RNF25

gene
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Also known as AO7FLJ13906

Summary

RNF25 (ring finger protein 25, HGNC:14662) is a protein-coding gene on chromosome 2q35, encoding E3 ubiquitin-protein ligase RNF25 (Q96BH1). E3 ubiquitin-protein ligase that plays a key role in the RNF14-RNF25 translation quality control pathway, a pathway that takes place when a ribosome has stalled during translation, and which promotes ubiquitination and degradation of translation factors on stalled ribosomes.

The protein encoded by this gene contains a RING finger motif. The mouse counterpart of this protein has been shown to interact with Rela, the p65 subunit of NF-kappaB (NFKB), and modulate NFKB-mediated transcription activity. The mouse protein also binds ubiquitin-conjugating enzymes (E2s) and is a substrate for E2-dependent ubiquitination.

Source: NCBI Gene 64320 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 84 total
  • MANE Select transcript: NM_022453

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14662
Approved symbolRNF25
Namering finger protein 25
Location2q35
Locus typegene with protein product
StatusApproved
AliasesAO7, FLJ13906
Ensembl geneENSG00000163481
Ensembl biotypeprotein_coding
OMIM616014
Entrez64320

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 13 protein_coding, 4 retained_intron, 1 nonsense_mediated_decay

ENST00000295704, ENST00000423170, ENST00000463188, ENST00000473034, ENST00000474339, ENST00000497832, ENST00000864475, ENST00000864476, ENST00000864477, ENST00000864478, ENST00000864479, ENST00000917058, ENST00000917059, ENST00000917060, ENST00000917061, ENST00000917062, ENST00000944909, ENST00000944910

RefSeq mRNA: 1 — MANE Select: NM_022453 NM_022453

CCDS: CCDS2420

Canonical transcript exons

ENST00000295704 — 10 exons

ExonStartEnd
ENSE00001144106218663892218664535
ENSE00001940096218671930218672002
ENSE00003464419218668239218668341
ENSE00003545290218668605218668679
ENSE00003563730218667912218667981
ENSE00003603318218666159218666230
ENSE00003605555218668079218668146
ENSE00003661908218665155218665247
ENSE00003662798218664739218664873
ENSE00003665191218665916218666059

Expression profiles

Bgee: expression breadth ubiquitous, 217 present calls, max score 91.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.1635 / max 103.4859, expressed in 1794 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
3398017.16351794

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
adenohypophysisUBERON:000219691.25gold quality
granulocyteCL:000009489.60gold quality
popliteal arteryUBERON:000225089.49gold quality
tibial arteryUBERON:000761089.49gold quality
prefrontal cortexUBERON:000045189.44gold quality
pituitary glandUBERON:000000789.25gold quality
descending thoracic aortaUBERON:000234589.19gold quality
left testisUBERON:000453389.06gold quality
right testisUBERON:000453489.06gold quality
stromal cell of endometriumCL:000225589.04gold quality
right frontal lobeUBERON:000281088.95gold quality
aortaUBERON:000094788.93gold quality
right lobe of thyroid glandUBERON:000111988.79gold quality
right coronary arteryUBERON:000162588.78gold quality
cerebellar hemisphereUBERON:000224588.76gold quality
right hemisphere of cerebellumUBERON:001489088.74gold quality
esophagogastric junction muscularis propriaUBERON:003584188.71gold quality
cerebellar cortexUBERON:000212988.65gold quality
mucosa of stomachUBERON:000119988.62gold quality
colonic epitheliumUBERON:000039788.61gold quality
lower esophagus muscularis layerUBERON:003583388.61gold quality
lower esophagusUBERON:001347388.59gold quality
anterior cingulate cortexUBERON:000983588.52gold quality
left coronary arteryUBERON:000162688.48gold quality
cingulate cortexUBERON:000302788.48gold quality
calcaneal tendonUBERON:000370188.45gold quality
Brodmann (1909) area 9UBERON:001354088.39gold quality
thoracic aortaUBERON:000151588.35gold quality
left uterine tubeUBERON:000130388.33gold quality
body of uterusUBERON:000985388.29gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes4.55

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 5)

  • Functional studies of the mouse counterpart (PMID:10500182)
  • RING finger protein AO7 supports NF-kappaB-mediated transcription by interacting with the transactivation domain of the p65 subunit. (PMID:12748188)
  • mutations having marked effects on function only minimally affect the intermolecular interactions between the AO7 RING and UbcH5B, establishing a high degree of complexity in activation through the RING-E2 interface. (PMID:26475854)
  • RNF25 plays an essential role in gefitinib resistance of Non-small cell lung cancer by mediating cross-talk between NF-kappaB and ERK pathways. (PMID:29789542)
  • Oxidative Stress Promotes Liver Cancer Metastasis via RNF25-Mediated E-Cadherin Protein Degradation. (PMID:38286671)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriornf25ENSDARG00000027182
mus_musculusRnf25ENSMUSG00000026171
rattus_norvegicusRnf25ENSRNOG00000016886
drosophila_melanogasterCG13344FBGN0033884
caenorhabditis_elegansWBGENE00021812

Protein

Protein identifiers

E3 ubiquitin-protein ligase RNF25Q96BH1 (reviewed: Q96BH1)

Alternative names: RING finger protein 25, RING finger protein AO7

All UniProt accessions (2): Q96BH1, H7C219

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin-protein ligase that plays a key role in the RNF14-RNF25 translation quality control pathway, a pathway that takes place when a ribosome has stalled during translation, and which promotes ubiquitination and degradation of translation factors on stalled ribosomes. Catalyzes ubiquitination of RPS27A in response to ribosome collisions, promoting activation of RNF14. RNF25 catalyzes ubiquitination of other ribosomal proteins on stalled ribosomes, such as RPL0, RPL1, RPL12, RPS13 and RPS17. Also involved in ubiquitination and degradation of stalled ETF1/eRF1. Independently of its function in the response to stalled ribosomes, mediates ubiquitination and subsequent proteasomal degradation of NKD2. May also stimulate transcription mediated by NF-kappa-B via its interaction with RELA/p65.

Subunit / interactions. Interacts with UBE2D2, and may also interact with UBE2E1 and UBE2E3. Interacts with RELA/p65.

Subcellular location. Cytoplasm.

Post-translational modifications. Ubiquitinated; autoubiquitinated.

Pathway. Protein modification; protein ubiquitination.

Similarity. Belongs to the RNF25 family.

RefSeq proteins (1): NP_071898* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR006575RWD_domDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR016135UBQ-conjugating_enzyme/RWDHomologous_superfamily
IPR039133RNF25Family

Pfam: PF05773, PF13639

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 (48 total): binding site 8, mutagenesis site 8, strand 8, helix 6, turn 5, compositionally biased region 5, sequence conflict 2, region of interest 2, chain 1, domain 1, modified residue 1, zinc finger region 1

Structure

Experimental structures (PDB)

5 structures.

PDBMethodResolution (Å)
5D1MX-RAY DIFFRACTION1.58
5D1LX-RAY DIFFRACTION1.62
5D1KX-RAY DIFFRACTION1.78
2DAYSOLUTION NMR
2DMFSOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96BH1-F168.520.40

Functional residue map

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

Ligand- & substrate-binding residues (8): 135; 138; 153; 155; 158; 161; 198; 201

Post-translational modifications (1): 450

Mutagenesis-validated functional residues (8):

PositionPhenotype
135–138abolished e3 ubiquitin-protein ligase activity.
137strongly reduced e3 ubiquitin-protein ligase activity, slightly reduced binding to ube2d2.
159reduced activation of nf-kappa-b.
161strongly reduced activation of nf-kappa-b.
165decreased e3 ubiquitin-protein ligase activity, increased binding to ube2d2.
199decreased e3 ubiquitin-protein ligase activity without affecting binding to ube2d2.
242decreased binding to ube2d2.
245decreased binding to ube2d2.

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

IDPathway
R-HSA-983168Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-1280218Adaptive Immune System
R-HSA-168256Immune System
R-HSA-983169Class I MHC mediated antigen processing & presentation

MSigDB gene sets: 96 (showing top): REACTOME_ADAPTIVE_IMMUNE_SYSTEM, REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION, REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, EFC_Q6, GOBP_TRANSLATION, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, GGAANCGGAANY_UNKNOWN, NF1_Q6_01, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_PROTEIN_POLYUBIQUITINATION, GOBP_TRANSLATIONAL_ELONGATION, GOBP_POSITIVE_REGULATION_OF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY, HAND1E47_01, SAGIV_CD24_TARGETS_DN

GO Biological Process (8): ubiquitin-dependent protein catabolic process (GO:0006511), protein ubiquitination (GO:0016567), obsolete positive regulation of NF-kappaB transcription factor activity (GO:0051092), rescue of stalled cytosolic ribosome (GO:0072344), protein K6-linked ubiquitination (GO:0085020), protein-RNA covalent cross-linking repair (GO:0160127), translational elongation (GO:0006414), translational termination (GO:0006415)

GO Molecular Function (7): ubiquitin-protein transferase activity (GO:0004842), zinc ion binding (GO:0008270), NF-kappaB binding (GO:0051059), ubiquitin protein ligase activity (GO:0061630), protein binding (GO:0005515), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), cytosol (GO:0005829), cytosolic ribosome (GO:0022626), cytoplasm (GO:0005737)

Reactome top-level categories

Rollup of top-3 pathways:

CategoryPathways
Class I MHC mediated antigen processing & presentation1
Immune System1
Adaptive Immune System1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
translation2
cellular anatomical structure2
protein ubiquitination1
modification-dependent protein catabolic process1
protein modification by small protein conjugation1
cytoplasmic translational elongation1
ribosome disassembly1
protein polyubiquitination1
rescue of stalled cytosolic ribosome1
macromolecule biosynthetic process1
protein-containing complex disassembly1
ubiquitin-like protein transferase activity1
transition metal ion binding1
RNA polymerase II-specific DNA-binding transcription factor binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
binding1
catalytic activity1
cation binding1
intracellular membrane-bounded organelle1
cytoplasm1
cytosol1
ribosome1
intracellular anatomical structure1

Protein interactions and networks

STRING

1072 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RNF25UBE2D2P51669541
RNF25FBXO42Q6P3S6512
RNF25UBE2D1P51668501
RNF25NKD2Q969F2464
RNF25HSD17B10Q99714459
RNF25ADGRG7Q96K78442
RNF25LCN2P30150432
RNF25LSM7Q9UK45423
RNF25ZNF319Q9P2F9417
RNF25GIT1Q9Y2X7410
RNF25RNF11Q9Y3C5405
RNF25PSMA6P34062403
RNF25GIT2Q14161401
RNF25RNF20Q5VTR2401
RNF25TMBIM1Q969X1399

IntAct

64 interactions, top by confidence:

ABTypeScore
RNF25UBE2D3psi-mi:“MI:0915”(physical association)0.850
UBE2D3RNF25psi-mi:“MI:0915”(physical association)0.850
STX18NBASpsi-mi:“MI:0914”(association)0.810
UBE2D1RNF25psi-mi:“MI:0915”(physical association)0.800
RNF25UBE2D2psi-mi:“MI:0915”(physical association)0.800
RNF25UBE2E3psi-mi:“MI:0915”(physical association)0.800
RNF25UBE2D1psi-mi:“MI:0915”(physical association)0.800
UBE2D2RNF25psi-mi:“MI:0915”(physical association)0.800
UBE2E3RNF25psi-mi:“MI:0915”(physical association)0.800
HSPA8GAKpsi-mi:“MI:0914”(association)0.760
RNF25UBE2D4psi-mi:“MI:0915”(physical association)0.750
RNF25UBE2E1psi-mi:“MI:0915”(physical association)0.750
UBE2D4RNF25psi-mi:“MI:0915”(physical association)0.750
RNF25UBE2E1psi-mi:“MI:0914”(association)0.750
UBE2E2RNF25psi-mi:“MI:0914”(association)0.740
UBE2E2RNF25psi-mi:“MI:0915”(physical association)0.740
STX5GOSR2psi-mi:“MI:0914”(association)0.670
KCTD21RNF25psi-mi:“MI:0915”(physical association)0.560
MEOX2RNF25psi-mi:“MI:0915”(physical association)0.560
PRKNRNF25psi-mi:“MI:0915”(physical association)0.560
UBE2D2UBBpsi-mi:“MI:0914”(association)0.530
MINDY3UBBpsi-mi:“MI:0914”(association)0.530
RNF25IVLpsi-mi:“MI:0914”(association)0.530

BioGRID (147): RNF25 (Two-hybrid), RNF25 (Affinity Capture-MS), RNF25 (Affinity Capture-MS), RNF25 (Co-crystal Structure), UBE2D2 (Reconstituted Complex), RNF25 (Biochemical Activity), UBE2E3 (Reconstituted Complex), RNF25 (Affinity Capture-MS), RNF25 (Affinity Capture-MS), RNF25 (Affinity Capture-MS), UBE2D4 (Affinity Capture-MS), UBE2E1 (Affinity Capture-MS), RNF25 (Affinity Capture-MS), RNF25 (Affinity Capture-MS), UBE2D3 (Affinity Capture-MS)

ESM2 similar proteins: A0A0G2JXN2, A2RRU4, A4D2P6, A6QM06, D3YYI7, E1BBQ2, E9PGG2, F1LQY6, O19131, P19438, P29590, P50555, P52734, P55199, P97260, P98174, Q0VCT3, Q12770, Q3TAA7, Q3ZCA1, Q496Y0, Q4R4I0, Q5E9N3, Q5MNU5, Q5R5T1, Q60953, Q66T02, Q69Z89, Q6GQT6, Q70EL4, Q7TNM2, Q7Z4K8, Q7Z6J9, Q8BUM9, Q8C190, Q8CE64, Q8HXH0, Q8N1F8, Q8N554, Q8TC41

Diamond homologs: D4A7V9, Q5E9N3, Q7SXJ6, Q96BH1, Q9QZ05, Q9QZR0, Q9P2K8

SIGNOR signaling

2 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”RNF25ubiquitination
RNF25“down-regulates quantity by destabilization”NKD2polyubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 42 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
Synthesis of active ubiquitin: roles of E1 and E2 enzymes555.8×4e-06
Negative regulators of DDX58/IFIH1 signaling549.4×5e-06
E3 ubiquitin ligases ubiquitinate target proteins529.3×4e-05
Antigen processing: Ubiquitination & Proteasome degradation1112.4×2e-07

GO biological processes:

GO termPartnersFoldFDR
protein K11-linked ubiquitination551.6×4e-06
protein monoubiquitination545.2×6e-06
protein K48-linked ubiquitination835.5×2e-08
protein K63-linked ubiquitination535.2×2e-05
protein polyubiquitination721.3×4e-06
ubiquitin-dependent protein catabolic process815.6×4e-06
protein ubiquitination77.6×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1405 predictions. Top by Δscore:

VariantEffectΔscore
2:218664536:C:CCacceptor_gain1.0000
2:218664733:CCTCA:Cdonor_loss1.0000
2:218664734:CTCA:Cdonor_loss1.0000
2:218664735:TCA:Tdonor_loss1.0000
2:218664736:CA:Cdonor_loss1.0000
2:218664737:A:ACdonor_gain1.0000
2:218664738:C:CCdonor_gain1.0000
2:218664738:CCTG:Cdonor_gain1.0000
2:218664772:AG:Adonor_gain1.0000
2:218664869:AGCTC:Aacceptor_gain1.0000
2:218664871:CTC:Cacceptor_gain1.0000
2:218664872:TC:Tacceptor_gain1.0000
2:218664873:CC:Cacceptor_gain1.0000
2:218664874:C:CCacceptor_gain1.0000
2:218664874:C:Tacceptor_gain1.0000
2:218664875:T:Gacceptor_loss1.0000
2:218664886:A:ACacceptor_gain1.0000
2:218664886:A:Cacceptor_gain1.0000
2:218665243:GCCTT:Gacceptor_gain1.0000
2:218665244:CCTTC:Cacceptor_gain1.0000
2:218665245:CTT:Cacceptor_gain1.0000
2:218665246:TT:Tacceptor_gain1.0000
2:218665247:TC:Tacceptor_loss1.0000
2:218665248:C:CCacceptor_gain1.0000
2:218665248:CT:Cacceptor_loss1.0000
2:218665249:T:Aacceptor_loss1.0000
2:218665911:TCTA:Tdonor_loss1.0000
2:218665912:CTACC:Cdonor_loss1.0000
2:218665913:TACCT:Tdonor_loss1.0000
2:218665914:A:Tdonor_loss1.0000

AlphaMissense

2941 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:218665229:A:GC198R0.999
2:218666176:A:GC138R0.999
2:218666185:A:GC135R0.999
2:218665220:A:GC201R0.998
2:218666008:A:GC161R0.998
2:218666026:G:CH155D0.998
2:218666214:A:GL125P0.998
2:218666214:A:TL125H0.998
2:218666227:C:GG121R0.998
2:218666227:C:TG121R0.998
2:218667919:A:GL117P0.998
2:218668100:A:GL89P0.998
2:218668306:G:TP51H0.998
2:218668648:A:GS25P0.998
2:218665215:T:AR202S0.997
2:218665215:T:GR202S0.997
2:218665216:C:AR202I0.997
2:218665216:C:GR202T0.997
2:218665219:C:GC201S0.997
2:218665220:A:TC201S0.997
2:218666006:G:CC161W0.997
2:218666015:G:CH158Q0.997
2:218666015:G:TH158Q0.997
2:218666017:G:CH158D0.997
2:218666024:G:CH155Q0.997
2:218666024:G:TH155Q0.997
2:218666163:A:GF142S0.997
2:218666174:G:CC138W0.997
2:218666183:A:CC135W0.997
2:218666184:C:GC135S0.997

dbSNP variants (sampled 300 via entrez): RS1000024451 (2:218665470 G>A,C), RS1000055970 (2:218669337 T>C), RS1000621972 (2:218667262 TTC>T), RS1000909845 (2:218666822 T>C,G), RS1001694844 (2:218670966 G>T), RS1002075817 (2:218672267 T>A), RS1002260138 (2:218665437 G>A,C), RS1002291461 (2:218665041 C>A,T), RS1002625019 (2:218666741 T>A), RS1004086499 (2:218673660 C>G,T), RS1004288255 (2:218668936 G>A), RS1004409318 (2:218670490 T>TA), RS1004641770 (2:218670200 T>TTAA), RS1004650828 (2:218670116 G>A), RS1005432265 (2:218664261 TCC>T)

Disease associations

OMIM: gene MIM:616014 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006661_114Male-pattern baldness2.000000e-16

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

21 total (human), top 21 by PubMed support.

ChemicalActions (top 5)PubMed papers
aristolochic acid Iincreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359decreases phosphorylation1
pirinixic aciddecreases expression, increases activity, affects binding1
sodium arseniteincreases expression1
di-n-butylphosphoric acidaffects expression1
cylindrospermopsinincreases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
Caffeineincreases phosphorylation1
Cisplatinincreases expression1
Diethylstilbestrolincreases expression1
Doxorubicindecreases expression1
Enzyme Inhibitorsdecreases activity, increases O-linked glycosylation1
Methyl Methanesulfonateincreases expression1
Rotenonedecreases expression1
Smokedecreases expression1
Dronabinoldecreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Lactic Aciddecreases 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): alopecia