PRPF8

protein-coding

pre-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]

Previous symbols:
  • RP13

MANE transcript

NM_006445.4

Inheritance

AD

ClinVar variants

P:99U:678B:627

Top phenotype

Retinitis pigmentosa 13

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr17:1,650,629-1,684,867

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~34.2 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

retinitis pigmentosaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019200

Submitter: Orphanet

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: Ambry Genetics

glaucomaLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0005041

Submitter: G2P

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

neurodevelopmental disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: G2P

retinitis pigmentosa 13DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0010806

Submitter: G2P

retinitis pigmentosa 13STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010806

Submitter: PanelApp Australia

retinitis pigmentosa 13STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0010806

Submitter: Labcorp Genetics (formerly Invitae)

PRPF8-related retinopathyDEFINITIVE

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)

Retinitis pigmentosa 13AD

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

Refs: 11468273; 20232351; 22039234Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRPF8 variants in ClinVar

16 Conditions Cataloged
not providedTotal: 1586
not specifiedTotal: 351
PRPF8-related disorderTotal: 148
Inborn genetic diseasesTotal: 108
Retinitis pigmentosaTotal: 87
Retinal dystrophyTotal: 83
Retinitis pigmentosa 13Total: 75
Neurodevelopmental disorderTotal: 4

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.

EffectPLPVUSLBBSum
synonymous
25
clinvar
606
clinvar
7
clinvar
638
missense
10
clinvar
44
clinvar
613
clinvar
14
clinvar
681
nonsense
6
clinvar
8
clinvar
10
clinvar
24
start loss
0
frameshift
13
clinvar
13
clinvar
10
clinvar
36
splice donor/acceptor (+/-2bp)
2
clinvar
3
clinvar
20
clinvar
25
Total316867862071404

Highest pathogenic variant AF is 0.0001338275

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_006445.4RefSeqNP_006436.342MANE Select
ENST00000304992.11EnsemblENSP00000304350.642MANE Select
ENST00000571958.1EnsemblENSP00000459095.12Standard
ENST00000572621.5EnsemblENSP00000460348.142Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
prpf8Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense8.284581.30e+30.3530.000087415433
Missense (PolyPhen)106537.480.197226315
Synonymous-4.386245001.250.00003124463
Loss of Function9.10141230.1140.000007361397

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000110.00011rare
Finnish0.0000920.000092rare
European (Non-Finnish)0.000130.00012rare
South Asian0.0000650.000065rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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