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25 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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PRPF3
pre-mRNA processing factor 3
Chromosome 1 · 1q21.2
NCBI Gene: 9129Ensembl: ENSG00000117360.14HGNC: HGNC:17348UniProt: O43395
198PubMed Papers
21Diseases
0Drugs
12Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub Gene
RESEARCH IMPACT
Trending
CLINICAL
OMIM Disease Gene
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
RNA bindingnucleusnucleoplasmCajal bodyretinitis pigmentosaRetinal dystrophyautosomal dominant retinitis pigmentosaeye disease
✦AI Summary

PRPF3 (pre-mRNA processing factor 3) is an RNA-binding protein that functions as a core component of the U4/U6•U5 tri-snRNP complex, essential for spliceosome assembly and pre-mRNA splicing 1. The protein facilitates spliceosomal complex assembly and catalytic activity through its role in the precatalytic B complex 2. SUMOylation of PRPF3 is required for proper U4/U6•U5 tri-snRNP formation and recruitment to active spliceosomes 1. PRPF3 mutations cause autosomal dominant retinitis pigmentosa (RP), a hereditary form of blindness 3. Pathogenic variants in PRPF3 cluster within the U4/U6 duplex three-way junction region, which normally binds multiple splicing factors including PRPF3 itself, disrupting snRNP biogenesis 2. Variants in RNU4-2 and RNU6 genes that interact with PRPF3 account for up to 1.2% of undiagnosed RP cases 2. Beyond inherited retinal disease, PRPF3 has emerged as a novel oncogene in hepatocellular carcinoma (HCC). Elevated PRPF3 expression promotes HCC cell proliferation and migration, associates with poorer overall and disease-free survival, and correlates with immune infiltration 45. PRPF3 upregulation is transcriptionally regulated by ZNF93 in HCC 5. These findings suggest PRPF3 has dual roles in disease: essential for normal splicing function but pathogenic when dysregulated.

Sources cited
1
PRPF3 is a component of the U4/U6 di-snRNP; SUMOylation of PRPF3 is required for U4/U6•U5 tri-snRNP formation and recruitment to active spliceosomes
PMID: 29741121
2
PRPF3 binds to the U4/U6 duplex three-way junction region; variants in U4/U6 snRNAs affect snRNP biogenesis and cause retinitis pigmentosa; such variants account for up to 1.2% of undiagnosed RP cases
PMID: 39830270
3
PRPF3 mutations cause autosomal dominant retinitis pigmentosa; mutations in general pre-mRNA splicing factors such as PRPF3 predominantly cause autosomal dominant RP
PMID: 23647439
4
PRPF3 is upregulated and amplified in hepatocellular carcinoma; high PRPF3 expression associates with poorer overall survival and disease-free survival; PRPF3 correlates with immune infiltration including CD4+ T, CD8+ T cells, macrophages, neutrophils, and dendritic cells
PMID: 31926109
5
PRPF3 promotes HCC cell proliferation and migration; ZNF93 acts as a transcription factor regulating PRPF3 by binding to its promoter; PRPF3 is identified as a novel oncogene in HCC
PMID: 39501301
Disease Associationsⓘ21
retinitis pigmentosaOpen Targets
0.76Strong
Retinal dystrophyOpen Targets
0.50Moderate
autosomal dominant retinitis pigmentosaOpen Targets
0.41Moderate
eye diseaseOpen Targets
0.37Weak
neurodegenerative diseaseOpen Targets
0.35Weak
smoking initiationOpen Targets
0.28Weak
HeadacheOpen Targets
0.25Weak
Abnormality of the skeletal systemOpen Targets
0.20Weak
headache disorderOpen Targets
0.20Weak
Hip painOpen Targets
0.19Weak
genetic disorderOpen Targets
0.19Weak
osteoarthritisOpen Targets
0.18Weak
skin agingOpen Targets
0.16Weak
ulcerative colitisOpen Targets
0.15Weak
functional lateralityOpen Targets
0.15Weak
Chronic painOpen Targets
0.15Weak
Abdominal Aortic AneurysmOpen Targets
0.14Weak
hepatocellular carcinomaOpen Targets
0.09Suggestive
age-related macular degenerationOpen Targets
0.08Suggestive
Stargardt diseaseOpen Targets
0.08Suggestive
Retinitis pigmentosa 18UniProt
Pathogenic Variants12
NM_004698.4(PRPF3):c.1481C>T (p.Thr494Met)Pathogenic
Retinitis pigmentosa 18|not provided|Retinitis pigmentosa|Retinal dystrophy
★★☆☆2026→ Residue 494
NM_004698.4(PRPF3):c.1477C>T (p.Pro493Ser)Pathogenic
Retinitis pigmentosa 18|not provided|Retinal dystrophy
★★☆☆2024→ Residue 493
NM_004698.4(PRPF3):c.1496A>C (p.His499Pro)Pathogenic
Retinitis pigmentosa|not provided
★★☆☆2024→ Residue 499
NM_004698.4(PRPF3):c.1345C>G (p.Arg449Gly)Pathogenic
Retinal dystrophy|not provided
★★☆☆2022→ Residue 449
NM_004698.4(PRPF3):c.591dup (p.Asp198Ter)Pathogenic
not provided
★☆☆☆2024→ Residue 198
NM_004698.4(PRPF3):c.1426+1G>APathogenic
not provided
★☆☆☆2024
NM_004698.4(PRPF3):c.1427-2A>CLikely pathogenic
not provided
★☆☆☆2023
NM_004698.4(PRPF3):c.1283-1G>ALikely pathogenic
not provided
★☆☆☆2023
NM_004698.4(PRPF3):c.1504G>C (p.Ala502Pro)Likely pathogenic
Retinitis pigmentosa 18
★☆☆☆2020→ Residue 502
NM_004698.4(PRPF3):c.1285G>T (p.Asp429Tyr)Pathogenic
Retinitis pigmentosa 18
★☆☆☆2019→ Residue 429
NM_004698.4(PRPF3):c.1532A>C (p.His511Pro)Likely pathogenic
Retinal dystrophy
★☆☆☆2017→ Residue 511
NM_004698.4(PRPF3):c.1466C>A (p.Ala489Asp)Pathogenic
Retinitis pigmentosa 18
☆☆☆☆2008→ Residue 489
View on ClinVar ↗
Related Genes
DHX8Protein interaction100%SNRNP70Protein interaction100%SNRPD3Protein interaction100%PRPF18Protein interaction100%SNRNP200Protein interaction100%SF3B5Protein interaction100%
Tissue Expression6 tissues
Bone Marrow
100%
Ovary
64%
Liver
50%
Lung
45%
Brain
29%
Heart
28%
Gene Interaction Network
Click a node to explore
PRPF3DHX8SNRNP70SNRPD3PRPF18SNRNP200SF3B5
PROTEIN STRUCTURE
Preparing viewer…
PDB7N2R · 2.28 Å · X-ray
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.09Highly Constrained
pLIⓘ
1.00Intolerant
Observed/Expected LoF0.03 [0.01–0.09]
RankingsWhere PRPF3 stands among ~20K protein-coding genes
  • #2,144of 20,598
    Most Researched198 · top quartile
  • #2,652of 5,498
    Most Pathogenic Variants12
  • #34of 17,882
    Most Constrained (LOEUF)0.09 · top 1%
Genes detectedPRPF3
Sources retrieved25 papers
Response time—
📄 Sources
25▼
1
PMID: 20301590
1.00
2
Integrative analysis based on ATAC-seq and RNA-seq reveals a novel oncogene PRPF3 in hepatocellular carcinoma.
PMID: 39501301
Clin Epigenetics · 2024
0.90
3
Optimized Prime Editing of Human Induced Pluripotent Stem Cells to Efficiently Generate Isogenic Models of Mendelian Diseases.
PMID: 39795970
Int J Mol Sci · 2024
0.84
4
In PD-1+ human colon cancer cells NIVOLUMAB promotes survival and could protect tumor cells from conventional therapies.
PMID: 35246475
J Immunother Cancer · 2022
0.80
5
De novo and inherited dominant variants in U4 and U6 snRNAs cause retinitis pigmentosa.
PMID: 39830270
medRxiv · 2025
0.70