MEX3B

gene
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Also known as DKFZp434J0617RNF195

Summary

MEX3B (mex-3 RNA binding family member B, HGNC:25297) is a protein-coding gene on chromosome 15q25.2, encoding RNA-binding protein MEX3B (Q6ZN04). RNA-binding protein.

This gene encodes an RNA-binding phosphoprotein that is part of the MEX3 (muscle excess 3) family of translational regulators. The encoded protein contains N-terminal nuclear export and nuclear localization signals and is exported from the cytoplasm to the nucleus. The protein binds to RNA via two KH domains and also colocalizes with MEX3A, Dcp1A decapping factor and Argonaute proteins within P (processing) bodies.

Source: NCBI Gene 84206 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 96 total
  • MANE Select transcript: NM_032246

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25297
Approved symbolMEX3B
Namemex-3 RNA binding family member B
Location15q25.2
Locus typegene with protein product
StatusApproved
AliasesDKFZp434J0617, RNF195
Ensembl geneENSG00000183496
Ensembl biotypeprotein_coding
OMIM611008
Entrez84206

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000329713, ENST00000558133

RefSeq mRNA: 1 — MANE Select: NM_032246 NM_032246

CCDS: CCDS10319

Canonical transcript exons

ENST00000329713 — 2 exons

ExonStartEnd
ENSE000013169838204177882044613
ENSE000014180468204545082046018

Expression profiles

Bgee: expression breadth ubiquitous, 161 present calls, max score 97.98.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.3084 / max 287.8475, expressed in 1550 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1512426.83171352
1512350.5080247
1512440.217487
1512430.196378
1512390.171247
1512360.115145
1512400.088231
1512410.075037
1512370.055617
1512380.049917

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
spermCL:000001997.98gold quality
ganglionic eminenceUBERON:000402393.63gold quality
right testisUBERON:000453492.59gold quality
left testisUBERON:000453392.58gold quality
cortical plateUBERON:000534392.38gold quality
testisUBERON:000047389.76gold quality
ventricular zoneUBERON:000305384.79gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.76gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.81gold quality
stromal cell of endometriumCL:000225576.93gold quality
endocervixUBERON:000045876.87gold quality
adult organismUBERON:000702374.14gold quality
ectocervixUBERON:001224971.89gold quality
left ovaryUBERON:000211971.58gold quality
body of uterusUBERON:000985371.53gold quality
uterine cervixUBERON:000000271.09gold quality
muscle layer of sigmoid colonUBERON:003580569.88gold quality
right ovaryUBERON:000211869.86gold quality
right hemisphere of cerebellumUBERON:001489069.65gold quality
cerebellar hemisphereUBERON:000224569.21gold quality
cerebellar cortexUBERON:000212969.11gold quality
prefrontal cortexUBERON:000045168.62gold quality
gall bladderUBERON:000211068.62gold quality
apex of heartUBERON:000209868.60gold quality
ovaryUBERON:000099268.36gold quality
cerebellumUBERON:000203767.75gold quality
endometriumUBERON:000129567.40gold quality
uterusUBERON:000099567.22gold quality
heart left ventricleUBERON:000208467.03gold quality
right coronary arteryUBERON:000162566.96gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no2.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

184 targeting MEX3B, 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-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-3163100.0077.238605
HSA-MIR-1277-5P100.0073.955056
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-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-29A-3P100.0073.111835
HSA-MIR-29B-3P100.0073.181833
HSA-MIR-29C-3P100.0073.151833
HSA-MIR-4262100.0073.263931
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-5692A100.0074.406850
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-126-5P100.0072.713180
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-366299.9973.825684

Literature-anchored findings (GeneRIF, showing 6)

  • 14-3-3 exerts combined effects on hMex-3B and acts as a major regulator of the sorting between distinct classes of RNA granules (PMID:18779327)
  • Mex3b role in the Runx3 degradation in gastric cancer. (PMID:29417297)
  • MEX3B mediates resistance to cancer immunotherapy by binding to the 3’ UTR of HLA-A to destabilize the HLA-A mRNA and thus downregulate HLA-A expression on the surface of tumor cells. (PMID:29496759)
  • he suppressed IL-37 secretion caused by a type 2 milieu can enhance Mex3B-mediated TLR3 activation and subsequent TSLP production in nasal epithelial cells and therefore promotes eosinophilic inflammation in patients with eosinophilic chronic rhinosinusitis with nasal polyps. (PMID:31330219)
  • MEX3B inhibits collagen production in eosinophilic nasal polyps by downregulating epithelial cell TGFBR3 mRNA stability. (PMID:36976645)
  • Molecular mechanism of specific HLA-A mRNA recognition by the RNA-binding-protein hMEX3B to promote tumor immune escape. (PMID:38326406)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriomex3bENSDARG00000058369
mus_musculusMex3bENSMUSG00000057706
rattus_norvegicusMex3bENSRNOG00000025142

Paralogs (3): MEX3C (ENSG00000176624), MEX3D (ENSG00000181588), MEX3A (ENSG00000254726)

Protein

Protein identifiers

RNA-binding protein MEX3BQ6ZN04 (reviewed: Q6ZN04)

Alternative names: RING finger and KH domain-containing protein 3, RING finger protein 195

All UniProt accessions (1): Q6ZN04

UniProt curated annotations — full annotation on UniProt →

Function. RNA-binding protein. May be involved in post-transcriptional regulatory mechanisms.

Subcellular location. Nucleus. Cytoplasm. P-body. Cytoplasmic granule.

Tissue specificity. Highest levels found in fetal brain and testis. Detected in the adult intestinal epithelium, specifically in goblet cell at protein level.

Post-translational modifications. Phosphorylation at Ser-462 creates a docking site for 14-3-3, which stabilizes the protein and modulates its ability to bind RNA.

Domain organisation. Binds RNA through its KH domains.

Isoforms (2)

UniProt IDNamesCanonical?
Q6ZN04-11yes
Q6ZN04-32

RefSeq proteins (1): NP_115622* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001841Znf_RINGDomain
IPR004087KH_domDomain
IPR004088KH_dom_type_1Domain
IPR013083Znf_RING/FYVE/PHDHomologous_superfamily
IPR036612KH_dom_type_1_sfHomologous_superfamily
IPR047226KH-I_MEX3_rpt2Domain
IPR047227MEX3Family
IPR047228KH-I_MEX3_rpt1Domain

Pfam: PF00013, PF13920

UniProt features (18 total): region of interest 4, modified residue 3, domain 2, splice variant 2, sequence conflict 2, compositionally biased region 2, chain 1, mutagenesis site 1, zinc finger region 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
9JNMX-RAY DIFFRACTION2.2
9JNLX-RAY DIFFRACTION2.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6ZN04-F162.960.33

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): 4, 288, 462

Mutagenesis-validated functional residues (1):

PositionPhenotype
177prevents rna binding.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 190 (showing top): AHRARNT_01, TGGTGCT_MIR29A_MIR29B_MIR29C, PAX4_01, TTTGTAG_MIR520D, TATTATA_MIR374, AP2_Q3, GGGTGGRR_PAX4_03, FREAC3_01, TGCTGAY_UNKNOWN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, ATTCTTT_MIR186, ACATATC_MIR190, GFI1_01, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, LEF1_Q6

GO Biological Process (2): protein phosphorylation (GO:0006468), protein autophosphorylation (GO:0046777)

GO Molecular Function (6): RNA binding (GO:0003723), calcium ion binding (GO:0005509), zinc ion binding (GO:0008270), nucleic acid binding (GO:0003676), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (5): P-body (GO:0000932), nucleoplasm (GO:0005654), cytosol (GO:0005829), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
binding2
phosphorylation1
protein modification process1
protein phosphorylation1
nucleic acid binding1
metal ion binding1
transition metal ion binding1
cation binding1
cytoplasmic ribonucleoprotein granule1
nuclear lumen1
cytoplasm1
intracellular membrane-bounded organelle1
intracellular anatomical structure1

Protein interactions and networks

STRING

1250 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
MEX3BDZIP3Q86Y13848
MEX3BDCP1AQ9NPI6808
MEX3BAGO1Q9UL18775
MEX3BSNUPNO95149774
MEX3BHNRNPKP61978714
MEX3BATXN1P54253694
MEX3BRUNX3Q13761554
MEX3BAGO2Q9UKV8487
MEX3BMEX3AA1L020435
MEX3BSUZ12Q15022431
MEX3BDAZ1Q9NQZ3430
MEX3BPTBP2Q9UKA9414
MEX3BDACT3Q96B18410
MEX3BTTC9BQ8N6N2404
MEX3BIRGQQ8WZA9400

IntAct

23 interactions, top by confidence:

ABTypeScore
ENPP6SCAMP1psi-mi:“MI:0914”(association)0.640
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
MEX3BUBE2D3psi-mi:“MI:0915”(physical association)0.550
PIP4K2AAP3B1psi-mi:“MI:0914”(association)0.530
EPB41L1AP3B1psi-mi:“MI:0914”(association)0.530
YWHABPLEKHG3psi-mi:“MI:0914”(association)0.480
USP7MEX3Bpsi-mi:“MI:0407”(direct interaction)0.440
MEX3BYWHAEpsi-mi:“MI:0915”(physical association)0.400
SFNMEX3Bpsi-mi:“MI:0915”(physical association)0.400
ATP13A2MEX3Bpsi-mi:“MI:0915”(physical association)0.370
MEX3BNUDT3psi-mi:“MI:0915”(physical association)0.370
SNUPNMEX3Bpsi-mi:“MI:0915”(physical association)0.370
YWHAHFOXO6psi-mi:“MI:0914”(association)0.350
CREB3L2PLEKHG3psi-mi:“MI:0914”(association)0.350
PIP4K2ASAP18psi-mi:“MI:0914”(association)0.350
RPS11ESYT2psi-mi:“MI:2364”(proximity)0.270
ZNF800MED19psi-mi:“MI:2364”(proximity)0.270
RAP1GAPMEX3Bpsi-mi:“MI:0915”(physical association)0.000
UBE2D3MEX3Bpsi-mi:“MI:0915”(physical association)0.000

BioGRID (239): MEX3B (Affinity Capture-MS), MEX3B (Affinity Capture-MS), MEX3B (Affinity Capture-MS), SUZ12 (Affinity Capture-Western), HOTAIR (Affinity Capture-RNA), MEX3B (Affinity Capture-Western), MEX3B (Affinity Capture-RNA), MEX3B (Protein-RNA), HLA-A (Affinity Capture-RNA), MEX3B (Two-hybrid), MEX3B (Two-hybrid), AGO1 (Proximity Label-MS), AGO2 (Proximity Label-MS), AGO3 (Proximity Label-MS), AGO4 (Proximity Label-MS)

ESM2 similar proteins: A1L020, A1L3F4, A7X8B3, A7X8B5, A7X8B7, A7X8B9, A7X8C2, A7X8C4, A7X8C7, A7X8C9, A7X8D2, A7X8D4, A7XW25, O97775, O97776, O97952, O97960, P06401, P10275, P84550, P84551, P89463, Q01JD1, Q05A36, Q0VDT2, Q3UE17, Q5PQQ7, Q5U5Q3, Q69Z36, Q6QT55, Q6ZK57, Q6ZN04, Q71FD5, Q7RTV3, Q7TSJ6, Q7XQN1, Q7XT42, Q84SL2, Q86XN8, Q8BQ89

Diamond homologs: A1E2V0, A1L020, A1L3F4, A5D8Q0, A9JTP3, A9ULZ2, D3ZDI6, E3SCZ8, O08863, O10296, O10324, O14064, O15392, O62640, O70201, O88738, P40629, P41435, P41436, P41437, P41454, P47732, P98170, Q05AK5, Q0WPJ7, Q13489, Q13490, Q28ER3, Q28H51, Q50L39, Q557E7, Q5BKL8, Q5R881, Q5RAH9, Q60989, Q62210, Q69Z36, Q6I6F4, Q6J1J1, Q6NTT6

SIGNOR signaling

3 interactions.

AEffectBMechanism
Ub:E2“up-regulates activity”MEX3Bubiquitination
MEX3B“down-regulates quantity by destabilization”SNUPNpolyubiquitination
HOTAIR“up-regulates activity”MEX3Bbinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 23 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-host interactions539.9×4e-06
SARS-CoV-1 Infection532.4×1e-05
SARS-CoV-2-host interactions527.0×2e-05
SARS-CoV-2 Infection518.3×9e-05
SARS-CoV Infections615.1×3e-05
Viral Infection Pathways79.8×7e-05
Membrane Trafficking58.4×2e-03
Vesicle-mediated transport57.9×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance89
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

224 predictions. Top by Δscore:

VariantEffectΔscore
15:82044622:CAGGG:Cacceptor_gain0.9900
15:82044640:G:GCacceptor_gain0.9900
15:82045445:CCTA:Cdonor_loss0.9900
15:82045447:TA:Tdonor_loss0.9900
15:82044626:G:Cacceptor_gain0.9800
15:82044626:G:GCacceptor_gain0.9800
15:82044611:AACC:Aacceptor_loss0.9700
15:82044612:ACCTA:Aacceptor_loss0.9700
15:82044613:CCTA:Cacceptor_loss0.9700
15:82044614:CTA:Cacceptor_loss0.9700
15:82044615:T:Gacceptor_loss0.9700
15:82044630:G:Tacceptor_gain0.9700
15:82045448:A:ACdonor_gain0.9700
15:82045449:C:CCdonor_gain0.9700
15:82044629:C:CTacceptor_gain0.9600
15:82044610:CAAC:Cacceptor_gain0.9500
15:82044623:A:Tacceptor_gain0.9500
15:82045449:CCTTG:Cdonor_gain0.9500
15:82044640:G:Cacceptor_gain0.9300
15:82044622:C:Tacceptor_gain0.9100
15:82044609:ACAAC:Aacceptor_gain0.9000
15:82044610:CAACC:Cacceptor_gain0.9000
15:82044614:C:CCacceptor_gain0.9000
15:82045448:AC:Adonor_gain0.9000
15:82045449:CC:Cdonor_gain0.9000
15:82044612:AC:Aacceptor_gain0.8900
15:82044613:CC:Cacceptor_gain0.8900
15:82044755:C:CAdonor_gain0.8900
15:82044897:T:Cdonor_gain0.8900
15:82045501:A:ACdonor_gain0.8900

AlphaMissense

3678 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
15:82043170:A:CI567S1.000
15:82043170:A:GI567T1.000
15:82043170:A:TI567N1.000
15:82043176:A:CI565S1.000
15:82043176:A:GI565T1.000
15:82043176:A:TI565N1.000
15:82043179:G:TA564D1.000
15:82043199:G:CC557W1.000
15:82043200:C:AC557F1.000
15:82043200:C:GC557S1.000
15:82043200:C:TC557Y1.000
15:82043201:A:GC557R1.000
15:82043201:A:TC557S1.000
15:82043208:G:CC554W1.000
15:82043209:C:AC554F1.000
15:82043209:C:GC554S1.000
15:82043209:C:TC554Y1.000
15:82043210:A:CC554G1.000
15:82043210:A:GC554R1.000
15:82043210:A:TC554S1.000
15:82043242:G:TA543D1.000
15:82043243:C:GA543P1.000
15:82043244:G:CC542W1.000
15:82043245:C:AC542F1.000
15:82043245:C:GC542S1.000
15:82043245:C:TC542Y1.000
15:82043246:A:GC542R1.000
15:82043246:A:TC542S1.000
15:82043253:G:CC539W1.000
15:82043254:C:AC539F1.000

dbSNP variants (sampled 300 via entrez): RS1000524415 (15:82041723 T>G), RS1000819819 (15:82046297 GGA>G), RS1001077648 (15:82044880 G>A,C), RS1001238891 (15:82045121 C>G,T), RS1002087386 (15:82047021 G>A,T), RS1002148219 (15:82042698 C>G,T), RS1002439659 (15:82046877 C>G), RS1002862019 (15:82045197 G>A), RS1002867013 (15:82045631 T>C), RS1003091185 (15:82042392 A>G), RS1003582278 (15:82046024 G>A,T), RS1003610088 (15:82046203 G>A,C), RS1004439831 (15:82047520 T>C,G), RS1004886824 (15:82041310 T>A), RS1004958830 (15:82041563 G>A)

Disease associations

OMIM: gene MIM:611008 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

StudyTraitp-value
GCST000298_9Body mass index7.000000e-06
GCST002401_7Post-traumatic stress disorder4.000000e-06
GCST005352_3Paclitaxel disposition in epithelial ovarian cancer6.000000e-06
GCST006291_62Spherical equivalent or myopia (age of diagnosis)2.000000e-10
GCST006976_60Macular thickness4.000000e-10
GCST007277_21Tourette syndrome7.000000e-06
GCST008839_116Height2.000000e-13
GCST010002_102Refractive error3.000000e-27

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0004847age at onset

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, affects expression, affects cotreatment6
trichostatin Adecreases expression, affects cotreatment3
sodium arsenitedecreases expression, increases expression3
Estradiolaffects expression, affects cotreatment, increases expression, decreases expression3
methylmercuric chlorideincreases expression, affects cotreatment2
entinostatdecreases expression, affects cotreatment2
Formaldehydeincreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Tretinoinincreases expression2
bisphenol Adecreases methylation1
2,5,2’,5’-tetrachlorobiphenylincreases expression1
titanium dioxidedecreases expression1
kojic acidincreases expression1
dimethylselenidedecreases expression, increases expression, increases oxidation1
tobacco tardecreases expression1
manganese chlorideincreases abundance, increases expression1
homosalateaffects cotreatment, decreases expression1
azoxystrobindecreases expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression, increases expression1
ICG 001affects expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression, increases expression1
licochalcone Bincreases expression1
picoxystrobindecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomideincreases expression1
Leflunomidedecreases expression1
Acetaminophenincreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

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

CellosaurusNameCategorySex
CVCL_B3AZAbcam HEK293T MEX3B KOTransformed cell lineFemale

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): post-traumatic stress disorder