Gene Gene information from NCBI Gene database.
Entrez ID 9129
Gene name Pre-mRNA processing factor 3
Gene symbol PRPF3
Synonyms (NCBI Gene)
HPRP3HPRP3PPRP3Prp3pRP18SNRNP90
Chromosome 1
Chromosome location 1q21.2
Summary 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
SNPs SNP information provided by dbSNP.
6
SNP ID Visualize variation Clinical significance Consequence
rs121434241 C>T Pathogenic Genic downstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs121434242 C>T Pathogenic Genic downstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs121434243 C>A Pathogenic Genic downstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs199721048 T>C Conflicting-interpretations-of-pathogenicity Coding sequence variant, synonymous variant, non coding transcript variant
rs1572263399 A>G Likely-pathogenic Genic downstream transcript variant, splice acceptor variant
miRNA miRNA information provided by mirtarbase database.
148
miRTarBase ID miRNA Experiments Reference
MIRT1265351 hsa-miR-1271 CLIP-seq
MIRT1265352 hsa-miR-1321 CLIP-seq
MIRT1265353 hsa-miR-199a-5p CLIP-seq
MIRT1265354 hsa-miR-199b-5p CLIP-seq
MIRT1265355 hsa-miR-204 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
29
GO ID Ontology Definition Evidence Reference
GO:0000244 Process Spliceosomal tri-snRNP complex assembly IDA 20595234
GO:0000375 Process RNA splicing, via transesterification reactions TAS 9328476
GO:0000398 Process MRNA splicing, via spliceosome IBA
GO:0000398 Process MRNA splicing, via spliceosome IDA 28781166
GO:0000398 Process MRNA splicing, via spliceosome IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
607301 17348 ENSG00000117360
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O43395
Protein name U4/U6 small nuclear ribonucleoprotein Prp3 (Pre-mRNA-splicing factor 3) (hPrp3) (U4/U6 snRNP 90 kDa protein)
Protein function Plays a role in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as component of the precatalytic spliceosome (spliceosome B complex). {ECO:0000269|PubMed:26912367, ECO:0000269|PubMed
PDB 1X4Q , 3JCR , 5O9Z , 6AH0 , 6AHD , 6QW6 , 6QX9 , 7N2N , 7N2R , 7N2S , 8H6E , 8H6J , 8H6K , 8H6L , 8Q7N , 8QO9 , 8QOZ , 8QP8 , 8QP9 , 8QPA , 8QPB , 8QPE , 8QXD , 8QZS , 8R08 , 8R09 , 8R0A , 8R0B , 8RM5 , 8Y6O
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01480 PWI 9 78 PWI domain Family
PF08572 PRP3 308 521 pre-mRNA processing factor 3 (PRP3) Domain
PF06544 DUF1115 544 673 Protein of unknown function (DUF1115) Domain
Tissue specificity TISSUE SPECIFICITY: Highly expressed in retina, liver, kidney and blood. Detected at lower levels in heart and brain. {ECO:0000269|PubMed:11773002}.
Sequence
Sequence length 683
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Spliceosome   mRNA Splicing - Major Pathway
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
16
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Retinal dystrophy Pathogenic; Likely pathogenic rs121434241, rs121434242, rs1657981991, rs1658082808 RCV001074785
RCV004814816
RCV001075175
RCV001074516
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa Pathogenic rs121434241, rs1658062720 RCV001003129
RCV001199729
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinitis pigmentosa 18 Pathogenic; Likely pathogenic rs121434241, rs121434242, rs121434243, rs1572263404, rs1658063448 RCV000003516
RCV000003517
RCV000003518
RCV001002720
RCV001261958
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Acute myeloid leukemia Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Atrophy Atrophy Pubtator 20309403 Associate
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma BEFREE 7774926
★☆☆☆☆
Found in Text Mining only
Carcinogenesis Carcinogenesis Pubtator 31926109 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Hepatocellular Hepatocellular carcinoma Pubtator 31926109 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Squamous Cell Squamous cell carcinoma Pubtator 32483193 Associate
★☆☆☆☆
Found in Text Mining only
Cataract Cataract HPO_DG
★☆☆☆☆
Found in Text Mining only
Conductive hearing loss Hearing Loss HPO_DG
★☆☆☆☆
Found in Text Mining only
Congenital hypoplasia of penis Congenital Hypoplasia Of Penis HPO_DG
★☆☆☆☆
Found in Text Mining only
Degenerative polyarthritis Arthritis BEFREE 31268737
★☆☆☆☆
Found in Text Mining only
Diabetes Mellitus Type 1 Diabetes mellitus, type 1 Pubtator 33154504 Associate
★☆☆☆☆
Found in Text Mining only