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9 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PRPF39
pre-mRNA processing factor 39
Chromosome 14 · 14q21.2
NCBI Gene: 55015Ensembl: ENSG00000185246.19HGNC: HGNC:20314UniProt: Q86UA1
45PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingmRNA 5'-splice site recognitionpre-mRNA 5'-splice site bindingU1 snRNPneurodegenerative diseaseinborn disorder of amino acid metabolismhemoglobin D diseasehead and neck squamous cell carcinoma
✦AI Summary

PRPF39 is a pre-mRNA splicing factor that functions as a homodimer to recruit U1 snRNP to weak 5' splice sites 1. Structurally, human PRPF39 forms a homodimer that interacts with the U1C CTD, functionally substituting for the yeast Prp39/Prp42 heterodimer despite increased splicing complexity in metazoans 23. The protein preferentially binds GC-rich RNA sequences and works alongside auxiliary factors including TIA1 and LUC7L isoforms to facilitate alternative splicing 1. Clinically, PRPF39 shows multiple disease relevance connections. PRPF39 expression variants affect cellular sensitivity to cisplatin chemotherapy; knockdown increases cisplatin resistance through altered expression of downstream signaling genes like MAP3K4 and TFPD2 4. Conversely, elevated circ-G004213 promotes cisplatin sensitivity in liver cancer via the miR-513b-5p/PRPF39 regulatory axis 5. Additionally, PRPF39 is overexpressed in certain cancers and serves as a DCAF15-dependent substrate for the anticancer drug E7070, suggesting therapeutic potential through targeted protein degradation 6. PRPF39 expression is regulated by NMD-inducing alternative splicing, indicating adaptive roles in cell-type-specific splicing efficiency 3.

Sources cited
1
PRPF39 is an alternative splicing factor that recruits U1 snRNP to weak 5' splice sites and preferentially binds GC-rich RNA
PMID: 36316087
2
Human PRPF39 homodimer interacts with U1C-CTD, mirroring yeast Prp42/Prp39 in U1 snRNP structure
PMID: 29051543
3
PRPF39 forms a functional homodimer that substitutes for yeast heterodimer; expression is controlled by NMD-inducing alternative splicing
PMID: 30949712
4
PRPF39 knockdown increases cisplatin resistance and affects expression of downstream genes including MAP3K4 and TFPD2
PMID: 22773733
5
PRPF39 is overexpressed in certain cancers and is a DCAF15-dependent substrate for E7070-mediated degradation
PMID: 31626998
6
circ-G004213 promotes cisplatin sensitivity in liver cancer via the miR-513b-5p/PRPF39 regulatory axis
PMID: 33864660
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.53Moderate
inborn disorder of amino acid metabolismOpen Targets
0.28Weak
hemoglobin D diseaseOpen Targets
0.05Suggestive
head and neck squamous cell carcinomaOpen Targets
0.05Suggestive
hereditary persistence of fetal hemoglobin-sickle cell disease syndromeOpen Targets
0.05Suggestive
Hereditary persistence of fetal hemoglobin - beta-thalassemiaOpen Targets
0.05Suggestive
hemolytic anemia due to glutathione reductase deficiencyOpen Targets
0.05Suggestive
galactokinase deficiencyOpen Targets
0.04Suggestive
Autosomal dominant methemoglobinemiaOpen Targets
0.04Suggestive
dominant beta-thalassemiaOpen Targets
0.04Suggestive
Hemoglobin E - beta-thalassemiaOpen Targets
0.04Suggestive
hemoglobin E-beta-thalassemia syndromeOpen Targets
0.04Suggestive
hemoglobin E diseaseOpen Targets
0.04Suggestive
delta-beta-thalassemiaOpen Targets
0.04Suggestive
Alpha-thalassemia - myelodysplastic syndromeOpen Targets
0.04Suggestive
alpha-thalassemia-myelodysplastic syndromeOpen Targets
0.04Suggestive
Hemoglobin C - beta-thalassemiaOpen Targets
0.04Suggestive
hemoglobin C-beta-thalassemia syndromeOpen Targets
0.04Suggestive
primary familial polycythemia due to EPO receptor mutationOpen Targets
0.04Suggestive
Blackfan-Diamond anemiaOpen Targets
0.04Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
DDX46Protein interaction100%SART1Protein interaction100%SNRPGProtein interaction100%SF3A2Protein interaction100%SNRPA1Protein interaction100%SF3B1Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
73%
Lung
45%
Liver
44%
Heart
33%
Brain
22%
Gene Interaction Network
Click a node to explore
PRPF39DDX46SART1SNRPGSF3A2SNRPA1SF3B1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted · UniProt Q86UA1
View on AlphaFold ↗
Constraintⓘ
LOEUFⓘ
0.48Moderately Constrained
pLIⓘ
0.99Intolerant
Observed/Expected LoF0.33 [0.24–0.48]
RankingsWhere PRPF39 stands among ~20K protein-coding genes
  • #9,505of 20,598
    Most Researched45
  • #2,816of 17,882
    Most Constrained (LOEUF)0.48 · top quartile
Genes detectedPRPF39
Sources retrieved9 papers
Response time—
📄 Sources
9▼
1
Human PRPF39 is an alternative splicing factor recruiting U1 snRNP to weak 5' splice sites.
PMID: 36316087
RNA · 2022
1.00
2
CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing.
PMID: 29051543
Nat Commun · 2017
0.89
3
Increased versatility despite reduced molecular complexity: evolution, structure and function of metazoan splicing factor PRPF39.
PMID: 30949712
Nucleic Acids Res · 2019
0.78
4
Functional consequences of PRPF39 on distant genes and cisplatin sensitivity.
PMID: 22773733
Hum Mol Genet · 2012
0.67
5
pSILAC method coupled with two complementary digestion approaches reveals PRPF39 as a new E7070-dependent DCAF15 substrate.
PMID: 31626998
J Proteomics · 2020
0.56