PRPF19: Pre-mRNA Processing Factor 19 – A Key Spliceosome Component and DNA Repair Protein
Comprehensive gene card for PRPF19, including genomic annotation, expression, mutations, and disease associations.
Gene Information Card
| Symbol | PRPF19 |
|---|---|
| Full Name | Pre-mRNA Processing Factor 19 |
| Gene Type | Protein coding |
| Chromosomal Location | 11q12.2 |
| NCBI Gene ID | 27339 ncbi.nlm.nih.gov/gene/27339 |
| Ensembl ID | ENSG00000110107 |
| UniProt ID | Q9UMS4 |
| OMIM ID | 608364 |
| HGNC ID | 17896 |
| Aliases | PRP19, PSO4, UBOX4, SNEV |
Description
PRPF19 (Pre-mRNA Processing Factor 19) encodes a member of the U-box protein family that functions as an E3 ubiquitin ligase. It is a core component of the spliceosome, essential for pre-mRNA splicing, and also participates in DNA repair, cell cycle regulation, and the DNA damage response. The protein is involved in the activation of the ATR-dependent DNA damage checkpoint and is required for homologous recombination repair.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Cancer (various types) | PRPF19 mutations or altered expression may disrupt splicing fidelity and DNA repair, contributing to genomic instability and tumorigenesis. | COSMIC database reports somatic mutations in multiple cancer types including breast, lung, and colorectal cancers. |
| Fanconi anemia-like phenotype (rare) | Biallelic PRPF19 variants have been associated with a syndrome featuring bone marrow failure, developmental delay, and increased cancer risk. | ClinVar and OMIM list pathogenic variants in PRPF19 linked to a Fanconi anemia-like disorder. |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Testis | 38.2 | High |
| Lymph node | 25.1 | High |
| Bone marrow | 22.8 | High |
| Brain | 12.5 | Medium |
| Liver | 9.3 | Medium |
| Heart | 7.1 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK 293 | 32.4 | Embryonic kidney cells; high expression |
| HeLa | 28.7 | Cervical carcinoma; high expression |
| K562 | 26.3 | Leukemia cell line; high expression |
| MCF7 | 18.9 | Breast cancer; moderate expression |
| HepG2 | 15.2 | Hepatocellular carcinoma; moderate expression |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.1250A>G (p.Tyr417Cys) | Missense | Rare | Reported in ClinVar as likely pathogenic; may impair spliceosome function. |
| c.1018C>T (p.Arg340Trp) | Missense | Rare | Associated with Fanconi anemia-like phenotype; loss of function. |
| c.1472_1473del (p.Glu491Valfs*2) | Frameshift | Rare | Predicted to cause nonsense-mediated decay; loss of function. |
Mutation functional classification
Loss of Function (LOF)
Frameshift and nonsense variants (e.g., p.Glu491Valfs*2) lead to truncated protein or mRNA decay, reducing PRPF19 activity in splicing and DNA repair.
Gain of Function (GOF)
No well-characterized gain-of-function mutations reported in PRPF19.
Dominant Negative (DN)
Missense variants such as p.Tyr417Cys may act in a dominant-negative manner by disrupting spliceosome assembly while retaining partial interaction.
View complete mutation data：
Gene Ontology (GO)
Pathways
• Spliceosome (KEGG hsa03040)
• mRNA surveillance pathway (KEGG hsa03015)
• Fanconi anemia pathway (KEGG hsa03460)
• Homologous recombination (KEGG hsa03440)
Protein Summary
PRPF19 is a 504-amino acid protein containing a U-box domain that confers E3 ubiquitin ligase activity. It forms a homotetramer and is a core component of the Nineteen Complex (NTC), which is essential for spliceosome activation and catalytic step II of splicing. Additionally, PRPF19 localizes to sites of DNA damage where it promotes ATR signaling and homologous recombination. Its dual role in RNA processing and genome maintenance underscores its importance in cellular homeostasis.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| No Data | ||||
