PRPF3: Pre-mRNA Processing Factor 3
A core component of the U4/U6-U5 tri-snRNP spliceosome complex involved in retinal degeneration
Gene Information Card
| Symbol | PRPF3 |
|---|---|
| Full Name | Pre-mRNA Processing Factor 3 |
| Gene Type | Protein coding |
| Chromosomal Location | 1q21.2 |
| NCBI Gene ID | 9129 ncbi.nlm.nih.gov/gene/9129 |
| Ensembl ID | ENSG00000117360 |
| UniProt ID | O43395 |
| OMIM ID | 607301 |
| HGNC ID | 9326 |
| Aliases | PRP3, HPRP3, RP18, SNRNP90 |
Description
PRPF3 encodes a 90 kDa protein that is a core component of the U4/U6-U5 tri-snRNP complex of the spliceosome. This protein is essential for pre-mRNA splicing, specifically in the assembly and stabilization of the tri-snRNP particle. Mutations in PRPF3 are a known cause of autosomal dominant retinitis pigmentosa (adRP), a progressive retinal degeneration disorder. The protein is ubiquitously expressed but retinal photoreceptors are particularly sensitive to splicing defects.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Retinitis pigmentosa 18 (RP18) | Dominant-negative mutations in PRPF3 disrupt tri-snRNP assembly, leading to splicing defects and photoreceptor cell death | ClinVar, OMIM #601414 |
| Retinitis pigmentosa (general) | PRPF3 mutations cause autosomal dominant RP through haploinsufficiency or dominant-negative effects on spliceosome function | NCBI Gene, PubMed |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 12.5 | Medium |
| Thyroid | 10.2 | Medium |
| Retina | 9.8 | Medium |
| Brain (cerebellum) | 8.1 | Medium |
| Heart | 7.5 | Medium |
| Liver | 6.3 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK 293 | 14.2 | High expression |
| K562 | 11.0 | Medium expression |
| HeLa | 9.5 | Medium expression |
| HepG2 | 7.8 | Medium expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1270C>T (p.Arg424Trp) | Missense | Reported in adRP families | Dominant-negative; disrupts tri-snRNP stability |
| c.1271G>A (p.Arg424Gln) | Missense | Reported in adRP families | Dominant-negative; similar effect to Arg424Trp |
| c.1288G>A (p.Val430Met) | Missense | Rare variant | Uncertain significance; possibly benign |
Mutation functional classification
Loss of Function (LOF)
Not established as primary mechanism; homozygous loss may be lethal.
Gain of Function (GOF)
Not reported.
Dominant Negative (DN)
Primary mechanism for adRP mutations (e.g., Arg424Trp, Arg424Gln); mutant protein interferes with wild-type PRPF3 function in tri-snRNP assembly.
View complete mutation data：
Gene Ontology (GO)
Pathways
• mRNA Splicing - Major Pathway (Reactome: R-HSA-72163)
• U4/U6-U5 tri-snRNP assembly (Reactome: R-HSA-5689877)
• Processing of Capped Intron-Containing Pre-mRNA (Reactome: R-HSA-72203)
Protein Summary
PRPF3 (also known as PRP3, HPRP3) is a 683-amino acid protein with a molecular weight of ~90 kDa. It contains a zinc finger domain and is localized to nuclear speckles. The protein is a stable component of the U4/U6-U5 tri-snRNP complex, where it interacts with PRPF4 and other spliceosomal factors to facilitate the assembly of the active spliceosome. PRPF3 is essential for pre-mRNA splicing, and its dysfunction leads to retinal degeneration due to the high splicing demand in photoreceptor cells.
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