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GeneE
26 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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PRPF31
pre-mRNA processing factor 31
Chromosome 19 Β· 19q13.42
NCBI Gene: 26121Ensembl: ENSG00000105618.15HGNC: HGNC:15446UniProt: Q8WWY3
279PubMed Papers
21Diseases
0Drugs
266Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedHub Gene
RESEARCH IMPACT
TrendingVariant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
snoRNA localizationspliceosomal tri-snRNP complex assemblymRNA splicing, via spliceosomeRNA bindingretinitis pigmentosaRetinal dystrophyautosomal dominant retinitis pigmentosaeye disease
✦AI Summary

PRPF31 (pre-mRNA processing factor 31) is a ubiquitously expressed spliceosomal component essential for pre-mRNA splicing 1. It functions as a critical assembly factor for the U4/U6/U5 tri-snRNP complex, a core building block of the spliceosome 2. This tri-snRNP complex binds directly to regulatory regions of U4 and U6 snRNAs, including sites where RP-associated variants cluster 3. Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa (RP11), a progressive retinal degeneration leading to visual impairment 1. Notably, PRPF31-RP exhibits incomplete penetrance due to haploinsufficiency, where reduced mutant allele expression determines disease manifestation 4. The retina-specific phenotype despite ubiquitous PRPF31 expression remains mechanistically complex 5. Patient-derived retinal organoids and RPE cells reveal that PRPF31 mutations cause selective mis-splicing of genes encoding splicing factors and ciliogenesis proteins, leading to photoreceptor death and RPE dysfunction with impaired phagocytosis and cilia defects 6. PRPF31 mutations also localize to the connecting cilium, establishing unexpected connections between spliceosomal function and ciliary biology 7. Gene augmentation and CRISPR/Cas9 correction successfully rescue defective phenotypes in patient cells, providing therapeutic proof-of-concept 5. PRPF31 variants account for significant RP cases in multiple populations 89.

Sources cited
1
PRPF31 is required for U4/U6/U5 tri-snRNP complex assembly in the spliceosome
PMID: 11867543
2
PRPF31 is a ubiquitously expressed splicing factor; mutations cause autosomal dominant retinitis pigmentosa with incomplete penetrance
PMID: 28663330
3
PRPF31-mutated retinal organoids and RPE cells show rod photoreceptor death and functional defects; gene augmentation rescues phenotypes
PMID: 35974011
4
PRPF31 mutations cause selective mis-splicing of splicing and ciliogenesis genes; RPE shows polarity disruption, reduced cilia, and phagocytic defects
PMID: 30315276
5
PRPF31 localizes to the connecting cilium; PRPF31-mutated cells exhibit ciliary defects
PMID: 26167768
6
PRPF3, PRPF8 and PRPF31 bind the U4/U6 duplex three-way junction; variants in RNU4-2 and RNU6 genes cluster in this binding region
PMID: 39830270
7
PRPF31-RP exhibits incomplete penetrance due to haploinsufficiency; no efficient treatment currently exists
PMID: 37714045
8
PRPF31 variants are among pathogenic genes causing retinitis pigmentosa in Japanese populations
PMID: 31213501
9
PRPF31 is identified as a disease-causing gene in Chinese families with retinitis pigmentosa
PMID: 31960602
Disease Associationsβ“˜21
retinitis pigmentosaOpen Targets
0.80Strong
Retinal dystrophyOpen Targets
0.57Moderate
autosomal dominant retinitis pigmentosaOpen Targets
0.42Moderate
eye diseaseOpen Targets
0.37Weak
Cone rod dystrophyOpen Targets
0.36Weak
cone-rod dystrophyOpen Targets
0.34Weak
retinopathyOpen Targets
0.27Weak
genetic disorderOpen Targets
0.19Weak
neurodegenerative diseaseOpen Targets
0.16Weak
Leber congenital amaurosisOpen Targets
0.11Weak
age-related macular degenerationOpen Targets
0.10Weak
colorectal carcinomaOpen Targets
0.08Suggestive
Stargardt diseaseOpen Targets
0.08Suggestive
X-linked retinal dysplasiaOpen Targets
0.08Suggestive
Familial exudative vitreoretinopathyOpen Targets
0.07Suggestive
choroidal dystrophy, central areolar, 1Open Targets
0.07Suggestive
severe early-childhood-onset retinal dystrophyOpen Targets
0.07Suggestive
Familial drusenOpen Targets
0.07Suggestive
reticular dystrophy of the retinal pigment epitheliumOpen Targets
0.07Suggestive
age related macular degeneration 2Open Targets
0.07Suggestive
Retinitis pigmentosa 11UniProt
Pathogenic Variants266
NM_015629.4(PRPF31):c.1040del (p.Leu347fs)Pathogenic
Retinal dystrophy|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 347
NM_015629.4(PRPF31):c.1060C>T (p.Arg354Ter)Pathogenic
Retinal dystrophy|Retinitis pigmentosa|not provided|PRPF31-related disorder
β˜…β˜…β˜†β˜†2026β†’ Residue 354
NM_015629.4(PRPF31):c.1084del (p.Lys361_Met362insTer)Pathogenic
Retinal dystrophy|not provided
β˜…β˜…β˜†β˜†2026β†’ Residue 361
NM_015629.4(PRPF31):c.322+4_322+7delPathogenic
not provided|Retinitis pigmentosa 11
β˜…β˜…β˜†β˜†2026
NM_015629.4(PRPF31):c.895T>C (p.Cys299Arg)Pathogenic
Retinal dystrophy|not provided|Retinitis pigmentosa|Retinitis pigmentosa 11|PRPF31-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 299
NM_015629.4(PRPF31):c.698-1G>APathogenic
Retinal dystrophy|not provided
β˜…β˜…β˜†β˜†2025
NM_015629.4(PRPF31):c.528-39_531delPathogenic
not provided|Retinitis pigmentosa 11|Retinal dystrophy
β˜…β˜…β˜†β˜†2025
NM_015629.4(PRPF31):c.856-2A>GPathogenic
not provided
β˜…β˜…β˜†β˜†2025
NM_015629.4(PRPF31):c.636del (p.Met212fs)Pathogenic
Retinal dystrophy|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 212
NM_015629.4(PRPF31):c.527+3A>GPathogenic
Retinitis pigmentosa 11|Retinal dystrophy|not provided
β˜…β˜…β˜†β˜†2025
NM_015629.4(PRPF31):c.1462_1472del (p.Lys488fs)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 488
NM_015629.4(PRPF31):c.220C>T (p.Gln74Ter)Pathogenic
not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 74
NM_015629.4(PRPF31):c.757G>A (p.Gly253Arg)Pathogenic
Retinitis pigmentosa 11|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 253
NM_015629.4(PRPF31):c.912_914dup (p.Val305dup)Likely pathogenic
Retinal dystrophy|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 305
NM_015629.4(PRPF31):c.469C>T (p.Gln157Ter)Pathogenic
Cone-rod dystrophy|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 157
NM_015629.4(PRPF31):c.239-2A>GPathogenic
Retinitis pigmentosa|not provided
β˜…β˜…β˜†β˜†2025
NM_015629.4(PRPF31):c.73_166dup (p.Asp56fs)Pathogenic
Retinal dystrophy|Retinitis pigmentosa|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 56
NM_015629.4(PRPF31):c.330_333del (p.His111fs)Pathogenic
Retinal dystrophy|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 111
NM_015629.4(PRPF31):c.973G>T (p.Glu325Ter)Pathogenic
not provided|Retinitis pigmentosa 11
β˜…β˜…β˜†β˜†2025β†’ Residue 325
NM_015629.4(PRPF31):c.866_879del (p.Arg289fs)Pathogenic
not provided|Retinitis pigmentosa 11
β˜…β˜…β˜†β˜†2025β†’ Residue 289
View on ClinVar β†—
Related Genes
MEPCEProtein interaction100%TUT1Protein interaction100%DAW1Protein interaction100%WDR53Protein interaction100%SNRPD3Protein interaction100%PRPF18Protein interaction100%
Tissue Expression6 tissues
Liver
100%
Ovary
88%
Brain
83%
Lung
73%
Bone Marrow
69%
Heart
62%
Gene Interaction Network
Click a node to explore
PRPF31MEPCETUT1DAW1WDR53SNRPD3PRPF18
PROTEIN STRUCTURE
Preparing viewer…
PDB2OZB Β· 2.60 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
0.35Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.21 [0.14–0.35]
RankingsWhere PRPF31 stands among ~20K protein-coding genes
  • #1,298of 20,598
    Most Researched279 Β· top 10%
  • #238of 5,498
    Most Pathogenic Variants266 Β· top 5%
  • #1,515of 17,882
    Most Constrained (LOEUF)0.35 Β· top 10%
Genes detectedPRPF31
Sources retrieved26 papers
Response timeβ€”
πŸ“„ Sources
26β–Ό
1
Genetic characteristics of retinitis pigmentosa in 1204 Japanese patients.
PMID: 31213501
J Med Genet Β· 2019
1.00
2
PMID: 20301590
0.90
3
Modeling PRPF31 retinitis pigmentosa using retinal pigment epithelium and organoids combined with gene augmentation rescue.
PMID: 35974011
NPJ Regen Med Β· 2022
0.80
4
An siRNA-based functional genomics screen for theΒ identification of regulators of ciliogenesis and ciliopathyΒ genes.
PMID: 26167768
Nat Cell Biol Β· 2015
0.70
5
PRPF31 alternative splicing and expression in human retina.
PMID: 19373678
Ophthalmic Genet Β· 2009
0.68