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26 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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RBM39
RNA binding motif protein 39
Chromosome 20 · 20q11.22
NCBI Gene: 9584Ensembl: ENSG00000131051.25HGNC: HGNC:15923UniProt: A0A384NQ03
282PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub GeneTranscription Factor
RESEARCH IMPACT
Trending
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
RNA bindingprotein-containing complexprotein bindingregulation of mRNA splicing, via spliceosomeneurodegenerative diseaseendometrial cancercolorectal carcinomaAbruptio Placentae
✦AI Summary

RBM39 (RNA binding motif protein 39) is an essential RNA-binding protein that functions primarily as a pre-mRNA splicing factor, promoting exon inclusion through regulation of exon cassette splicing 12. The protein associates with precursor mRNA splicing factors and plays a crucial role in maintaining proper RNA splicing patterns 1. Beyond its splicing function, RBM39 serves as a metabolic regulator, binding arginine to control expression of metabolic genes in hepatocellular carcinoma, creating feedback loops that sustain oncogenic metabolism 3. RBM39 also functions as a transcriptional coactivator, interacting with proteins like JMJD6 to regulate gene expression, including DGAT1 in clear cell renal cell carcinoma 4. Clinically, RBM39 represents a significant therapeutic target across multiple cancers. The protein can be pharmacologically targeted through sulfonamide drugs like indisulam, which promote RBM39 degradation via recruitment to the DCAF15 E3 ubiquitin ligase complex 15. RBM39 dependency is particularly pronounced in acute myeloid leukemia and B-cell acute lymphoblastic leukemia, where its targeting shows promising anti-tumor activity 26. Additionally, RBM39 degradation can enhance anti-tumor immunity by generating splicing-derived neoantigens 7.

Sources cited
1
RBM39 functions as pre-mRNA splicing factor and can be targeted by sulfonamide drugs
PMID: 28302793
2
RBM39 is essential for RNA splicing and AML survival
PMID: 30799057
3
RBM39 binds arginine to control metabolic gene expression in hepatocellular carcinoma
PMID: 37804830
4
RBM39 interacts with JMJD6 to regulate DGAT1 expression in renal cell carcinoma
PMID: 35764091
5
Indisulam promotes RBM39 degradation via DCAF15 E3 ligase recruitment
PMID: 31819272
6
RBM39 targeting shows anti-tumor activity in B-cell acute lymphoblastic leukemia
PMID: 39316649
7
RBM39 modulation can generate neoantigens to enhance anti-tumor immunity
PMID: 34171309
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.40Moderate
endometrial cancerOpen Targets
0.22Weak
colorectal carcinomaOpen Targets
0.17Weak
Abruptio PlacentaeOpen Targets
0.15Weak
skin cancerOpen Targets
0.15Weak
skin neoplasmOpen Targets
0.15Weak
actinic keratosisOpen Targets
0.13Weak
hepatocellular carcinomaOpen Targets
0.10Suggestive
neoplasmOpen Targets
0.09Suggestive
acute lymphoblastic leukemiaOpen Targets
0.09Suggestive
cancerOpen Targets
0.09Suggestive
Miyoshi myopathyOpen Targets
0.08Suggestive
triple-negative breast cancerOpen Targets
0.08Suggestive
non-small cell lung carcinomaOpen Targets
0.08Suggestive
cholangiocarcinomaOpen Targets
0.08Suggestive
neuroblastomaOpen Targets
0.08Suggestive
gastric cancerOpen Targets
0.06Suggestive
colorectal cancerOpen Targets
0.06Suggestive
basal cell carcinomaOpen Targets
0.05Suggestive
acute myeloid leukemiaOpen Targets
0.05Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
SAP18Protein interaction100%DHX9Protein interaction100%U2AF2Protein interaction99%SRRM1Protein interaction98%DDB1Protein interaction98%DDX5Protein interaction97%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
38%
Liver
28%
Lung
27%
Heart
16%
Brain
13%
Gene Interaction Network
Click a node to explore
RBM39SAP18DHX9U2AF2SRRM1DDB1DDX5
PROTEIN STRUCTURE
Preparing viewer…
PDB4YUD · 1.28 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.26Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.15 [0.09–0.26]
RankingsWhere RBM39 stands among ~20K protein-coding genes
  • #1,281of 20,598
    Most Researched282 · top 10%
  • #860of 17,882
    Most Constrained (LOEUF)0.26 · top 5%
Genes detectedRBM39
Sources retrieved26 papers
Response time—
📄 Sources
26▼
1
Arginine reprograms metabolism in liver cancer via RBM39.
PMID: 37804830
Cell · 2023
1.00
2
Pharmacologic modulation of RNA splicing enhances anti-tumor immunity.
PMID: 34171309
Cell · 2021
0.90
3
Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15.
PMID: 28302793
Science · 2017
0.80
4
RBM39 Promotes Base Excision Repair to Facilitate the Progression of HCC by Stabilising OGG1 mRNA.
PMID: 40364450
Cell Prolif · 2025
0.76
5
Targeting the RBM39-MEK5 axis synergizes with bortezomib to inhibit the malignant growth of multiple myeloma.
PMID: 40048740
Blood Adv · 2025
0.72