RNF186

gene
On this page

Also known as FLJ20225

Summary

RNF186 (ring finger protein 186, HGNC:25978) is a protein-coding gene on chromosome 1p36.13, encoding E3 ubiquitin-protein ligase RNF186 (Q9NXI6). E3 ubiquitin protein ligase that is part of an apoptotic signaling pathway activated by endoplasmic reticulum stress.

Enables ubiquitin protein ligase activity and ubiquitin protein ligase binding activity. Involved in several processes, including intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress; proteasome-mediated ubiquitin-dependent protein catabolic process; and protein ubiquitination. Acts upstream of with a positive effect on regulation of autophagosome assembly. Located in endoplasmic reticulum membrane. Is active in endoplasmic reticulum.

Source: NCBI Gene 54546 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 55 total — 1 likely-pathogenic
  • MANE Select transcript: NM_019062

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25978
Approved symbolRNF186
Namering finger protein 186
Location1p36.13
Locus typegene with protein product
StatusApproved
AliasesFLJ20225
Ensembl geneENSG00000178828
Ensembl biotypeprotein_coding
OMIM617163
Entrez54546

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000375121

RefSeq mRNA: 1 — MANE Select: NM_019062 NM_019062

CCDS: CCDS199

Canonical transcript exons

ENST00000375121 — 1 exons

ExonStartEnd
ENSE000014658201981402919815283

Expression profiles

Bgee: expression breadth broad, 76 present calls, max score 96.87.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4944 / max 156.5897, expressed in 30 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
106950.233522
106910.098717
106940.076515
106920.054011
106930.031712

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
jejunal mucosaUBERON:000039996.87gold quality
duodenumUBERON:000211495.50gold quality
corpus epididymisUBERON:000435992.47gold quality
nephron tubuleUBERON:000123191.19gold quality
body of pancreasUBERON:000115090.69gold quality
mucosa of transverse colonUBERON:000499188.47gold quality
kidney epitheliumUBERON:000481986.99gold quality
colonic mucosaUBERON:000031785.82gold quality
renal glomerulusUBERON:000007485.45gold quality
metanephric glomerulusUBERON:000473685.31gold quality
mucosa of sigmoid colonUBERON:000499384.67gold quality
pancreatic ductal cellCL:000207984.40silver quality
adult mammalian kidneyUBERON:000008284.16gold quality
rectumUBERON:000105283.55gold quality
pancreasUBERON:000126480.06gold quality
kidneyUBERON:000211378.53gold quality
cortex of kidneyUBERON:000122578.08gold quality
transverse colonUBERON:000115775.84gold quality
jejunumUBERON:000211575.22gold quality
ileal mucosaUBERON:000033173.98gold quality
vermiform appendixUBERON:000115473.67gold quality
caecumUBERON:000115371.95gold quality
metanephrosUBERON:000008171.27gold quality
small intestineUBERON:000210870.21gold quality
oocyteCL:000002369.43gold quality
caput epididymisUBERON:000435868.58gold quality
small intestine Peyer’s patchUBERON:000345467.29gold quality
intestineUBERON:000016065.98gold quality
secondary oocyteCL:000065565.67gold quality
large intestineUBERON:000005964.68gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-GEOD-125970yes15.67
E-ANND-3yes11.19

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

27 targeting RNF186, 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-548AW99.9972.573559
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-129799.9173.413162
HSA-MIR-26A-5P99.7873.522303
HSA-MIR-26B-5P99.7873.512305
HSA-MIR-6505-5P99.7369.251595
HSA-MIR-26A-1-3P99.6466.81788
HSA-MIR-26A-2-3P99.6466.82786
HSA-MIR-432899.5771.064094
HSA-MIR-569799.3967.741249
HSA-MIR-6853-3P99.3670.791558
HSA-MIR-316899.0867.751384
HSA-MIR-6814-5P99.0366.681273
HSA-MIR-10A-5P98.8969.85712
HSA-MIR-10B-5P98.8969.86711
HSA-MIR-6829-5P98.8665.121480
HSA-MIR-428998.2666.90810
HSA-MIR-4436B-3P98.2565.261494
HSA-MIR-6735-5P98.2465.361488
HSA-MIR-7843-5P98.1265.261421
HSA-MIR-4632-5P97.8265.381470
HSA-MIR-6879-5P97.7765.521521
HSA-MIR-464297.5267.60916
HSA-MIR-214-5P97.3466.50617
HSA-MIR-1266-3P96.2366.36778

Literature-anchored findings (GeneRIF, showing 10)

  • Single-nucleotide polymorphism in RNF186 gene is associated with ulcerative colitis. (PMID:23511034)
  • BNip1 functions as a downstream modulator of RNF186 to direct endoplasmic reticulum stress-associated apoptotic signaling. (PMID:23896122)
  • Our results confirmed significant association to rare non-synonymous coding variants in both IL23R and CARD9, previously identified from sequencing of CD loci, as well as identified a novel association in RNF186 (PMID:24068945)
  • a predicted protein-truncating variant (rs36095412, p.R179X, genotyped in 11,148 ulcerative colitis patients and 295,446 controls, MAF=up to 0.78%) in RNF186, a single-exon ring finger E3 ligase with strong colonic expression, protects against ulcerative colitis. (PMID:27503255)
  • RNF186 and Sestrin-2 bind each other through distinct C-terminal motifs and that Lys-13 in Sestrin-2 is a putative ubiquitin acceptor site. RNF186 knockdown increased Sestrin-2 protein levels and decreased mTORC1 activation. (PMID:31586034)
  • The Role of Tissue-Specific Ubiquitin Ligases, RNF183, RNF186, RNF182 and RNF152, in Disease and Biological Function. (PMID:32486221)
  • The role and mechanism of action of RNF186 in colorectal cancer through negative regulation of NF-kappaB. (PMID:32882406)
  • The E3 ubiquitin ligase RNF186 and RNF186 risk variants regulate innate receptor-induced outcomes. (PMID:34353900)
  • Ubiquitination of ATF6 by disease-associated RNF186 promotes the innate receptor-induced unfolded protein response. (PMID:34623328)
  • Systematic pan-cancer analysis of RNF186 with potential implications in progression and prognosis in human cancer. (PMID:38160786)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusRnf186ENSMUSG00000070661
rattus_norvegicusRnf186ENSRNOG00000017244

Protein

Protein identifiers

E3 ubiquitin-protein ligase RNF186Q9NXI6 (reviewed: Q9NXI6)

Alternative names: RING finger protein 186

All UniProt accessions (1): Q9NXI6

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin protein ligase that is part of an apoptotic signaling pathway activated by endoplasmic reticulum stress. Stimulates the expression of proteins specific of the unfolded protein response (UPR), ubiquitinates BNIP1 and regulates its localization to the mitochondrion and induces calcium release from the endoplasmic reticulum that ultimately leads to cell apoptosis. Plays a role in the maintenance of intestinal homeostasis and clearance of enteric pathogens. Upon NOD2 stimulation, ubiquitinates the ER stress sensor activating transcription factor 6/ATF6 and promotes the unfolded protein response UPR. Participates in basal level of autophagy maintenance by regulating the ubiquitination of EPHB2 and EPHB3. Upon stimulation by ligand EFNB1, ubiquitinates EPHB2 and further recruits MAP1LC3B for autophagy induction. Controls nutrient sensing by ubiquitinating Sestrin-2/SESN2, which is an intracellular sensor of cytosolic leucine and inhibitor of mTORC1 activity.

Subunit / interactions. Interacts with BNIP1.

Subcellular location. Endoplasmic reticulum membrane.

Post-translational modifications. Polyubiquitinated. ‘Lys-29’-linked autoubiquitination leads to proteasomal degradation.

Domain organisation. The RING-type domain is required for ubiquitination.

Pathway. Protein modification; protein ubiquitination.

RefSeq proteins (1): NP_061935* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR017907Znf_RING_CSConserved_site
IPR051435RING_finger_E3_ubiq-ligasesFamily

Enzyme classification (BRENDA):

  • EC 2.3.2.27 — RING-type E3 ubiquitin transferase (BRENDA: 28 organisms, 138 substrates, 10 inhibitors, 1 Km, 1 kcat entries)

Substrate kinetics (BRENDA)

1 substrates with measured Km, best-characterized 1. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
[UBE2W]-S-UBIQUITINYL-L-CYSTEINE0.30141

UniProt features (10 total): mutagenesis site 3, transmembrane region 2, sequence variant 2, chain 1, zinc finger region 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NXI6-F168.890.22

Functional residue map

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

Mutagenesis-validated functional residues (3):

PositionPhenotype
58–66loss of autoubiquitination; loss of bnip1 polyubiquitination; no effect on interaction with bnip1; decreased effect on c
60loss of ability to decrease sesn2 protein.
64exhibits a reduced ability to ubiquitinate ephb2 but retained ability to ubiquitinate ephb3.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): GOBP_RESPONSE_TO_ENDOPLASMIC_RETICULUM_STRESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, HNF1_Q6, GOBP_APOPTOTIC_SIGNALING_PATHWAY, RGTTAMWNATT_HNF1_01, GATA6_01, GOBP_PROTEIN_AUTOUBIQUITINATION, TGANTCA_AP1_C, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_POLYUBIQUITINATION, GOBP_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, HNF1_C, TGGNNNNNNKCCAR_UNKNOWN, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_PROTEIN_K63_LINKED_UBIQUITINATION

GO Biological Process (9): protein K29-linked ubiquitination (GO:0035519), proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161), protein autoubiquitination (GO:0051865), intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059), protein K63-linked ubiquitination (GO:0070534), protein localization to mitochondrion (GO:0070585), protein ubiquitination (GO:0016567), apoptotic process in response to mitochondrial fragmentation (GO:0140208), regulation of autophagosome assembly (GO:2000785)

GO Molecular Function (7): ubiquitin-protein transferase activity (GO:0004842), zinc ion binding (GO:0008270), ubiquitin protein ligase binding (GO:0031625), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (3): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein polyubiquitination2
ubiquitin-dependent protein catabolic process1
proteasomal protein catabolic process1
protein ubiquitination1
response to endoplasmic reticulum stress1
intrinsic apoptotic signaling pathway1
protein localization to organelle1
protein modification by small protein conjugation1
apoptotic process1
autophagosome assembly1
regulation of vacuole organization1
regulation of organelle assembly1
ubiquitin-like protein transferase activity1
transition metal ion binding1
ubiquitin-like protein ligase binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cation binding1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cellular anatomical structure1

Protein interactions and networks

STRING

420 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RNF186OTUD3Q5T2D3620
RNF186RNF183Q96D59620
RNF186PLA2G2EQ9NZK7609
RNF186RNF182Q8N6D2576
RNF186CARD9Q9H257524
RNF186RNF175Q8N4F7504
RNF186BNIP1Q12981469
RNF186RNF150Q9ULK6454
RNF186SVOPLQ8N434449
RNF186ZNRF4Q8WWF5447
RNF186IL23RQ5VWK5432
RNF186KBTBD3Q8NAB2429
RNF186SLC25A45Q8N413414
RNF186BTNL2Q9UIR0410
RNF186INAVAQ3KP66403

IntAct

13 interactions, top by confidence:

ABTypeScore
RNF186psi-mi:“MI:0915”(physical association)0.560
PBX3RNF186psi-mi:“MI:0915”(physical association)0.560
SCAND1RNF186psi-mi:“MI:0915”(physical association)0.560
UBE2D2RNF186psi-mi:“MI:0915”(physical association)0.370
RNF186UBE2Hpsi-mi:“MI:0915”(physical association)0.370
RNF186TFRCpsi-mi:“MI:0914”(association)0.350
RNF186psi-mi:“MI:0915”(physical association)0.000
PBX3RNF186psi-mi:“MI:0915”(physical association)0.000
SCAND1RNF186psi-mi:“MI:0915”(physical association)0.000

BioGRID (22): RNF186 (PCA), RNF186 (Two-hybrid), RNF186 (Two-hybrid), RNF186 (Two-hybrid), SESN2 (Reconstituted Complex), RNF186 (Reconstituted Complex), EPHB2 (Affinity Capture-MS), EPHB3 (Affinity Capture-MS), TOLLIP (Affinity Capture-MS), TFRC (Affinity Capture-MS), TRIM21 (Affinity Capture-MS), EPHB2 (Affinity Capture-Western), EPHB3 (Affinity Capture-Western), RNF186 (Affinity Capture-Western), RNF186 (Affinity Capture-Western)

ESM2 similar proteins: A6NCL7, A6NCQ9, A6QP29, A6QQV9, B1AVH7, B5DFA1, D2H0G5, D2H6Z0, D2H788, D3ZBM4, D4A723, E1C2W7, O95153, Q0QWG9, Q3SWY0, Q3T0Y9, Q3U0L2, Q3UV31, Q3V3A7, Q5RF77, Q60943, Q6INB3, Q6PGG2, Q7TNF8, Q7Z465, Q80TI1, Q810L3, Q8BG47, Q8BRJ3, Q8BXP5, Q8C0R7, Q8C432, Q8CEF8, Q8HYZ0, Q8N0U2, Q8N6D2, Q8N8N0, Q8NC24, Q8QZS5, Q8TED9

Diamond homologs: A0A7I2V3R4, A6NIN4, D2H788, D3ZBM4, O70277, O75382, Q13049, Q3T0Y9, Q6IMG5, Q6INB3, Q8C432, Q8CH72, Q8K0W3, Q8N6D2, Q9DCB3, Q9FY48, Q9H0X6, Q9NXI6, Q9R1R2, Q58EC8, Q9D241, Q9VE61, D2H6Z0, D4A723, E1C2W7, P36406, P36407, Q3SWY0, Q68EV7, Q6GND7, Q6NRD3, Q8BG47, Q8BGX0, Q8N8N0, Q8QZS5, E7ERA6, P33288, Q3UV31, Q96D59

SIGNOR signaling

1 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”RNF186ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance50
Likely benign4
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
3767281NC_000001.11:g.19676448_19875998delLikely pathogenic

SpliceAI

141 predictions. Top by Δscore:

VariantEffectΔscore
1:19814668:A:ACdonor_gain0.8600
1:19814669:C:CCdonor_gain0.8600
1:19814838:G:Tdonor_gain0.8500
1:19814834:CGG:Cdonor_gain0.7600
1:19814669:CTT:Cdonor_gain0.7300
1:19814837:TG:Tdonor_gain0.7000
1:19814836:G:GCdonor_gain0.6500
1:19814497:GTGCT:Gacceptor_loss0.6300
1:19814499:GCTGG:Gacceptor_loss0.6300
1:19814566:C:CTacceptor_gain0.6300
1:19814500:C:CCacceptor_gain0.6100
1:19814662:GCACT:Gdonor_loss0.6100
1:19814663:CACT:Cdonor_loss0.6100
1:19814664:ACTTA:Adonor_loss0.6100
1:19814665:CT:Cdonor_loss0.6100
1:19814666:T:TCdonor_loss0.6100
1:19814667:TAC:Tdonor_loss0.6100
1:19814668:ACTTC:Adonor_loss0.6100
1:19814669:C:CAdonor_loss0.6100
1:19814661:TGCAC:Tdonor_loss0.6000
1:19814786:C:CTdonor_gain0.5900
1:19814498:TG:Tacceptor_gain0.5700
1:19814878:T:TAdonor_gain0.5700
1:19814493:CCGGG:Cacceptor_gain0.5500
1:19814577:C:Tacceptor_gain0.5500
1:19814787:C:CTdonor_gain0.5500
1:19814512:C:CTacceptor_gain0.5400
1:19814578:G:Tacceptor_gain0.5400
1:19814669:CT:Cdonor_gain0.5300
1:19814576:CCGGG:Cacceptor_gain0.5200

AlphaMissense

1443 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:19814916:G:CF62L0.993
1:19814916:G:TF62L0.993
1:19814918:A:GF62L0.993
1:19814940:C:AK54N0.989
1:19814940:C:GK54N0.989
1:19814904:G:CC66W0.984
1:19814858:A:GC82R0.983
1:19814984:A:GC40R0.981
1:19814906:A:GC66R0.980
1:19814913:G:CC63W0.979
1:19814914:C:TC63Y0.978
1:19814856:G:CC82W0.975
1:19814905:C:TC66Y0.974
1:19814915:A:GC63R0.974
1:19814917:A:GF62S0.974
1:19814975:A:GC43R0.973
1:19814974:C:GC43S0.972
1:19814975:A:TC43S0.972
1:19814917:A:CF62C0.969
1:19814846:G:TR86S0.968
1:19814930:A:GC58R0.968
1:19814830:A:TV91D0.967
1:19814849:A:GC85R0.967
1:19814922:A:CH60Q0.966
1:19814922:A:TH60Q0.966
1:19814983:C:GC40S0.966
1:19814984:A:TC40S0.966
1:19814848:C:GC85S0.965
1:19814849:A:TC85S0.965
1:19814847:G:CC85W0.963

dbSNP variants (sampled 300 via entrez): RS1002502163 (1:19813623 A>C), RS1003768412 (1:19814664 A>C), RS1003816950 (1:19816070 G>A), RS1003982515 (1:19816371 G>T), RS1004311936 (1:19816657 C>T), RS1004417911 (1:19816166 C>T), RS1005826765 (1:19813982 C>T), RS1006288097 (1:19816093 G>A), RS1006322648 (1:19815493 A>C), RS1007717131 (1:19816706 T>C), RS1008250187 (1:19814114 C>A,T), RS1008602260 (1:19814335 C>G,T), RS1009763148 (1:19815846 A>C), RS1010249420 (1:19815572 G>A,C), RS1011180434 (1:19817096 C>G,T)

Disease associations

OMIM: gene MIM:617163 | disease phenotypes: MIM:300310

GenCC curated gene-disease

Mondo (1): immunodeficiency 61 (MONDO:0010296)

Orphanet (3): Non-syndromic agammaglobulinemia (Orphanet:229717), X-linked agammaglobulinemia (Orphanet:47), X-linked common variable immunodeficiency phenotype due to SH3KBP1 deficiency (Orphanet:696945)

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST000311_7Ulcerative colitis7.000000e-09
GCST000624_1Ulcerative colitis3.000000e-08
GCST000624_11Ulcerative colitis2.000000e-10
GCST000624_21Ulcerative colitis2.000000e-21
GCST001938_4Ulcerative colitis7.000000e-09
GCST004131_40Inflammatory bowel disease1.000000e-19
GCST004133_1Ulcerative colitis3.000000e-42
GCST005537_152Chronic inflammatory diseases (ankylosing spondylitis, Crohn’s disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy)1.000000e-24
GCST005537_153Chronic inflammatory diseases (ankylosing spondylitis, Crohn’s disease, psoriasis, primary sclerosing cholangitis, ulcerative colitis) (pleiotropy)8.000000e-20

MeSH disease descriptors (1)

DescriptorNameTree numbers
C538057Agammaglobulinemia, X-linked, type 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression2
pirinixic acidaffects binding, decreases expression, increases activity1
terbufosincreases methylation1
2-amino-3,8-dimethylimidazo(4,5-f)quinoxalinedecreases expression1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridinedecreases expression1
CGP 52608affects binding, increases reaction1
Arsenicaffects methylation1
Fonofosincreases methylation1
Parathionincreases methylation1
Rotenonedecreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1increases expression1
Okadaic Acidincreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): immunodeficiency 61