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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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NCBP2
nuclear cap binding protein subunit 2
Chromosome 3 · 3q29
NCBI Gene: 22916Ensembl: ENSG00000114503.11HGNC: HGNC:7659UniProt: F6WVI0
120PubMed Papers
20Diseases
1Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Hub GeneTransporter
CLINICAL
Clinical Trials
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
RNA bindingnuclear-transcribed mRNA catabolic process, nonsense-mediated decaymRNA export from nucleusregulation of translational initiationHIV infectionneurodegenerative diseasedengue diseaseacrocephalosyndactyly
✦AI Summary

NCBP2 (nuclear cap binding protein subunit 2) is a core component of the cap-binding complex (CBC) that binds co-transcriptionally to the 5' m7G cap of pre-mRNAs [UniProt]. In the CBC, NCBP2 recognizes capped RNAs but requires NCBP1 to stabilize the complex into a high-affinity cap-binding state [UniProt]. The CBC-NCBP2 complex mediates multiple RNA metabolism processes: it promotes mRNA splicing, nonsense-mediated decay (NMD), and nuclear export by recruiting the TREX machinery through ALYREF interaction 1. The complex also regulates microRNA biogenesis and acts as a negative regulator of mRNA deadenylation [UniProt]. In cancer, NCBP2 shows aberrant expression across multiple tumor types, with increased expression in 24 of 32 cancer types examined 2. High NCBP2 expression is associated with worse overall survival, disease-specific survival, and progression-free survival in pancreatic adenocarcinoma and endometrial carcinoma 2. In oral squamous cell carcinoma, NCBP2 depletion reduces cell proliferation, migration, and invasion 3. In head and neck squamous cell carcinoma, NCBP2 expression inversely correlates with immune infiltration and immunotherapy response, with NCBP2 knockdown upregulating CCL4/CCL5 chemokines 4. Additionally, the antisense RNA NCBP2-AS2 regulates ovarian cancer stem cell activity through the MEK/ERK/STAT3 pathway 5, while a mitochondrial microprotein form (NCBP2-AS2) regulates energy metabolism and neurogenesis, with downregulation observed in Alzheimer's disease 6.

Sources cited
1
NCBP2 shows increased expression in 24/32 cancer types and is a risk factor for overall survival, disease-specific survival, and progression-free survival in pancreatic adenocarcinoma and endometrial carcinoma
PMID: 40124611
2
NCBP2 depletion reduces oral squamous cell carcinoma cell proliferation, migration, and invasion; high NCBP2 expression associates with worse survival in HPV-negative OSCC
PMID: 36635327
3
NCBP2 expression inversely correlates with immune infiltration and immunotherapy response in head and neck squamous cell carcinoma; NCBP2 knockdown upregulates CCL4/CCL5 expression
PMID: 37067401
4
CBC-NCBP2 complex recruits mRNA export machinery through ALYREF interaction; the RRM domain of ALYREF makes direct contact with both NCBP1 and NCBP2
PMID: 39282949
5
NCBP2-AS2 microprotein regulates mitochondrial ATPase subunit transport, energy metabolism, and neurogenesis; expression is downregulated in Alzheimer's disease
PMID: 39975220
6
Antisense RNA NCBP2-AS2 regulates ovarian cancer stem cell activity through the MEK/ERK/STAT3 signaling pathway
PMID: 37483091
Disease Associationsⓘ20
HIV infectionOpen Targets
0.59Moderate
neurodegenerative diseaseOpen Targets
0.54Moderate
acrocephalosyndactylyOpen Targets
0.37Weak
dengue diseaseOpen Targets
0.37Weak
ulcerative colitisOpen Targets
0.36Weak
Crohn's diseaseOpen Targets
0.20Weak
rheumatoid arthritisOpen Targets
0.09Suggestive
COVID-19Open Targets
0.09Suggestive
neoplasmOpen Targets
0.09Suggestive
hepatocellular carcinomaOpen Targets
0.09Suggestive
cancerOpen Targets
0.09Suggestive
oral squamous cell carcinomaOpen Targets
0.08Suggestive
posterior cortical atrophyOpen Targets
0.07Suggestive
major depressive disorderOpen Targets
0.07Suggestive
chronic obstructive pulmonary diseaseOpen Targets
0.06Suggestive
attention deficit hyperactivity disorderOpen Targets
0.06Suggestive
obsessive-compulsive disorderOpen Targets
0.06Suggestive
cornea transplantationOpen Targets
0.05Suggestive
pancreatic adenocarcinomaOpen Targets
0.04Suggestive
acute myeloid leukemiaOpen Targets
0.03Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Drug Targets1
OBEFAZIMODPhase III
Cap binding complex modulator
ulcerative colitis
Related Genes
SF3B3Protein interaction100%SNRNP200Protein interaction100%SF3B2Protein interaction100%MFAP1Protein interaction100%SNRPGProtein interaction100%SF3A2Protein interaction100%
Tissue Expression6 tissues
Brain
100%
Heart
79%
Bone Marrow
72%
Ovary
60%
Lung
56%
Liver
53%
Gene Interaction Network
Click a node to explore
NCBP2SF3B3SNRNP200SF3B2MFAP1SNRPGSF3A2
PROTEIN STRUCTURE
Preparing viewer…
PDB1H2V · 2.00 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.66LoF Tolerant
pLIⓘ
0.58Intermediate
Observed/Expected LoF0.37 [0.21–0.66]
RankingsWhere NCBP2 stands among ~20K protein-coding genes
  • #3,929of 20,598
    Most Researched120 · top quartile
  • #4,869of 17,882
    Most Constrained (LOEUF)0.66
Genes detectedNCBP2
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
NCBP2 predicts the prognosis and the immunotherapy response of cancers: a pan-cancer analysis.
PMID: 40124611
PeerJ · 2025
1.00
2
NCBP2-AS2 is a mitochondrial microprotein, regulates energy metabolism and neurogenesis, and is downregulated in Alzheimer's disease.
PMID: 39975220
bioRxiv · 2025
0.90
3
m7G-related genes-NCBP2 and EIF4E3 determine immune contexture in head and neck squamous cell carcinoma by regulating CCL4/CCL5 expression.
PMID: 37067401
Mol Carcinog · 2023
0.80
4
NCBP2 and TFRC are novel prognostic biomarkers in oral squamous cell carcinoma.
PMID: 36635327
Cancer Gene Ther · 2023
0.70
5
NCBP3 positively impacts mRNA biogenesis.
PMID: 32960271
Nucleic Acids Res · 2020
0.60