ILRUN

gene
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Also known as FLJ22195dJ391O22.4

Summary

ILRUN (inflammation and lipid regulator with UBA-like and NBR1-like domains, HGNC:21215) is a protein-coding gene on chromosome 6p21.31, encoding Protein ILRUN (Q9H6K1). Negative regulator of innate antiviral response.

This gene encodes a protein with N-terminal ubiquitin-associated (UBA)-like and central neighbor of BRCA1 gene 1 (NBR1)-like domains. The protein acts an inhibitor of antiviral and proinflammatory cytokine transcription and as a regulator of the renin-angiotensin-aldosterone system (RAAS).

Source: NCBI Gene 64771 — RefSeq curated summary.

At a glance

  • GWAS associations: 75
  • Clinical variants (ClinVar): 6 total
  • MANE Select transcript: NM_024294

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:21215
Approved symbolILRUN
Nameinflammation and lipid regulator with UBA-like and NBR1-like domains
Location6p21.31
Locus typegene with protein product
StatusApproved
AliasesFLJ22195, dJ391O22.4
Ensembl geneENSG00000196821
Ensembl biotypeprotein_coding
OMIM612217
Entrez64771

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 8 protein_coding

ENST00000374021, ENST00000374023, ENST00000374026, ENST00000857868, ENST00000857869, ENST00000857870, ENST00000857871, ENST00000943487

RefSeq mRNA: 2 — MANE Select: NM_024294 NM_022758, NM_024294

CCDS: CCDS4795, CCDS4796

Canonical transcript exons

ENST00000374023 — 5 exons

ExonStartEnd
ENSE000009295103464660134646798
ENSE000014297983460655534606904
ENSE000014621873469644634696767
ENSE000014621943458728834590600
ENSE000036851253465462534654779

Expression profiles

Bgee: expression breadth ubiquitous, 290 present calls, max score 97.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.8901 / max 204.1649, expressed in 1788 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
732626.75201735
732641.8309930
732650.4292218
732610.3801158
732600.2605107
732630.166267
732590.071139

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
gastrocnemiusUBERON:000138897.89gold quality
tendon of biceps brachiiUBERON:000818897.74gold quality
muscle of legUBERON:000138397.66gold quality
hindlimb stylopod muscleUBERON:000425297.62gold quality
medial globus pallidusUBERON:000247796.53gold quality
buccal mucosa cellCL:000233696.45gold quality
muscle organUBERON:000163096.20gold quality
islet of LangerhansUBERON:000000696.17gold quality
apex of heartUBERON:000209896.17gold quality
right testisUBERON:000453495.89gold quality
left testisUBERON:000453395.77gold quality
globus pallidusUBERON:000187595.56gold quality
heart left ventricleUBERON:000208495.17gold quality
cerebellar hemisphereUBERON:000224595.09gold quality
amniotic fluidUBERON:000017395.07gold quality
right frontal lobeUBERON:000281095.06gold quality
cerebellar cortexUBERON:000212995.04gold quality
cardiac ventricleUBERON:000208295.02gold quality
right hemisphere of cerebellumUBERON:001489094.90gold quality
right atrium auricular regionUBERON:000663194.79gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451194.69gold quality
testisUBERON:000047394.60gold quality
tendonUBERON:000004394.57gold quality
lower esophagusUBERON:001347394.37gold quality
lower esophagus muscularis layerUBERON:003583394.36gold quality
prefrontal cortexUBERON:000045194.33gold quality
right lobe of liverUBERON:000111494.28gold quality
heartUBERON:000094894.15gold quality
cardiac atriumUBERON:000208194.11gold quality
skeletal muscle tissueUBERON:000113494.09gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes8.65
E-GEOD-110499no331.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

208 targeting ILRUN, 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-6867-5P100.0082.213464
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-8485100.0077.574731
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4283100.0066.422097
HSA-MIR-9-5P100.0072.282361
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-5193100.0067.261744
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-4455100.0065.481587
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-186-5P99.9970.833707
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-569699.9872.364487
HSA-MIR-477599.9875.006394
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-6888-3P99.9765.951170
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062

Literature-anchored findings (GeneRIF, showing 9)

  • Ethanol, but not acetaldehyde, inhibited PPAR-beta transactivation. (PMID:18003597)
  • DSCR2 was found to interact with PPARbeta and to inhibit it. (PMID:18793612)
  • up-regulated expression by repetitive low-grade oxidative stress through p38MAPK or NF-kappaB pathways (PMID:19059477)
  • C6orf106 promotes invasion in NSCLC cells. Finally, C6orf106 upregulates vimentin, and downregulates E-cadherin and P120ctn. (PMID:25736925)
  • High C6orf106 expression was significantly correlated with lymph node metastasis in triple-negative breast cancer. (PMID:25953261)
  • High C6orf106 expression is associated with innate antiviral response. (PMID:29802199)
  • C6orf106 facilitates invasion and proliferation of pancreatic cancer cells, likely via activating ERK-P90RSK signaling pathway. (PMID:30311108)
  • we detected a novel obesity and BMI-associated locus at PKHD1 and novel variants driving associations at previously established signals (e.g. rs205262 at the SNRPC/C6orf106 locus and rs112446794 at the PRDM6-CEP120 locus). (PMID:30677029)
  • ILRUN Downregulates ACE2 Expression and Blocks Infection of Human Cells by SARS-CoV-2. (PMID:33963054)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioilrunENSDARG00000078075
mus_musculusIlrunENSMUSG00000056692
rattus_norvegicusIlrunENSRNOG00000038883

Protein

Protein identifiers

Protein ILRUNQ9H6K1 (reviewed: Q9H6K1)

Alternative names: Inflammation and lipid regulator with UBA-like and NBR1-like domains protein

All UniProt accessions (2): Q9H6K1, Q5TH58

UniProt curated annotations — full annotation on UniProt →

Function. Negative regulator of innate antiviral response. Blocks IRF3-dependent cytokine production such as IFNA, IFNB and TNF. Interacts with IRF3 and inhibits IRF3 recruitment to type I IFN promoter sequences while also reducing nuclear levels of the coactivators EP300 and CREBBP.

Subunit / interactions. Interacts with IRF3; the interaction inhibits IRF3 binding to its DNA consensus sequence.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Expressed in lung (at protein level).

Induction. Expression is increased in presence of dsRNA such as poly(I:C).

Isoforms (2)

UniProt IDNamesCanonical?
Q9H6K1-11yes
Q9H6K1-22

RefSeq proteins (2): NP_073595, NP_077270* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR009060UBA-like_sfHomologous_superfamily
IPR013783Ig-like_foldHomologous_superfamily
IPR032350Nbr1_FWDomain
IPR039517C6orf106_UBA-likeDomain

Pfam: PF14555, PF16158

UniProt features (17 total): strand 8, modified residue 3, compositionally biased region 2, chain 1, region of interest 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6VHIX-RAY DIFFRACTION2.46

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H6K1-F171.260.38

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 (3): 215, 222, 272

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 233 (showing top): ELVIDGE_HYPOXIA_DN, MODULE_255, GOBP_REGULATION_OF_DEFENSE_RESPONSE_TO_VIRUS, AAGCCAT_MIR135A_MIR135B, MODULE_317, GOBP_NEGATIVE_REGULATION_OF_TYPE_I_INTERFERON_PRODUCTION, TGACCTY_ERR1_Q2, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_MACROAUTOPHAGY, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_BIOTIC_STIMULUS, CAGCAGG_MIR370, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, GOBP_NEGATIVE_REGULATION_OF_DEFENSE_RESPONSE_TO_VIRUS, GOBP_DEFENSE_RESPONSE_TO_OTHER_ORGANISM

GO Biological Process (8): macroautophagy (GO:0016236), negative regulation of type I interferon production (GO:0032480), negative regulation of tumor necrosis factor production (GO:0032720), negative regulation of DNA binding (GO:0043392), innate immune response (GO:0045087), negative regulation of defense response to virus (GO:0050687), negative regulation of protein localization to nucleus (GO:1900181), immune system process (GO:0002376)

GO Molecular Function (2): ubiquitin binding (GO:0043130), protein binding (GO:0005515)

GO Cellular Component (6): phagophore assembly site (GO:0000407), nucleus (GO:0005634), cytoplasm (GO:0005737), centrosome (GO:0005813), cytosol (GO:0005829), nuclear speck (GO:0016607)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cytoplasm2
autophagosome assembly1
autophagy1
negative regulation of cytokine production1
regulation of type I interferon production1
type I interferon production1
tumor necrosis factor production1
regulation of tumor necrosis factor production1
negative regulation of tumor necrosis factor superfamily cytokine production1
DNA binding1
negative regulation of binding1
regulation of DNA binding1
immune response1
defense response to symbiont1
negative regulation of response to biotic stimulus1
negative regulation of defense response1
negative regulation of response to external stimulus1
regulation of defense response to virus1
defense response to virus1
protein localization to nucleus1
regulation of protein localization to nucleus1
negative regulation of protein localization1
biological_process1
ubiquitin-like protein binding1
binding1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
centriole1
microtubule organizing center1
nuclear ribonucleoprotein granule1

Protein interactions and networks

STRING

566 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ILRUNBLTP3AQ6BDS2588
ILRUNA0A2U3TZT1A0A2U3TZT1575
ILRUNNUDT3O95989542
ILRUNSPDEFO95238476
ILRUNC17orf67Q0P5P2446
ILRUNSNRPCP09234428
ILRUNRSRC2Q7L4I2401
ILRUNTDP2O95551381
ILRUNPACSIN1Q9BY11377
ILRUNSCMH1Q96GD3370
ILRUNC3orf38Q5JPI3368
ILRUNZBTB38Q8NAP3356
ILRUNZNF704Q6ZNC4350
ILRUNDYMQ7RTS9349
ILRUNFAM219BQ5XKK7349

IntAct

14 interactions, top by confidence:

ABTypeScore
HSPA8GAKpsi-mi:“MI:0914”(association)0.760
MCOLN1MCOLN2psi-mi:“MI:0914”(association)0.530
BAG2HGSpsi-mi:“MI:0914”(association)0.530
ILRUNRPSApsi-mi:“MI:0915”(physical association)0.370
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
HSPBP1HGSpsi-mi:“MI:0914”(association)0.350
STK26psi-mi:“MI:0914”(association)0.350
hspa1a_hspa1b_human-1SHTN1psi-mi:“MI:0914”(association)0.350
HSPA8SBNO1psi-mi:“MI:0914”(association)0.350
HSPA8PLEKHG3psi-mi:“MI:0914”(association)0.350
ILRUNUBA1psi-mi:“MI:0220”(ubiquitination reaction)0.000

BioGRID (19): C6orf106 (Biochemical Activity), C6orf106 (Affinity Capture-MS), C6orf106 (Biochemical Activity), C6orf106 (Affinity Capture-MS), C6orf106 (Affinity Capture-MS), C6orf106 (Affinity Capture-RNA), C6orf106 (Affinity Capture-RNA), UBC (Affinity Capture-Western), PPARA (Affinity Capture-Western), PPARG (Affinity Capture-Western), C6orf106 (Affinity Capture-MS), C6orf106 (Affinity Capture-MS), C6orf106 (Affinity Capture-MS), C6orf106 (Affinity Capture-MS), C6orf106 (Affinity Capture-MS)

ESM2 similar proteins: A0A8M1NHK4, A3KFF6, A6H8J1, O49429, O80678, O80910, P12348, P55265, P94017, P97765, Q08B53, Q13434, Q32SG5, Q3T1I4, Q3TJZ6, Q3UMQ8, Q3UPH1, Q4R3M1, Q5F3N9, Q5FWT1, Q5R679, Q5XJA3, Q5Z8L1, Q66H68, Q6ICG8, Q6P870, Q7G6K7, Q7ZYB4, Q8AVN9, Q8LA32, Q8R478, Q8R4X3, Q93YP4, Q94JZ8, Q969T9, Q96M27, Q9C5P0, Q9C6S1, Q9D529, Q9FF15

Diamond homologs: M1BJF6, P97432, Q14596, Q3TT38, Q501R9, Q5BL31, Q5F3N9, Q5RC94, Q9H6K1, Q9SB64

SIGNOR signaling

1 interactions.

AEffectBMechanism
SMURF1unknownILRUNubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance2
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1485 predictions. Top by Δscore:

VariantEffectΔscore
6:34646598:CA:Cdonor_loss1.0000
6:34646599:ACCT:Adonor_gain1.0000
6:34646600:CCTC:Cdonor_gain1.0000
6:34646806:C:CTacceptor_gain1.0000
6:34646807:A:Tacceptor_gain1.0000
6:34647433:C:Adonor_gain1.0000
6:34654620:CTTA:Cdonor_gain1.0000
6:34654621:TTA:Tdonor_loss1.0000
6:34654622:TA:Tdonor_loss1.0000
6:34654623:A:ACdonor_gain1.0000
6:34654623:AC:Adonor_gain1.0000
6:34654624:C:CAdonor_gain1.0000
6:34654624:CC:Cdonor_gain1.0000
6:34654624:CCA:Cdonor_gain1.0000
6:34654624:CCAG:Cdonor_gain1.0000
6:34654624:CCAGA:Cdonor_gain1.0000
6:34654775:GGTTC:Gacceptor_gain1.0000
6:34654776:GTTC:Gacceptor_gain1.0000
6:34654777:TTC:Tacceptor_gain1.0000
6:34654778:TC:Tacceptor_gain1.0000
6:34654779:CC:Cacceptor_gain1.0000
6:34654780:C:CCacceptor_gain1.0000
6:34654780:C:Tacceptor_gain1.0000
6:34654781:T:Gacceptor_loss1.0000
6:34654782:A:ACacceptor_gain1.0000
6:34654782:A:Cacceptor_gain1.0000
6:34696440:GCTCA:Gdonor_loss1.0000
6:34696441:CTCAC:Cdonor_loss1.0000
6:34696442:TCAC:Tdonor_loss1.0000
6:34696443:CA:Cdonor_loss1.0000

AlphaMissense

1972 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
6:34606896:A:GW174R1.000
6:34606896:A:TW174R1.000
6:34646603:C:AG170V1.000
6:34646603:C:TG170E1.000
6:34646604:C:GG170R1.000
6:34646604:C:TG170R1.000
6:34646633:C:GR160P1.000
6:34646635:C:AW159C1.000
6:34646635:C:GW159C1.000
6:34646636:C:GW159S1.000
6:34646637:A:GW159R1.000
6:34646637:A:TW159R1.000
6:34646643:C:GG157R1.000
6:34646643:C:TG157R1.000
6:34646668:G:CS148R1.000
6:34646668:G:TS148R1.000
6:34646670:T:GS148R1.000
6:34646681:A:TV144D1.000
6:34646768:A:GL115P1.000
6:34646768:A:TL115H1.000
6:34646785:C:AW109C1.000
6:34646785:C:GW109C1.000
6:34646787:A:GW109R1.000
6:34646787:A:TW109R1.000
6:34654639:C:GR100P1.000
6:34654641:C:AW99C1.000
6:34654641:C:GW99C1.000
6:34654642:C:GW99S1.000
6:34654643:A:GW99R1.000
6:34654643:A:TW99R1.000

dbSNP variants (sampled 300 via entrez): RS1000018719 (6:34635586 A>G), RS1000030053 (6:34631426 C>A), RS1000046463 (6:34644728 G>A,C), RS1000099588 (6:34604543 A>G), RS1000103682 (6:34622657 T>C), RS1000163018 (6:34629788 A>G), RS1000171823 (6:34673560 CATT>C), RS1000174315 (6:34688555 G>A), RS1000180333 (6:34671289 C>G,T), RS1000214843 (6:34587185 C>A), RS1000229661 (6:34694659 C>A), RS1000234433 (6:34671511 A>G,T), RS1000271472 (6:34654118 T>C), RS1000322227 (6:34621657 G>A,C), RS1000328324 (6:34593631 T>G)

Disease associations

OMIM: gene MIM:612217 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

75 associations (top):

StudyTraitp-value
GCST000174_18Height4.000000e-12
GCST000372_16Height8.000000e-11
GCST000755_24HDL cholesterol4.000000e-09
GCST000760_43Cholesterol, total5.000000e-11
GCST001876_2Pubertal anthropometrics9.000000e-08
GCST001956_63Height8.000000e-13
GCST002221_12Cholesterol, total4.000000e-15
GCST002285_9Chagas cardiomyopathy in Tripanosoma cruzi seropositivity1.000000e-06
GCST002783_262Body mass index3.000000e-10
GCST002783_36Body mass index2.000000e-09
GCST002783_617Body mass index2.000000e-10
GCST004146_25Chronic lymphocytic leukemia2.000000e-08
GCST004235_77Total cholesterol levels2.000000e-13
GCST004495_10BMI (adjusted for smoking behaviour)3.000000e-07
GCST004495_11BMI (adjusted for smoking behaviour)3.000000e-09
GCST004497_82Body mass index (joint analysis main effects and smoking interaction)3.000000e-09
GCST004497_83Body mass index (joint analysis main effects and smoking interaction)2.000000e-07
GCST004499_14BMI in non-smokers3.000000e-07
GCST004499_15BMI in non-smokers6.000000e-09
GCST005195_144Coronary artery disease2.000000e-11
GCST005196_96Coronary artery disease1.000000e-11
GCST006612_103LDL cholesterol3.000000e-08
GCST006802_28Body mass index2.000000e-09
GCST007293_46Body fat distribution (arm fat ratio)2.000000e-06
GCST007294_11Body fat distribution (trunk fat ratio)1.000000e-16
GCST007294_30Body fat distribution (trunk fat ratio)1.000000e-09
GCST007295_155Body fat distribution (leg fat ratio)1.000000e-24
GCST007295_161Body fat distribution (leg fat ratio)5.000000e-16
GCST008070_6HDL cholesterol levels4.000000e-07
GCST008075_181HDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)8.000000e-10

EFO canonical traits (22, from GWAS)

EFO IDTrait name
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0004574total cholesterol measurement
EFO:0001382puberty
EFO:0004340body mass index
EFO:0004318smoking behavior
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004341body fat distribution
EFO:0004329alcohol drinking
EFO:0004338body weight
EFO:0008039BMI-adjusted hip circumference
EFO:0010100multisite chronic pain
EFO:0000195metabolic syndrome
EFO:0004614apolipoprotein A 1 measurement
EFO:0004615apolipoprotein B measurement
EFO:0004918age at diagnosis
EFO:0006935thalamus volume
EFO:0004920progression free survival
EFO:0007789BMI-adjusted waist circumference
EFO:0004587lymphocyte count
EFO:0005091monocyte count
EFO:0004532serum gamma-glutamyl transferase measurement
EFO:0007788BMI-adjusted waist-hip ratio

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Estradiolincreases expression, decreases expression2
Valproic Acidincreases expression2
Cadmium Chlorideincreases abundance, increases expression2
FR900359decreases phosphorylation1
bisphenol Aincreases methylation1
afimoxifenedecreases expression1
sodium arseniteincreases expression1
cobaltous chlorideincreases expression1
nickel sulfateincreases expression1
dimethylarsinous acidincreases expression1
abrineincreases expression1
bisphenol Sdecreases methylation1
Fulvestrantdecreases expression1
Vorinostatdecreases expression1
Air Pollutantsincreases expression, increases abundance1
Benzo(a)pyreneincreases mutagenesis1
Cadmiumincreases abundance, increases expression1
Seleniumincreases expression1
Thimerosaldecreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutionincreases expression1
Tretinoinincreases expression1
Aflatoxin B1decreases methylation1
Lithium Chlorideincreases expression1
Copper Sulfateincreases expression1
Acrylamideincreases expression1
Raloxifene Hydrochloridedecreases expression1
Particulate Matterincreases abundance, increases expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E1SXHAP1 C6orf106 (-) 2Cancer cell lineMale
CVCL_E1SYHAP1 C6orf106 (-) 3Cancer cell lineMale
CVCL_XM38HAP1 C6orf106 (-) 1Cancer cell lineMale

Clinical trials (associated diseases)

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