDC1ILF3psi-mi:“MI:0915”(physical association)0.400
ILF3SPARCpsi-mi:“MI:0915”(physical association)0.400
USP12ILF3psi-mi:“MI:0915”(physical association)0.400

BioGRID (1314): ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), PLSCR1 (Two-hybrid), RBPMS (Two-hybrid), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS), ILF3 (Affinity Capture-MS)

ESM2 similar proteins: A5D7P8, A6QLK2, F1LQ48, O55047, O95628, P25916, P35226, P59326, P97855, Q08CW1, Q0VCY1, Q0VCZ3, Q12906, Q13148, Q13283, Q1ECX4, Q32KX7, Q32LC7, Q3SWT1, Q3ZBD9, Q4R5D9, Q5FVP2, Q5PRC7, Q5R601, Q5R8L2, Q5RB87, Q5SDR3, Q5U2U0, Q5ZLN5, Q64213, Q66K94, Q6DE02, Q6NRF9, Q86UE8, Q8BGW5, Q8BT14, Q8C0V0, Q8R2Y9, Q90ZY6, Q91YT7

Diamond homologs: O88532, Q08E27, Q0VD35, Q12906, Q562A2, Q5R6Y5, Q5REX3, Q5U231, Q5ZIL4, Q6DCD0, Q6DD04, Q6GL57, Q6GPM1, Q6NXA4, Q6PCR6, Q7TP98, Q91550, Q91WM1, Q96KR1, Q96SI9, Q9H898, Q9JIL3, Q9JKU6, Q9UPR6, Q9Z1X4, A2RFW8, A8AWC2, B5XKB7, B8GAM6, C0MCR4, P0DF14, P0DF15, P51400, P55265, P55266, P66670, P66672, P78563, P97473, P97616

SIGNOR signaling

4 interactions.

AEffectBMechanism
AKT“up-regulates activity”ILF3phosphorylation
PRKCB“up-regulates activity”ILF3phosphorylation
AKT1“up-regulates activity”ILF3phosphorylation
ILF3“form complex”NF90-NF45binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 226 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
SARS-CoV-1 modulates host translation machinery611.8×2e-04
Nonsense-Mediated Decay (NMD)710.4×1e-04
mRNA Polyadenylation1810.1×6e-11
SARS-CoV-1-host interactions910.1×2e-05
SARS-CoV-2 modulates host translation machinery710.0×2e-04
Eukaryotic Translation Initiation59.8×3e-03
Cap-dependent Translation Initiation59.8×3e-03
Formation of the ternary complex, and subsequently, the 43S complex79.6×2e-04

GO biological processes:

GO termPartnersFoldFDR
positive regulation of cytoplasmic translation630.2×9e-06
alternative mRNA splicing, via spliceosome620.5×5e-05
negative regulation of mRNA splicing, via spliceosome519.4×4e-04
stress granule assembly618.3×8e-05
regulation of alternative mRNA splicing, via spliceosome1012.4×3e-06
mRNA export from nucleus812.0×4e-05
regulation of translational initiation511.9×3e-03
mitophagy711.3×2e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance184
Likely benign14
Benign1

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
2423585NC_000002.11:g.(?202501451)(202633608_?)delPathogenic
375383NM_033066.3(MPP4):c.946T>C (p.Trp316Arg)Pathogenic

SpliceAI

2701 predictions. Top by Δscore:

VariantEffectΔscore
19:10654484:CAAGG:Cdonor_loss1.0000
19:10654485:AAGGT:Adonor_loss1.0000
19:10654486:AGG:Adonor_loss1.0000
19:10654487:GGT:Gdonor_loss1.0000
19:10654488:G:GGdonor_gain1.0000
19:10654488:GT:Gdonor_loss1.0000
19:10654489:T:Adonor_loss1.0000
19:10670515:GA:Gacceptor_gain1.0000
19:10670968:CCCTA:Cacceptor_loss1.0000
19:10670969:CCTA:Cacceptor_loss1.0000
19:10670970:CTAG:Cacceptor_loss1.0000
19:10670971:TAGC:Tacceptor_loss1.0000
19:10670972:A:AGacceptor_gain1.0000
19:10670972:A:ATacceptor_loss1.0000
19:10670973:G:GGacceptor_gain1.0000
19:10670973:GC:Gacceptor_gain1.0000
19:10670973:GCGTC:Gacceptor_gain1.0000
19:10671199:GCTGG:Gdonor_gain1.0000
19:10671201:TGGG:Tdonor_loss1.0000
19:10671202:GG:Gdonor_gain1.0000
19:10671203:GG:Gdonor_gain1.0000
19:10671203:GGTA:Gdonor_loss1.0000
19:10671204:G:GAdonor_loss1.0000
19:10671204:G:GGdonor_gain1.0000
19:10671205:T:Adonor_loss1.0000
19:10671353:CTCA:Cacceptor_loss1.0000
19:10671355:CA:Cacceptor_loss1.0000
19:10671356:A:AGacceptor_gain1.0000
19:10671356:AG:Aacceptor_gain1.0000
19:10671357:G:Aacceptor_gain1.0000

AlphaMissense

5837 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:10671001:G:CD11H1.000
19:10671002:A:CD11A1.000
19:10671002:A:TD11V1.000
19:10671034:T:CY22H1.000
19:10671034:T:GY22D1.000
19:10671037:C:TP23S1.000
19:10671038:C:AP23Q1.000
19:10671053:T:AL28Q1.000
19:10671053:T:CL28P1.000
19:10671062:T:AV31D1.000
19:10671065:A:CQ32P1.000
19:10671066:G:CQ32H1.000
19:10671066:G:TQ32H1.000
19:10671086:A:TE39V1.000
19:10671087:G:CE39D1.000
19:10671087:G:TE39D1.000
19:10671091:G:CA41P1.000
19:10671092:C:AA41E1.000
19:10671095:T:AL42H1.000
19:10671095:T:CL42P1.000
19:10671095:T:GL42R1.000
19:10671097:A:GK43E1.000
19:10671098:A:TK43I1.000
19:10671099:A:CK43N1.000
19:10671099:A:TK43N1.000
19:10671104:T:AV45E1.000
19:10671106:T:CS46P1.000
19:10671390:T:AL89Q1.000
19:10671390:T:CL89P1.000
19:10671395:G:AG91R1.000

dbSNP variants (sampled 300 via entrez): RS1000108372 (19:10652476 A>G), RS1000131095 (19:10666195 G>C), RS1000247357 (19:10688890 C>G,T), RS1000327142 (19:10661056 A>G), RS1000378202 (19:10660806 T>G), RS1000384819 (19:10675259 T>G), RS1000464346 (19:10665145 T>G), RS1000608634 (19:10655535 A>G,T), RS1000618445 (19:10669433 G>T), RS1000675365 (19:10656563 C>G), RS1000690525 (19:10692424 C>A,G,T), RS1000713933 (19:10659901 A>C,G), RS1000869936 (19:10664524 C>G), RS1000889708 (19:10679245 T>C), RS1000958155 (19:10655653 T>A)

Disease associations

OMIM: gene MIM:603182 | disease phenotypes: MIM:607225, MIM:614424

GenCC curated gene-disease

Mondo (4): infantile-onset ascending hereditary spastic paralysis (MONDO:0011797), Joubert syndrome 14 (MONDO:0013745), intellectual disability (MONDO:0001071), strabismus (MONDO:0003432)

Orphanet (2): Infantile-onset ascending hereditary spastic paralysis (Orphanet:293168), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

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

GWAS associations

14 associations (top):

StudyTraitp-value
GCST001762_723Obesity-related traits7.000000e-06
GCST002647_162Height8.000000e-11
GCST002702_28Height2.000000e-16
GCST002738_5Psoriasis3.000000e-07
GCST002874_22Psoriasis2.000000e-06
GCST003268_37Psoriasis vulgaris8.000000e-07
GCST004991_1White matter microstructure in first episode schizophrenia (left inferior parietal cortex)9.000000e-08
GCST005527_36Psoriasis3.000000e-17
GCST006959_18Rheumatoid arthritis9.000000e-10
GCST007400_34Systemic lupus erythematosus7.000000e-06
GCST007576_284Chronotype1.000000e-12
GCST008103_119Bipolar disorder5.000000e-06
GCST010456_3Anthracycline-induced cardiotoxicity in early breast cancer5.000000e-06
GCST011624_3Tau burden6.000000e-08

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0004530triglyceride measurement
EFO:1001494psoriasis vulgaris
EFO:0005674white matter microstructure measurement
EFO:0008328chronotype measurement
EFO:0005257response to anthracycline-based chemotherapy
EFO:1001482cardiotoxicity
EFO:0004760t-tau measurement

MeSH disease descriptors (3)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D013285StrabismusC10.292.562.887; C11.590.810
C537217Hereditary spastic paralysis, infantile onset ascending (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5465305 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 366 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL2105734SEPANTRONIUM BROMIDE2366

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs76966440ILF30.000

ChEMBL bioactivities

6 potent at pChembl≥5 of 6 total, top 6 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
7.76Kd17.44nMCHEMBL5653589
7.76ED5017.44nMCHEMBL5653589
6.79Kd163nMCHEMBL5411686
6.24Kd571nMSEPANTRONIUM BROMIDE
5.03Kd9386nMCHEMBL3752910
5.03ED509386nMCHEMBL3752910

PubChem BioAssay actives

4 with measured affinity, of 10 total; 4 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148583: Binding affinity to human ILF3 incubated for 45 mins by Kinobead based pull down assaykd0.0174uM
1,3-dimethylnaphtho[2,3-f]benzimidazol-3-ium-4,11-dione iodide2025132: Binding affinity to ILF3 (unknown origin) assessed as dissociation constant at upto 1 uM by SPR methodkd0.1630uM
1-(2-methoxyethyl)-2-methyl-3-(pyrazin-2-ylmethyl)benzo[f]benzimidazol-3-ium-4,9-dione bromide2025132: Binding affinity to ILF3 (unknown origin) assessed as dissociation constant at upto 1 uM by SPR methodkd0.5710uM
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148583: Binding affinity to human ILF3 incubated for 45 mins by Kinobead based pull down assaykd9.3857uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, increases abundance, increases expression4
Tretinoindecreases expression4
methylmercuric chlorideincreases expression, affects cotreatment3
bisphenol Adecreases expression3
bisphenol Faffects cotreatment, decreases expression, increases expression2
cobaltous chloridedecreases expression2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression2
Benzo(a)pyrenedecreases expression, increases methylation2
Caffeinedecreases phosphorylation, increases expression2
Ozoneincreases oxidation, affects expression, increases abundance, affects cotreatment2
Valproic Acidaffects expression, decreases expression2
FR900359affects phosphorylation1
TAK-243decreases sumoylation1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
deoxynivalenolincreases expression1
sodium arsenatedecreases expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, decreases expression, affects localization, increases expression1
trichostatin Adecreases expression, affects cotreatment1
beta-lapachonedecreases expression, increases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
butyraldehydedecreases expression1
sulindac sulfidedecreases expression1
coumarinincreases phosphorylation1
cupric oxidedecreases phosphorylation1
nivalenolincreases expression1
methacrylaldehydeaffects cotreatment, increases oxidation1
beta-methylcholineaffects expression1
epigallocatechin gallateincreases expression1
tamibarotenedecreases expression1

ChEMBL screening assays

4 unique, capped per target: 4 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5379142BindingBinding affinity to ILF3 (unknown origin) assessed as dissociation constant at upto 1 uM by SPR methodPioneering 4,11-Dioxo-4,11-dihydro-1H-anthra[2,3-d]imidazol-3-ium Compounds as Promising Survivin Inhibitors by Targeting ILF3/NF110 for Cancer Therapy. — J Med Chem

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT00461656PHASE4COMPLETEDPovidone-iodine Antisepsis for Strabismus Surgery
NCT01901588PHASE4COMPLETEDEfficacy of Single-Shot Dexmedetomidine Versus Placebo in Preventing Pediatric Emergence Delirium in Strabismus Surgery
NCT02379546PHASE4COMPLETEDThe Effect of Anaesthesia Depth on Oculo-cardiac Reflex
NCT03349515PHASE4COMPLETEDThe Effect of Povidone-iodine Ophthalmic Surgical Prep Solution on Respiration in Children Undergoing Strabismus Surgery With General Anesthesia.
NCT04549844PHASE4UNKNOWNPeribulbar Block for Prevention of Oculocardiac Reflex
NCT06035757PHASE4RECRUITINGThe Occurrence of Emergence Agitation in Pediatric Strabismus Surgery
NCT06560268PHASE4NOT_YET_RECRUITINGLow Flow Anesthesia in Children Undergoing Strabismus Surgery
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT00000128PHASE3UNKNOWNA Trial of Bifocals in Myopic Children With Esophoria
NCT00001864PHASE3COMPLETEDAmblyopia (Lazy Eye) Treatment Study
NCT00038753PHASE3UNKNOWNVision In Preschoolers Study (VIP Study)
NCT01584843PHASE3COMPLETEDEfficacy and Safety of GSK1358820 (Botulinum Toxin Type A) in Patients With Strabismus
NCT04060771PHASE3UNKNOWNPost-Operative Nausea and Vomiting in Children Submitted to Strabismus Surgery
NCT06863675PHASE3NOT_YET_RECRUITINGHighly Aspherical Lenslet (HAL) and Binocular Vision (BV) Disorders [HALT X(T) Study]
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT00478907PHASE2COMPLETEDPrevention of Complications of Eye Surgery
NCT06689943PHASE2NOT_YET_RECRUITINGPain After Strabismus Surgery
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT00917982PHASE1UNKNOWNThe Effect of Vision Therapy/Orthoptic on Motor & Sensory Status of the 3 to 7 Years Old Strabismic Patients
NCT02246556PHASE1TERMINATEDDichoptic Virtual Reality Therapy for Amblyopia in Adults
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities