HomeAboutRankingsData Sources
© 2026 GeneE
🧬
GeneE
9 sources retrieved · Most recent: April 2026 · Index updated 15 days ago
ⓘGeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
PRPF40B
pre-mRNA processing factor 40B
Chromosome 12 · 12q13.12
NCBI Gene: 25766Ensembl: ENSG00000110844.14HGNC: HGNC:25031UniProt: A0A8Z5ADK7
25PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingnuclear bodyRNA bindingmRNA splicing, via spliceosomenephronophthisisacute myeloid leukemiacervical squamous cell carcinomaglioma
✦AI Summary

PRPF40B is a splicing regulatory factor that functions as a repressor of alternative exon inclusion, primarily affecting genes with A-rich intronic motifs and weak 5' splice sites 1. As a mammalian ortholog of the yeast U1 snRNP-associated factor Prp40, PRPF40B interacts directly with splicing factors SF1 and U2AF65, and localizes to nuclear speckles where it modulates alternative splice site selection 2. Notably, PRPF40B regulates NTRK2 alternative splicing to promote production of the full-length TRKB receptor isoform, which is critical for neuronal differentiation and synaptic plasticity 3. In hematologic malignancies, PRPF40B mutations are recurrent in myelodysplastic syndromes and acute myeloid leukemia, where reduced PRPF40B expression is associated with leukemogenesis 1 4. Loss of PRPF40B activates hypoxia-responsive gene signatures and iron metabolism pathways in myeloid cells, suggesting a role in repressing pro-leukemic processes 1. Beyond blood disorders, PRPF40B regulates circMAN1A2 to control glioblastoma ferroptosis and temozolomide sensitivity 5. These findings establish PRPF40B as a multifunctional splicing factor with disease relevance across hematologic and neurologic contexts.

Sources cited
1
PRPF40B acts as a repressor of exon inclusion, regulates hundreds of alternative splicing targets with A-rich downstream intronic motifs and weak splice sites, and low expression correlates with leukemogenesis
PMID: 31088860
2
PRPF40B is a mammalian Prp40 ortholog that interacts with SF1 and U2AF65, localizes to nuclear speckles, and modulates alternative splice site selection in the Fas gene
PMID: 25605964
3
PRPF40B regulates NTRK2 alternative splicing to promote TRKB-FL isoform production, essential for neuronal differentiation and synaptic plasticity
PMID: 41360765
4
PRPF40B is identified as a recurrently mutated spliceosomal gene in myelodysplastic syndrome and acute myeloid leukemia
PMID: 23645565
5
PRPF40B regulates circMAN1A2 expression, affecting glioblastoma sensitivity to temozolomide through ferroptosis and NRF2 degradation pathways
PMID: 40583858
Disease Associationsⓘ20
nephronophthisisOpen Targets
0.26Weak
acute myeloid leukemiaOpen Targets
0.19Weak
cervical squamous cell carcinomaOpen Targets
0.19Weak
gliomaOpen Targets
0.19Weak
myelodysplastic syndromeOpen Targets
0.19Weak
acute lymphoblastic leukemiaOpen Targets
0.18Weak
bile duct carcinomaOpen Targets
0.18Weak
breast ductal adenocarcinomaOpen Targets
0.18Weak
gastric intestinal type adenocarcinomaOpen Targets
0.18Weak
head and neck squamous cell carcinomaOpen Targets
0.18Weak
Hepatobiliary NeoplasmOpen Targets
0.18Weak
HER2 Positive Breast CarcinomaOpen Targets
0.18Weak
kidney neoplasmOpen Targets
0.18Weak
lung carcinomaOpen Targets
0.18Weak
melanomaOpen Targets
0.18Weak
prostate adenocarcinomaOpen Targets
0.18Weak
rectal adenocarcinomaOpen Targets
0.18Weak
skin basal cell carcinomaOpen Targets
0.18Weak
squamous cell lung carcinomaOpen Targets
0.18Weak
urinary bladder carcinomaOpen Targets
0.18Weak
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
C9orf78Shared pathway100%CWC15Shared pathway100%SF3B3Protein interaction100%SF3B2Protein interaction100%SART1Protein interaction100%SNRPGProtein interaction100%
Tissue Expression6 tissues
Ovary
100%
Heart
54%
Brain
30%
Liver
27%
Lung
24%
Bone Marrow
6%
Gene Interaction Network
Click a node to explore
PRPF40BC9orf78CWC15SF3B3SF3B2SART1SNRPG
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q6NWY9
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.54Moderately Constrained
pLIⓘ
0.02Tolerant
Observed/Expected LoF0.43 [0.34–0.54]
RankingsWhere PRPF40B stands among ~20K protein-coding genes
  • #13,044of 20,598
    Most Researched25
  • #3,442of 17,882
    Most Constrained (LOEUF)0.54 · top quartile
Genes detectedPRPF40B
Sources retrieved9 papers
Response time—
📄 Sources
9▼
1
Human PRPF40B regulates hundreds of alternative splicing targets and represses a hypoxia expression signature.
PMID: 31088860
RNA · 2019
1.00
2
PRPF40A induces inclusion of exons in GC-rich regions important for human myeloid cell differentiation.
PMID: 38943321
Nucleic Acids Res · 2024
0.89
3
Regulation of NTRK2 alternative splicing by PRPF40B controls neural differentiation and synaptic plasticity.
PMID: 41360765
Cell Death Dis · 2025
0.78
4
The changing mutational landscape of acute myeloid leukemia and myelodysplastic syndrome.
PMID: 23645565
Mol Cancer Res · 2013
0.67
5
Prp40 pre-mRNA processing factor 40 homolog B (PRPF40B) associates with SF1 and U2AF65 and modulates alternative pre-mRNA splicing in vivo.
PMID: 25605964
RNA · 2015
0.56