PRPF3 Gene

Name	pre-mRNA processing factor 3
Description	The removal of introns from nuclear pre-mRNAs occurs on complexes called spliceosomes, which are made up of 4 small nuclear ribonucleoprotein (snRNP) particles and an undefined number of transiently associated splicing factors. This gene product is one of several proteins that associate with U4 and U6 snRNPs. Mutations in this gene are associated with retinitis pigmentosa-18. [provided by RefSeq, Jul 2008]
Summary	{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\nPRPF3 is a ubiquitously expressed core component of the spliceosome that is essential for the proper processing of pre‐mRNAs. Several independent studies have shown that mutations in PRPF3—often clustered in a conserved region in exon 11 (such as the recurrent Thr494Met and Pro493Ser substitutions)—lead to defects in splicing and are causative of autosomal dominant retinitis pigmentosa. Despite its broad expression, the retina, which exhibits particularly high levels of splicing activity, appears especially vulnerable to these impaired interactions and abnormal spliceosome assembly, ultimately triggering photoreceptor degeneration."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "6"}]}, {"type": "t", "text": "\n"}]}, {"type": "t", "text": "\n\n"}, {"type": "p", "children": [{"type": "t", "text": "\nAt the molecular level, PRPF3 (the human orthologue of yeast Hprp3p) contributes to the formation and stability of the U4/U6 snRNP and U4/U6∙U5 tri-snRNP complexes, acting in concert with other spliceosomal proteins. Its proper function is tightly regulated by post‐translational modifications—such as phosphorylation by CK2 and SUMOylation—that modulate its ability to interact with key partners including PRPF4, PAP‐1, and SPF30. Disruption of these interactions by disease‐linked mutations not only impairs the recycling and assembly of spliceosomal complexes but also leads to abnormal nuclear aggregation, particularly in photoreceptor cells, thereby linking defective splicing directly to the retinal degeneration observed in retinitis pigmentosa."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "7", "end_ref": "14"}]}, {"type": "t", "text": "\n"}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Christina F Chakarova, Matthew M Hims, Hanno Bolz, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutations in HPRP3, a third member of pre-mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/11.1.87"}], "href": "https://doi.org/10.1093/hmg/11.1.87"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "11773002"}], "href": "https://pubmed.ncbi.nlm.nih.gov/11773002"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "María Martínez-Gimeno, María José Gamundi, Imma Hernan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutations in the pre-mRNA splicing-factor genes PRPF3, PRPF8, and PRPF31 in Spanish families with autosomal dominant retinitis pigmentosa."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Invest Ophthalmol Vis Sci (2003)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1167/iovs.02-0871"}], "href": "https://doi.org/10.1167/iovs.02-0871"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "12714658"}], "href": "https://pubmed.ncbi.nlm.nih.gov/12714658"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Yuko Wada, Toshitaka Itabashi, Hajime Sato, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Clinical features of a Japanese family with autosomal dominant retinitis pigmentosa associated with a Thr494Met mutation in the HPRP3 gene."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Graefes Arch Clin Exp Ophthalmol (2004)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s00417-004-0923-x"}], "href": "https://doi.org/10.1007/s00417-004-0923-x"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15085354"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15085354"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Veronika Vaclavik, Marie-Claire Gaillard, L Tiab, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Variable phenotypic expressivity in a Swiss family with autosomal dominant retinitis pigmentosa due to a T494M mutation in the PRPF3 gene."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Vis (2010)"}]}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "20309403"}], "href": "https://pubmed.ncbi.nlm.nih.gov/20309403"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Goranka Tanackovic, Adriana Ransijn, Philippe Thibault, et al. "}, {"type": "b", "children": [{"type": "t", "text": "PRPF mutations are associated with generalized defects in spliceosome formation and pre-mRNA splicing in patients with retinitis pigmentosa."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2011)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/ddr094"}], "href": "https://doi.org/10.1093/hmg/ddr094"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "21378395"}], "href": "https://pubmed.ncbi.nlm.nih.gov/21378395"}]}, {"type": "r", "ref": 6, "children": [{"type": "t", "text": "Zilin Zhong, Ming Yan, Wan Sun, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Two novel mutations in PRPF3 causing autosomal dominant retinitis pigmentosa."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Sci Rep (2016)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/srep37840"}], "href": "https://doi.org/10.1038/srep37840"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "27886254"}], "href": "https://pubmed.ncbi.nlm.nih.gov/27886254"}]}, {"type": "r", "ref": 7, "children": [{"type": "t", "text": "Hiroshi Maita, Hirotake Kitaura, Hiroyoshi Ariga, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Association of PAP-1 and Prp3p, the products of causative genes of dominant retinitis pigmentosa, in the tri-snRNP complex."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Exp Cell Res (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.yexcr.2004.08.022"}], "href": "https://doi.org/10.1016/j.yexcr.2004.08.022"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15541726"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15541726"}]}, {"type": "r", "ref": 8, "children": [{"type": "t", "text": "Antonella Comitato, Carmine Spampanato, Christina Chakarova, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutations in splicing factor PRPF3, causing retinal degeneration, form detrimental aggregates in photoreceptor cells."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2007)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/ddm118"}], "href": "https://doi.org/10.1093/hmg/ddm118"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17517693"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17517693"}]}, {"type": "r", "ref": 9, "children": [{"type": "t", "text": "Berta Pozzi, Laureano Bragado, Cindy L Will, et al. "}, {"type": "b", "children": [{"type": "t", "text": "SUMO conjugation to spliceosomal proteins is required for efficient pre-mRNA splicing."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Nucleic Acids Res (2017)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/nar/gkx213"}], "href": "https://doi.org/10.1093/nar/gkx213"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "28379520"}], "href": "https://pubmed.ncbi.nlm.nih.gov/28379520"}]}, {"type": "r", "ref": 10, "children": [{"type": "t", "text": "Juana Maria Gonzalez-Santos, Anan Wang, Joses Jones, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Central region of the human splicing factor Hprp3p interacts with Hprp4p."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2002)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M111461200"}], "href": "https://doi.org/10.1074/jbc.M111461200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "11971898"}], "href": "https://pubmed.ncbi.nlm.nih.gov/11971898"}]}, {"type": "r", "ref": 11, "children": [{"type": "t", "text": "Juana Maria Gonzalez-Santos, Huibi Cao, Rongqi Cathleen Duan, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Mutation in the splicing factor Hprp3p linked to retinitis pigmentosa impairs interactions within the U4/U6 snRNP complex."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Hum Mol Genet (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1093/hmg/ddm300"}], "href": "https://doi.org/10.1093/hmg/ddm300"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "17932117"}], "href": "https://pubmed.ncbi.nlm.nih.gov/17932117"}]}, {"type": "r", "ref": 12, "children": [{"type": "t", "text": "S Lehnert, C Götz, S Kartarius, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Protein kinase CK2 interacts with the splicing factor hPrp3p."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Oncogene (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/sj.onc.1210882"}], "href": "https://doi.org/10.1038/sj.onc.1210882"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18026141"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18026141"}]}, {"type": "r", "ref": 13, "children": [{"type": "t", "text": "John T Little, Melissa S Jurica "}, {"type": "b", "children": [{"type": "t", "text": "Splicing factor SPF30 bridges an interaction between the prespliceosome protein U2AF35 and tri-small nuclear ribonucleoprotein protein hPrp3."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "J Biol Chem (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1074/jbc.M707984200"}], "href": "https://doi.org/10.1074/jbc.M707984200"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18211889"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18211889"}]}, {"type": "r", "ref": 14, "children": [{"type": "t", "text": "Janka Dörr, Sabine Kartarius, Claudia Götz, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Contribution of the individual subunits of protein kinase CK2 and of hPrp3p to the splicing process."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biochem (2008)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1007/s11010-008-9820-7"}], "href": "https://doi.org/10.1007/s11010-008-9820-7"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "18553058"}], "href": "https://pubmed.ncbi.nlm.nih.gov/18553058"}]}]}]}
Synonyms	PRP3, SNRNP90, HPRP3P, RP18, HPRP3, PRP3P
Proteins	PRPF3_HUMAN
NCBI Gene ID	9129
API
Download Associations
Predicted Functions
Co-expressed Genes
Expression in Tissues and Cell Lines

Functional Associations

PRPF3 has 8,181 functional associations with biological entities spanning 8 categories (molecular profile, organism, chemical, disease, phenotype or trait, functional term, phrase or reference, structural feature, cell line, cell type or tissue, gene, protein or microRNA) extracted from 135 datasets.

Click the + buttons to view associations for PRPF3 from the datasets below.

If available, associations are ranked by standardized value

Harmonizome 3.0

PRPF3 Gene

Functional Associations

Please acknowledge the Harmonizome in your publications by citing the following reference(s):

	Dataset	Summary
	Achilles Cell Line Gene Essentiality Profiles	cell lines with fitness changed by PRPF3 gene knockdown relative to other cell lines from the Achilles Cell Line Gene Essentiality Profiles dataset.
	Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PRPF3 gene relative to other tissues from the Allen Brain Atlas Adult Human Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles	tissues with high or low expression of PRPF3 gene relative to other tissues from the Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles dataset.
	Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles	tissue samples with high or low expression of PRPF3 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray	tissue samples with high or low expression of PRPF3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by Microarray dataset.
	Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq	tissue samples with high or low expression of PRPF3 gene relative to other tissue samples from the Allen Brain Atlas Developing Human Brain Tissue Gene Expression Profiles by RNA-seq dataset.
	Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles	tissues with high or low expression of PRPF3 gene relative to other tissues from the Allen Brain Atlas Prenatal Human Brain Tissue Gene Expression Profiles dataset.
	BioGPS Cell Line Gene Expression Profiles	cell lines with high or low expression of PRPF3 gene relative to other cell lines from the BioGPS Cell Line Gene Expression Profiles dataset.
	BioGPS Human Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PRPF3 gene relative to other cell types and tissues from the BioGPS Human Cell Type and Tissue Gene Expression Profiles dataset.
	BioGPS Mouse Cell Type and Tissue Gene Expression Profiles	cell types and tissues with high or low expression of PRPF3 gene relative to other cell types and tissues from the BioGPS Mouse Cell Type and Tissue Gene Expression Profiles dataset.
	Carcinogenome Chemical Perturbation Carcinogenicity Signatures	small molecule perturbations changing expression of PRPF3 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
	CCLE Cell Line Gene CNV Profiles	cell lines with high or low copy number of PRPF3 gene relative to other cell lines from the CCLE Cell Line Gene CNV Profiles dataset.
	CCLE Cell Line Gene Expression Profiles	cell lines with high or low expression of PRPF3 gene relative to other cell lines from the CCLE Cell Line Gene Expression Profiles dataset.
	CCLE Cell Line Proteomics	Cell lines associated with PRPF3 protein from the CCLE Cell Line Proteomics dataset.
	ChEA Transcription Factor Binding Site Profiles	transcription factor binding site profiles with transcription factor binding evidence at the promoter of PRPF3 gene from the CHEA Transcription Factor Binding Site Profiles dataset.
	ChEA Transcription Factor Targets	transcription factors binding the promoter of PRPF3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets dataset.
	ChEA Transcription Factor Targets 2022	transcription factors binding the promoter of PRPF3 gene in low- or high-throughput transcription factor functional studies from the CHEA Transcription Factor Targets 2022 dataset.
	ClinVar Gene-Phenotype Associations	phenotypes associated with PRPF3 gene from the curated ClinVar Gene-Phenotype Associations dataset.
	ClinVar Gene-Phenotype Associations 2025	phenotypes associated with PRPF3 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
	CM4AI U2OS Cell Map Protein Localization Assemblies	assemblies containing PRPF3 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
	CMAP Signatures of Differentially Expressed Genes for Small Molecules	small molecule perturbations changing expression of PRPF3 gene from the CMAP Signatures of Differentially Expressed Genes for Small Molecules dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores	cellular components containing PRPF3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores dataset.
	COMPARTMENTS Curated Protein Localization Evidence Scores 2025	cellular components containing PRPF3 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
	COMPARTMENTS Experimental Protein Localization Evidence Scores	cellular components containing PRPF3 protein in low- or high-throughput protein localization assays from the COMPARTMENTS Experimental Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores	cellular components co-occuring with PRPF3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores dataset.
	COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025	cellular components co-occuring with PRPF3 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
	CORUM Protein Complexes	protein complexs containing PRPF3 protein from the CORUM Protein Complexes dataset.
	COSMIC Cell Line Gene CNV Profiles	cell lines with high or low copy number of PRPF3 gene relative to other cell lines from the COSMIC Cell Line Gene CNV Profiles dataset.
	COSMIC Cell Line Gene Mutation Profiles	cell lines with PRPF3 gene mutations from the COSMIC Cell Line Gene Mutation Profiles dataset.
	CTD Gene-Chemical Interactions	chemicals interacting with PRPF3 gene/protein from the curated CTD Gene-Chemical Interactions dataset.
	CTD Gene-Disease Associations	diseases associated with PRPF3 gene/protein from the curated CTD Gene-Disease Associations dataset.
	DeepCoverMOA Drug Mechanisms of Action	small molecule perturbations with high or low expression of PRPF3 protein relative to other small molecule perturbations from the DeepCoverMOA Drug Mechanisms of Action dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores	diseases involving PRPF3 gene from the DISEASES Curated Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Curated Gene-Disease Association Evidence Scores 2025	diseases involving PRPF3 gene from the DISEASES Curated Gene-Disease Association Evidence Scores 2025 dataset.
	DISEASES Experimental Gene-Disease Association Evidence Scores 2025	diseases associated with PRPF3 gene in GWAS datasets from the DISEASES Experimental Gene-Disease Assocation Evidence Scores 2025 dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores	diseases co-occuring with PRPF3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores dataset.
	DISEASES Text-mining Gene-Disease Association Evidence Scores 2025	diseases co-occuring with PRPF3 gene in abstracts of biomedical publications from the DISEASES Text-mining Gene-Disease Assocation Evidence Scores 2025 dataset.
	DisGeNET Gene-Disease Associations	diseases associated with PRPF3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Disease Associations dataset.
	DisGeNET Gene-Phenotype Associations	phenotypes associated with PRPF3 gene in GWAS and other genetic association datasets from the DisGeNET Gene-Phenoptype Associations dataset.
	ENCODE Histone Modification Site Profiles	histone modification site profiles with high histone modification abundance at PRPF3 gene from the ENCODE Histone Modification Site Profiles dataset.