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10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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CPSF3
cleavage and polyadenylation specific factor 3
Chromosome 2 Β· 2p25.1
NCBI Gene: 51692Ensembl: ENSG00000119203.14HGNC: HGNC:2326UniProt: G5E9W3
148PubMed Papers
21Diseases
0Drugs
3Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
positive regulation of G1/S transition of mitotic cell cycleco-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathwayRNA endonuclease activitymRNA cleavage and polyadenylation specificity factor complexneurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizuresneurodegenerative diseaseneurodevelopmental disorder with hypotonia, microcephaly, and seizurescomplex neurodevelopmental disorder
✦AI Summary

CPSF3 is a multifunctional endonuclease and core component of the cleavage and polyadenylation specificity factor (CPSF) complex that regulates 3'-end processing of pre-mRNAs and histone transcripts 1. As an mRNA 3'-end-processing endonuclease, CPSF3 recognizes polyadenylation signals and catalyzes cleavage, enabling poly(A) addition and transcriptional termination 2. It also possesses 5' to 3' exonuclease activity for degrading downstream cleavage products in histone pre-mRNA processing 3. CPSF3 regulates alternative polyadenylation (APA), controlling 3'UTR length and miRNA accessibility to modulate gene expression 45. Additionally, CPSF3 is required for S-phase cell cycle progression 1. Clinically, CPSF3 is significantly overexpressed across multiple cancers including acute myeloid leukemia, Ewing's sarcoma, ovarian cancer, esophageal squamous cell carcinoma, glioblastoma, pancreatic cancer, and bladder cancer, correlating with poor patient prognosis 62437. CPSF3 inhibition via small-molecule inhibitors (JTE-607, benzoxaboroles) induces transcriptional readthrough, reduces histone expression, triggers apoptosis, and suppresses tumor growth in multiple cancer models 68. A homozygous pathogenic variant in CPSF3 causes neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures, underscoring its essential role in normal development.

Sources cited
1
CPSF3 is an mRNA 3'-end-processing endonuclease involved in pre-mRNA and histone 3'-end formation; required for S-phase cell cycle progression
PMID: 30507380
2
CPSF3 inhibition by JTE-607 represents a synthetic lethal target in AML and Ewing's sarcoma; prevents pre-mRNA release and causes R-loop formation
PMID: 31819276
3
CPSF3 is a critical dependency in ovarian cancer; its inhibition lengthens 3'UTRs, reduces intronic polyadenylation, and causes transcriptional readthrough
PMID: 37992178
4
CPSF3 regulates alternative polyadenylation of CNIH2 in esophageal squamous cell carcinoma; overexpression associates with poor prognosis and promotes tumor progression
PMID: 38718887
5
CPSF3 regulation of alternative polyadenylation controls MYC expression in glioblastoma stem cells; CPSF3 inhibition reduces GSC viability
PMID: 38503731
6
CPSF3 inhibition disrupts histone mRNA processing in pancreatic cancer, reduces histone expression, destabilizes chromatin, and arrests cells in S-phase
PMID: 38191171
7
Benzoxaboroles directly inhibit CPSF3 endonuclease activity and block transcriptional termination across multiple cancer cell lines
PMID: 37967558
8
CPSF3 is elevated in bladder cancer and associated with poor overall and disease-free survival; promotes cancer cell proliferation and G1/S transition
PMID: 41071397
Disease Associationsβ“˜21
neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizuresOpen Targets
0.60Moderate
neurodegenerative diseaseOpen Targets
0.53Moderate
neurodevelopmental disorder with hypotonia, microcephaly, and seizuresOpen Targets
0.42Moderate
complex neurodevelopmental disorderOpen Targets
0.37Weak
dengue diseaseOpen Targets
0.37Weak
diabetic ketoacidosisOpen Targets
0.11Weak
hepatocellular carcinomaOpen Targets
0.10Weak
preeclampsiaOpen Targets
0.10Weak
breast cancerOpen Targets
0.09Suggestive
lung adenocarcinomaOpen Targets
0.08Suggestive
obstructive sleep apneaOpen Targets
0.06Suggestive
coronary artery diseaseOpen Targets
0.06Suggestive
colorectal carcinomaOpen Targets
0.06Suggestive
neoplasmOpen Targets
0.05Suggestive
aortic valve stenosisOpen Targets
0.05Suggestive
vascular diseaseOpen Targets
0.04Suggestive
cancerOpen Targets
0.04Suggestive
triple-negative breast cancerOpen Targets
0.03Suggestive
liver cancerOpen Targets
0.02Suggestive
esophageal squamous cell carcinomaOpen Targets
0.02Suggestive
Neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizuresUniProt
Pathogenic Variants3
NM_016207.4(CPSF3):c.761-1G>TLikely pathogenic
HP:0001252; HP:0001776; HP:0000252; HP:0001270; HP:0000592
β˜†β˜†β˜†β˜†2024
NM_016207.4(CPSF3):c.1403G>A (p.Gly468Glu)Pathogenic
Neurodevelopmental disorder with hypotonia, microcephaly, and seizures
β˜†β˜†β˜†β˜†2022β†’ Residue 468
Single allelePathogenic
Neurodevelopmental disorder with microcephaly, hypotonia, nystagmus, and seizures
β˜†β˜†β˜†β˜†
View on ClinVar β†—
Related Genes
SNRPGProtein interaction100%SNRPFProtein interaction100%SNRPBProtein interaction100%SNRPEProtein interaction100%WDR77Protein interaction100%CSTF1Protein interaction99%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
94%
Liver
55%
Lung
54%
Heart
53%
Ovary
43%
Gene Interaction Network
Click a node to explore
CPSF3SNRPGSNRPFSNRPBSNRPEWDR77CSTF1
PROTEIN STRUCTURE
Preparing viewer…
PDB8T1Q Β· 1.70 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.01LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.77 [0.59–1.01]
RankingsWhere CPSF3 stands among ~20K protein-coding genes
  • #3,062of 20,598
    Most Researched148 Β· top quartile
  • #3,956of 5,498
    Most Pathogenic Variants3
  • #9,824of 17,882
    Most Constrained (LOEUF)1.01
Genes detectedCPSF3
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
CPSF3-dependent pre-mRNA processing as a druggable node in AML and Ewing's sarcoma.
PMID: 31819276
Nat Chem Biol Β· 2020
1.00
2
Therapeutic targeting of CPSF3-dependent transcriptional termination in ovarian cancer.
PMID: 37992178
Sci Adv Β· 2023
0.90
3
CPSF3 regulates alternative polyadenylation of CNIH2 to promote esophageal squamous cell carcinoma progression.
PMID: 38718887
Cancer Lett Β· 2024
0.80
4
RBBP6 maintains glioblastoma stem cells through CPSF3-dependent alternative polyadenylation.
PMID: 38503731
Cell Discov Β· 2024
0.70
5
CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing.
PMID: 38191171
RNA Β· 2024
0.60