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25 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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PRPF40A
pre-mRNA processing factor 40A
Chromosome 2 Β· 2q23.3
NCBI Gene: 55660Ensembl: ENSG00000196504.21HGNC: HGNC:16463UniProt: A0A7N4I394
197PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
FUNCTIONAL ROLE
Hub Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
RNA bindingprotein bindingmembranenuclear matrixneurodegenerative diseaseblood coagulation diseasepost term pregnancytype 2 diabetes mellitus
✦AI Summary

PRPF40A is a spliceosomal component that functions primarily as a regulator of pre-mRNA splicing with specialized roles in exon inclusion. In myeloid cells, PRPF40A acts as an activator of cassette exon inclusion, particularly for exons flanked by short, GC-rich introns localized to nuclear speckles 1. PRPF40A is globally required for microexon splicing (exons ≀30 nt) in neuronal cells, where it coregulates microexons with SRRM4 in a size-dependent manner 2. Mechanistically, PRPF40A contains tandem WW domains that recognize proline-rich motifs in spliceosomal proteins SF1 and SF3A1, promoting early spliceosome assembly and bridging 5' and 3' splice site recognition 3. An intramolecular autoinhibitory mechanism within PRPF40A enhances binding selectivity for high-affinity partners. Beyond splicing, PRPF40A knockdown increases myeloid cell death and reduces proliferation 1. Clinically, PRPF40A expression correlates with hypoxia markers in non-small cell lung cancer 4 and associates with overall survival in mantle cell lymphoma 5. PRPF40A is also implicated in pediatric acute myeloid leukemia pathogenesis as a hub gene regulated by miR-133 6.

Sources cited
1
PRPF40A activates cassette exon inclusion of exons in GC-rich regions and is required for myeloid cell survival and differentiation
PMID: 38943321
2
PRPF40A is globally required for microexon splicing in neuronal cells and coregulates microexons with SRRM4
PMID: 39389624
3
PRPF40A tandem WW domains recognize proline-rich motifs in SF1 and SF3A1 to promote spliceosome assembly, regulated by intramolecular autoinhibition
PMID: 38719828
4
PRPF40A is overexpressed in non-small cell lung cancer and correlates with hypoxia markers
PMID: 28258342
5
PRPF40A is a hub gene associated with overall survival in mantle cell lymphoma
PMID: 32219041
6
PRPF40A is a top hub gene in pediatric acute myeloid leukemia and is regulated by miR-133
PMID: 36160019
Disease Associationsβ“˜20
neurodegenerative diseaseOpen Targets
0.53Moderate
blood coagulation diseaseOpen Targets
0.35Weak
post term pregnancyOpen Targets
0.31Weak
type 2 diabetes mellitusOpen Targets
0.30Weak
Graves diseaseOpen Targets
0.24Weak
response to xenobiotic stimulusOpen Targets
0.24Weak
metabolic diseaseOpen Targets
0.23Weak
adolescent idiopathic scoliosisOpen Targets
0.22Weak
Abnormality of refractionOpen Targets
0.21Weak
lower urinary tract calculusOpen Targets
0.21Weak
hypertensionOpen Targets
0.21Weak
glomerulonephritisOpen Targets
0.21Weak
mixed connective tissue diseaseOpen Targets
0.19Weak
bipolar disorderOpen Targets
0.18Weak
dyspepsiaOpen Targets
0.11Weak
stomach diseaseOpen Targets
0.11Weak
iron metabolism diseaseOpen Targets
0.07Suggestive
ovarian neoplasmOpen Targets
0.06Suggestive
hemoglobin D diseaseOpen Targets
0.05Suggestive
Blackfan-Diamond anemiaOpen Targets
0.05Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar β†—
Related Genes
CWC15Shared pathway100%C9orf78Shared pathway100%NCBP2LShared pathway100%SF3A2Protein interaction100%SF3B1Protein interaction100%CDC5LProtein interaction100%
Tissue Expression

No tissue expression data available for this gene.

Gene Interaction Network
Click a node to explore
PRPF40ACWC15C9orf78NCBP2LSF3A2SF3B1CDC5L
PROTEIN STRUCTURE
Preparing viewer…
PDB1UZC Β· NMR
View on RCSB β†—
RankingsWhere PRPF40A stands among ~20K protein-coding genes
  • #2,153of 20,598
    Most Researched197 Β· top quartile
Genes detectedPRPF40A
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
PRPF40A induces inclusion of exons in GC-rich regions important for human myeloid cell differentiation.
PMID: 38943321
Nucleic Acids Res Β· 2024
1.00
2
Conserved role for spliceosomal component PRPF40A in microexon splicing.
PMID: 39389624
RNA Β· 2024
0.90
3
Intramolecular autoinhibition regulates the selectivity of PRPF40A tandem WW domains for proline-rich motifs.
PMID: 38719828
Nat Commun Β· 2024
0.80
4
Identification of key gene modules and hub genes of human mantle cell lymphoma by coexpression network analysis.
PMID: 32219041
PeerJ Β· 2020
0.70
5
Prp40 and early events in splice site definition.
PMID: 26494226
Wiley Interdiscip Rev RNA Β· 2016
0.64