PRPF8
protein-codingpre-mRNA processing factor 8, the group of Spliceosomal C complex|U5 small nuclear ribonucleoprotein|JAMM/MPN+ metallopeptidase family|Spliceosomal Bact complex|Spliceosomal P complex
Gene summary
Pre-mRNA splicing occurs in 2 sequential transesterification steps. The protein encoded by this gene is a component of both U2- and U12-dependent spliceosomes, and found to be essential for the catalytic step II in pre-mRNA splicing process. It contains several WD repeats, which function in protein-protein interactions. This protein has a sequence similarity to yeast Prp8 protein. This gene is a candidate gene for autosomal dominant retinitis pigmentosa. [provided by RefSeq, Jul 2008]
- RP13
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~34.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0019200
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0700092
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0005041
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0700092
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0700092
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0010806
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0010806
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0010806
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0700234
Submitter: ClinGen
The *PRPF8* gene (previously called *PRPC8*) was first reported in relation to autosomal dominant retinitis pigmentosa in 2001 (McKie et al., PMID: 11468273). PRPF8-related retinitis pigmentosa is now estimated to cause 2-3% of cases of autosomal dominant retinitis pigmentosa, characterized by classic presentation of night blindness and constriction of visual fields in multiple large families. We found PRPF8-related disease is inherited in an autosomal dominant pattern, with monoallelic disease-associated *PRPF8* variants causing classic retinitis pigmentosa; age of onset and severity of disease appears to be variable, with some published families displaying reduced penetrance (PMID: 22039234). Despite variability in severity, cases share overlapping phenotypes consistent with a single spectrum of disease, and consistent with criteria outlined by the ClinGen Lumping and Splitting Working Group, these cases have been lumped into a single disease entity, PRPF8-related retinopathy. Other non-retinal diseases related to *PRPF8* (glaucoma, myeloid leukemia) have also been described but have been excluded from this curation. 9 suspected disease-causing variants (2 nonsense and 7 missense or other variants) that have been reported in 9 probands in 7 publications (PMIDs: 17061239, 11468723, 11910553, 18695108, 29087248, 28076437, 22039234) were scored in this curation. Most of the reported variants are missense substitutions near the terminal exon of the coding sequence; several nonsense variants in the same region have also been associated with PRPF8-related disease in multiple publications (PMIDs: 29087248, 28076437). Only a few disease-causing variants have been described outside of this C-terminal region (PMIDs: 28761320, 22039234). Some variants (p.H2309P and p.H2309R) are reported to associate with a worse visual prognosis than others (such as p.R2310K, PMID: 20232351). More evidence is available in the literature but has not been included in this curation as the maximum for genetic evidence has already been reached. The mechanism of pathogenicity appears to be loss of spliceosome function; PRPF8 is the largest protein found in the spliceosome, and appears to inhibit the helicase activity of Brr2/SNRPN200 (PMID: 23727230). C-terminal mutations located in the Jab1 domain of PRPF8 are thought to result in reduction of PRPF8 interaction with a Brr2 (PMID: 19098916). Nonsense variants have also been associated with disease; it is predicted that C-terminal stop mutations may escape nonsense mediated decay, resulting in a truncated protein product that also reduces Brr2 interaction and increases helicase activity (PMID: 23704370). While genotype-phenotype correlations have not been well established, all reported retinopathy-causing variants except one (PMID: 33994920) are located in the C-terminal portion of the gene. The *PRPF8* gene is highly conserved in mammalian and lower vertebrate species, as it encodes a component of splicing machinery. The gene-disease association is supported by multiple cell culture models from model organisms and patient-derived tissue, demonstrating the role of PRPF8 in splicing. Multiple vertebrate and invertebrate models also support the gene-disease association. A drosophila mutant, in which adult eye morphology is dramatically disrupted, is consistent with a role for PRPF8 in photoreceptors (PMID: 32424050). A zebrafish mutant also demonstrates gross neurological differences and splicing disruption, supporting the role of the PRPF8 in splicing and snRNP assembly (PMID: 23714367). Retinal structures in mouse models demonstrate late-onset degenerative changes (PMID: 20811066). In summary, PRPF8 is definitively associated with PRPF8-related retinopathy; to date, the only associated phenotype is retinitis pigmentosa. The association with retinopathy has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This classification has been approved by the ClinGen Retina GCEP on April 6th, 2023 (SOP Version 9).
Clinical Genomic Database (CGD)
Manifestation: Ophthalmologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PRPF8 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006445.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 25 | 606 | 7 | 638 | ||
| missense | 10 | 44 | 613 | 14 | 681 | |
| nonsense | 6 | 8 | 10 | 24 | ||
| start loss | 0 | |||||
| frameshift | 13 | 13 | 10 | 36 | ||
| splice donor/acceptor (+/-2bp) | 2 | 3 | 20 | 25 | ||
| Total | 31 | 68 | 678 | 620 | 7 | 1404 |
Highest pathogenic variant AF is 0.0001338275
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006436.3 | 42 | MANE Select | |
| Ensembl | ENSP00000304350.6 | 42 | MANE Select | |
| Ensembl | ENSP00000459095.1 | 2 | Standard | |
| Ensembl | ENSP00000460348.1 | 42 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| prpf8 | Danio rerio | Structure: myeloid leukocyte Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Spliceosome - Homo sapiens (human)
- mRNA Processing
- Metabolism of RNA
- mRNA Splicing - Major Pathway
- mRNA Splicing - Minor Pathway
Biological Process
- spliceosomal tri-snRNP complex assembly
- RNA splicing, via transesterification reactions
- mRNA splicing, via spliceosome
- mRNA processing
- RNA splicing
Molecular Function
- second spliceosomal transesterification activity
- RNA binding
- protein binding
- U6 snRNA binding
- U1 snRNA binding
Cellular Component
- nucleus
- nucleoplasm
- U5 snRNP
- membrane
- nuclear speck
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000572621
- Coding exons
- 42
- Length
- 34254
- Individuals with no LoFs
- 125719
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 29
- Defined
- 125748
- p
- 0.000115
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 8.28 | 458 | 1.30e+3 | 0.353 | 0.0000874 | 15433 |
| Missense (PolyPhen) | 106 | 537.48 | 0.19722 | 6315 | ||
| Synonymous | -4.38 | 624 | 500 | 1.25 | 0.0000312 | 4463 |
| Loss of Function | 9.10 | 14 | 123 | 0.114 | 0.00000736 | 1397 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00013 | 0.00012 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions as a scaffold that mediates the ordered assembly of spliceosomal proteins and snRNAs. Required for the assembly of the U4/U6-U5 tri-snRNP complex. Functions as scaffold that positions spliceosomal U2, U5 and U6 snRNAs at splice sites on pre-mRNA substrates, so that splicing can occur. Interacts with both the 5' and the 3' splice site. {ECO:0000269|PubMed:20595234, ECO:0000303|PubMed:15840809}.;
- Disease
- DISEASE: Retinitis pigmentosa 13 (RP13) [MIM:600059]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269|PubMed:11468273, ECO:0000269|PubMed:11910553, ECO:0000269|PubMed:12714658, ECO:0000269|PubMed:17317632, ECO:0000269|Ref.36}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.210
Intolerance Scores
- LoFtool
- 0.184
- RVIS EVS
- -3.03
- RVIS percentile EVS
- 0.5
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.986
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |