RNF149

gene
On this page

Also known as FLJ90504

Summary

RNF149 (ring finger protein 149, HGNC:23137) is a protein-coding gene on chromosome 2q11.2, encoding E3 ubiquitin-protein ligase RNF149 (Q8NC42). E3 ubiquitin-protein ligase.

Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in ubiquitin-dependent protein catabolic process. Predicted to act upstream of or within cellular response to xenobiotic stimulus; negative regulation of MAPK cascade; and regulation of protein stability. Located in membrane.

Source: NCBI Gene 284996 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 37 total
  • Druggable target: yes
  • MANE Select transcript: NM_173647

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23137
Approved symbolRNF149
Namering finger protein 149
Location2q11.2
Locus typegene with protein product
StatusApproved
AliasesFLJ90504
Ensembl geneENSG00000163162
Ensembl biotypeprotein_coding
Entrez284996

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 9 protein_coding, 3 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000295317, ENST00000424632, ENST00000463726, ENST00000478404, ENST00000485752, ENST00000490553, ENST00000878916, ENST00000878917, ENST00000878918, ENST00000878919, ENST00000878920, ENST00000878921, ENST00000878922, ENST00000963872

RefSeq mRNA: 1 — MANE Select: NM_173647 NM_173647

CCDS: CCDS2051

Canonical transcript exons

ENST00000295317 — 7 exons

ExonStartEnd
ENSE00001072165101294014101294082
ENSE00001072167101294931101295181
ENSE00001072168101288973101289055
ENSE00001130251101286081101286177
ENSE00001164142101275601101277281
ENSE00001783996101308129101308701
ENSE00003577829101281859101282057

Expression profiles

Bgee: expression breadth ubiquitous, 262 present calls, max score 99.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 52.1482 / max 3238.0759, expressed in 1821 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
2993751.00071821
299381.0168778
299390.130755

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bloodUBERON:000017899.16gold quality
monocyteCL:000057698.52gold quality
leukocyteCL:000073898.48gold quality
spleenUBERON:000210698.01gold quality
granulocyteCL:000009497.99gold quality
right lungUBERON:000216797.69gold quality
bone marrow cellCL:000209297.56gold quality
oviduct epitheliumUBERON:000480497.24gold quality
buccal mucosa cellCL:000233697.11gold quality
upper arm skinUBERON:000426396.96gold quality
vermiform appendixUBERON:000115496.80gold quality
upper lobe of left lungUBERON:000895296.80gold quality
bone marrowUBERON:000237196.79gold quality
upper lobe of lungUBERON:000894896.59gold quality
nasal cavity epitheliumUBERON:000538496.32gold quality
pericardiumUBERON:000240796.31gold quality
pharyngeal mucosaUBERON:000035596.26gold quality
penisUBERON:000098996.07gold quality
cartilage tissueUBERON:000241896.06gold quality
skin of abdomenUBERON:000141696.03gold quality
lower esophagus mucosaUBERON:003583496.00gold quality
esophagus mucosaUBERON:000246995.85gold quality
skin of legUBERON:000151195.77gold quality
lower lobe of lungUBERON:000894995.74gold quality
zone of skinUBERON:000001495.70gold quality
esophagus squamous epitheliumUBERON:000692095.61gold quality
vaginaUBERON:000099695.58gold quality
body of pancreasUBERON:000115095.47gold quality
omental fat padUBERON:001041495.40gold quality
peritoneumUBERON:000235895.39gold quality

Single-cell (SCXA)

Detected in 7 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-HCAD-15yes1100.04
E-MTAB-7052yes464.15
E-CURD-46yes16.06
E-MTAB-9801yes8.57
E-CURD-88yes4.34
E-CURD-119yes4.31
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): STAT3

miRNA regulators (miRDB)

108 targeting RNF149, 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-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-3120-5P100.0065.56965
HSA-MIR-5692A100.0074.406850
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-477599.9875.006394
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-60799.9773.625593
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-314899.9775.066478
HSA-MIR-590-3P99.9674.346478
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-302E99.9670.742669
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426

Literature-anchored findings (GeneRIF, showing 1)

  • Data show that RNF149 (RING finger protein 149) interacts with wild-type BRAF. (PMID:22628551)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusRnf149ENSMUSG00000048234
rattus_norvegicusRnf149ENSRNOG00000013946

Paralogs (9): RNF13 (ENSG00000082996), RNF215 (ENSG00000099999), ZNRF4 (ENSG00000105428), RNF167 (ENSG00000108523), RNF130 (ENSG00000113269), RNF128 (ENSG00000133135), RNF150 (ENSG00000170153), RNF133 (ENSG00000188050), RNF148 (ENSG00000235631)

Protein

Protein identifiers

E3 ubiquitin-protein ligase RNF149Q8NC42 (reviewed: Q8NC42)

Alternative names: DNA polymerase-transactivated protein 2, RING finger protein 149, RING-type E3 ubiquitin transferase RNF149

All UniProt accessions (2): Q8NC42, F8WCD0

UniProt curated annotations — full annotation on UniProt →

Function. E3 ubiquitin-protein ligase. Ubiquitinates BRAF, inducing its proteasomal degradation.

Subcellular location. Membrane.

Domain organisation. The RING-type zinc finger domain mediates binding to an E2 ubiquitin-conjugating enzyme.

Pathway. Protein modification; protein ubiquitination.

RefSeq proteins (1): NP_775918* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR003137PA_domainDomain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR042712RNF149_RING-H2Domain
IPR046450PA_dom_sfHomologous_superfamily

Pfam: PF02225, PF13639

UniProt features (15 total): sequence variant 4, glycosylation site 2, compositionally biased region 2, signal peptide 1, chain 1, transmembrane region 1, domain 1, zinc finger region 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8NC42-F175.150.37

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 (1): 345

Glycosylation sites (2): 145, 52

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 245 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, MCBRYAN_TERMINAL_END_BUD_UP, GOBP_NEGATIVE_REGULATION_OF_MAPK_CASCADE, BRUECKNER_TARGETS_OF_MIRLET7A3_DN, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, FOSTER_TOLERANT_MACROPHAGE_DN, MARTINEZ_RB1_TARGETS_DN, MCBRYAN_PUBERTAL_BREAST_3_4WK_UP, MCBRYAN_PUBERTAL_BREAST_5_6WK_UP, GOBP_POST_TRANSLATIONAL_PROTEIN_MODIFICATION, GOBP_REGULATION_OF_PROTEIN_STABILITY, GUO_HEX_TARGETS_DN, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, CHANDRAN_METASTASIS_UP

GO Biological Process (5): ubiquitin-dependent protein catabolic process (GO:0006511), protein ubiquitination (GO:0016567), regulation of protein stability (GO:0031647), negative regulation of MAPK cascade (GO:0043409), cellular response to xenobiotic stimulus (GO:0071466)

GO Molecular Function (4): zinc ion binding (GO:0008270), ubiquitin protein ligase activity (GO:0061630), transferase activity (GO:0016740), metal ion binding (GO:0046872)

GO Cellular Component (5): cytoplasm (GO:0005737), late endosome (GO:0005770), endoplasmic reticulum (GO:0005783), Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
cytoplasm2
endomembrane system2
intracellular membrane-bounded organelle2
protein ubiquitination1
modification-dependent protein catabolic process1
protein modification by small protein conjugation1
regulation of biological quality1
MAPK cascade1
regulation of MAPK cascade1
negative regulation of intracellular signal transduction1
response to xenobiotic stimulus1
cellular response to chemical stimulus1
transition metal ion binding1
ubiquitin-protein transferase activity1
ubiquitin-like protein ligase activity1
catalytic activity1
cation binding1
intracellular anatomical structure1
endosome1

Protein interactions and networks

STRING

824 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RNF149ZNF319Q9P2F9517
RNF149KAAG1Q9UBP8433
RNF149TBC1D8O95759409
RNF149ZNF805Q5CZA5400
RNF149ZNF207O43670383
RNF149FAM151BQ6UXP7378
RNF149JOSD1Q15040365
RNF149SETDB2Q96T68362
RNF149RNFT1Q5M7Z0358
RNF149RNF25Q96BH1347
RNF149LRRC57Q8N9N7346
RNF149ANO10Q9NW15338
RNF149LONRF3Q496Y0336
RNF149UBA2Q9UBT2334
RNF149B3GNT4Q9C0J1325

IntAct

101 interactions, top by confidence:

ABTypeScore
LSMEM2STX7psi-mi:“MI:0914”(association)0.740
SLC20A1LIN7Apsi-mi:“MI:0914”(association)0.640
PDGFRBPIK3R2psi-mi:“MI:0914”(association)0.610
MANSC1KLRG2psi-mi:“MI:0914”(association)0.530
TSPAN3MAP1LC3B2psi-mi:“MI:0914”(association)0.530
TSPAN17UPK3BL1psi-mi:“MI:0914”(association)0.530
PCDHB7C2CD2Lpsi-mi:“MI:0914”(association)0.530
ACVR1BMPR1Apsi-mi:“MI:0914”(association)0.530
MRAP2GOLIM4psi-mi:“MI:0914”(association)0.530
MRAP2PODXLpsi-mi:“MI:0914”(association)0.530
DLK1SCAMP3psi-mi:“MI:0914”(association)0.530
HFEADAM10psi-mi:“MI:0914”(association)0.530
KCNE3RIOK3psi-mi:“MI:0914”(association)0.530
SNAP23psi-mi:“MI:0914”(association)0.350
LAMP1HAX1psi-mi:“MI:0914”(association)0.350
BTNL8TMEM131Lpsi-mi:“MI:0914”(association)0.350
TNFRSF10AMAP1LC3B2psi-mi:“MI:0914”(association)0.350
RUSF1MAP1LC3B2psi-mi:“MI:0914”(association)0.350
TPCN2DDX11L8psi-mi:“MI:0914”(association)0.350
PCDHGB4FAM171A2psi-mi:“MI:0914”(association)0.350
TMEM30AUPK3BL1psi-mi:“MI:0914”(association)0.350
SLC20A1MPP2psi-mi:“MI:0914”(association)0.350
MRAP2GOSR1psi-mi:“MI:0914”(association)0.350
LITAFSDCBPpsi-mi:“MI:0914”(association)0.350
ARRDC3ZNF593psi-mi:“MI:0914”(association)0.350
HEPACAM2TNFRSF10Bpsi-mi:“MI:0914”(association)0.350
TMEM231TNFRSF10Bpsi-mi:“MI:0914”(association)0.350

BioGRID (640): RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS), RNF149 (Affinity Capture-MS)

ESM2 similar proteins: A1L3I3, A2A699, A2AWH2, A4IHZ3, A6NKQ9, A6QNY1, A8MVW0, B4R1D8, B6VH76, B6VH77, B6VH79, D3YY23, O00220, O43278, O55034, O75074, O88204, O95502, P08751, P21563, P22618, P48778, Q04756, Q3U2C5, Q3U4N7, Q496H8, Q4R6Y5, Q4TUC0, Q5HZW5, Q6QNF4, Q7TPG6, Q7TQH7, Q7Z4F1, Q86T13, Q86VZ4, Q8BY98, Q8C2B3, Q8C4W3, Q8CB67, Q8IXA5

Diamond homologs: A5WWA0, E9QAU8, G3X9R7, O22197, O22755, O43567, O54965, O64763, P0C034, P0CH30, P0DPR2, Q06003, Q07G42, Q08D68, Q0II22, Q0VD51, Q10R93, Q14B02, Q29RU0, Q2TA44, Q3U2C5, Q4KLR8, Q4R6Y5, Q5NCP0, Q5RCV8, Q5RF74, Q5SPX3, Q5SSZ7, Q5XF85, Q641J8, Q66HG0, Q68DV7, Q69U49, Q6AY01, Q6DIP3, Q6IRP0, Q6NML0, Q6NQG7, Q6NRX0, Q6Y290

SIGNOR signaling

2 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”RNF149ubiquitination
RNF149“down-regulates quantity by destabilization”BRAFpolyubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 123 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
Interferon gamma signaling610.8×2e-03

GO biological processes:

GO termPartnersFoldFDR
T cell receptor signaling pathway812.2×3e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance26
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1362 predictions. Top by Δscore:

VariantEffectΔscore
2:101281853:GCTCA:Gdonor_loss1.0000
2:101281854:CTCA:Cdonor_loss1.0000
2:101281855:TCA:Tdonor_loss1.0000
2:101281856:CACCT:Cdonor_loss1.0000
2:101281857:A:ACdonor_gain1.0000
2:101281858:C:CCdonor_gain1.0000
2:101281858:C:CGdonor_loss1.0000
2:101282054:CTCC:Cacceptor_gain1.0000
2:101282059:T:TCacceptor_gain1.0000
2:101282066:T:Cacceptor_gain1.0000
2:101282066:T:TCacceptor_gain1.0000
2:101282072:C:CTacceptor_gain1.0000
2:101288971:A:ACdonor_gain1.0000
2:101288972:C:CCdonor_gain1.0000
2:101294084:T:Cacceptor_gain1.0000
2:101295177:TGTTC:Tacceptor_gain1.0000
2:101295180:TC:Tacceptor_gain1.0000
2:101295181:CC:Cacceptor_gain1.0000
2:101295181:CCTG:Cacceptor_loss1.0000
2:101295182:C:CCacceptor_gain1.0000
2:101281858:CCTAG:Cdonor_gain0.9900
2:101281862:G:Cdonor_gain0.9900
2:101282053:TCTCC:Tacceptor_gain0.9900
2:101282054:CTCCC:Cacceptor_gain0.9900
2:101282055:TCC:Tacceptor_gain0.9900
2:101282055:TCCC:Tacceptor_gain0.9900
2:101282056:CC:Cacceptor_gain0.9900
2:101282056:CCC:Cacceptor_gain0.9900
2:101282057:CC:Cacceptor_gain0.9900
2:101282058:C:CCacceptor_gain0.9900

AlphaMissense

2597 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:101286115:C:GC309S1.000
2:101286116:A:TC309S1.000
2:101286125:A:GC306R1.000
2:101286144:C:AW299C1.000
2:101286144:C:GW299C1.000
2:101286146:A:GW299R1.000
2:101286146:A:TW299R1.000
2:101286156:G:CC295W1.000
2:101286157:C:TC295Y1.000
2:101286158:A:GC295R1.000
2:101286168:A:CF291L1.000
2:101286168:A:TF291L1.000
2:101286170:A:GF291L1.000
2:101289029:A:CC269W1.000
2:101289031:A:GC269R1.000
2:101286112:T:AK310I0.999
2:101286114:A:CC309W0.999
2:101286115:C:AC309F0.999
2:101286115:C:TC309Y0.999
2:101286116:A:GC309R0.999
2:101286121:G:TP307Q0.999
2:101286122:G:AP307S0.999
2:101286123:A:CC306W0.999
2:101286124:C:GC306S0.999
2:101286124:C:TC306Y0.999
2:101286125:A:CC306G0.999
2:101286125:A:TC306S0.999
2:101286142:A:GL300P0.999
2:101286157:C:AC295F0.999
2:101286157:C:GC295S0.999

dbSNP variants (sampled 300 via entrez): RS1000017454 (2:101287388 T>C), RS1000051823 (2:101303370 A>C), RS1000112217 (2:101286001 TTGTTTCTAGTCAATAATGAAACTGAA>T), RS1000146863 (2:101294170 G>A), RS1000215349 (2:101296851 T>A), RS1000272204 (2:101302870 C>G,T), RS1000302319 (2:101272201 G>A,T), RS1000388412 (2:101291059 T>A), RS1000413495 (2:101308865 C>T), RS1000414478 (2:101310504 A>G), RS1000489782 (2:101310263 C>T), RS1000669921 (2:101298586 A>C,T), RS1000722437 (2:101304721 T>C), RS1000725474 (2:101277491 C>A,T), RS1000818170 (2:101297165 C>A,T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST000745_14Pancreatic cancer4.000000e-06
GCST009391_1106Metabolite levels9.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:00104473-hydroxyanthranilic acid measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6195769 (PROTEIN-PROTEIN INTERACTION)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Cyclosporinedecreases expression, increases expression2
aristolochic acid Iincreases expression1
GSK-J4increases expression1
ethylbenzeneincreases expression1
triphenyl phosphateaffects expression1
arseniteincreases reaction, affects binding1
methylparabenincreases expression1
ochratoxin Adecreases expression1
2-xyleneincreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
corosolic acidincreases expression1
abrinedecreases expression1
Resveratrolaffects cotreatment, increases expression1
Temozolomideincreases expression1
Sunitinibincreases expression1
Gemcitabineincreases expression1
Arsenicincreases expression1
Benzeneincreases expression1
Benzo(a)pyreneaffects methylation1
Calcitriolincreases expression1
Golddecreases expression1
Methylene Chlorideincreases expression1
Phenobarbitalaffects expression1
Plant Extractsincreases expression, affects cotreatment1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Tolueneincreases expression1
Trichloroethyleneincreases expression1

ChEMBL screening assays

11 unique, capped per target: 11 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL6076617BindingSiHyT-mediated degrader activity at RNF149/EGFR mutant in human HCC827 cels assessed as induction of EGFR degradation at 0.1 uM cells incubated in serum-free media for 8 hrs followed by incubation with compound for 24 hrs by western blot anDevelopment of Novel Silicon-Based Hydrophobic Tags (SiHyT) for Targeted Proteins Degradation. — J Med Chem

Cellosaurus cell lines

2 cell lines: 1 cancer cell line, 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B2DXAbcam HeLa RNF149 KOCancer cell lineFemale
CVCL_D9QSUbigene HEK293 RNF149 KOTransformed cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.