Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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

Show/Hide all (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
rs1572263404	G>T	Pathogenic	Coding sequence variant, missense variant, genic downstream transcript variant, non coding transcript variant

148

Show/Hide all (148)

miRTarBase ID	miRNA	Experiments
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
MIRT1265356	hsa-miR-211	CLIP-seq
MIRT1265357	hsa-miR-2355-3p	CLIP-seq
MIRT1265358	hsa-miR-3150b-3p	CLIP-seq
MIRT1265359	hsa-miR-3169	CLIP-seq
MIRT1265360	hsa-miR-345	CLIP-seq
MIRT1265361	hsa-miR-346	CLIP-seq
MIRT1265362	hsa-miR-3591-3p	CLIP-seq
MIRT1265363	hsa-miR-3664-3p	CLIP-seq
MIRT1265364	hsa-miR-377	CLIP-seq
MIRT1265365	hsa-miR-3929	CLIP-seq
MIRT1265366	hsa-miR-4251	CLIP-seq
MIRT1265367	hsa-miR-4277	CLIP-seq
MIRT1265368	hsa-miR-4287	CLIP-seq
MIRT1265369	hsa-miR-4288	CLIP-seq
MIRT1265370	hsa-miR-4303	CLIP-seq
MIRT1265371	hsa-miR-4329	CLIP-seq
MIRT1265372	hsa-miR-4419b	CLIP-seq
MIRT1265373	hsa-miR-4433	CLIP-seq
MIRT1265374	hsa-miR-4459	CLIP-seq
MIRT1265375	hsa-miR-4469	CLIP-seq
MIRT1265376	hsa-miR-4478	CLIP-seq
MIRT1265377	hsa-miR-451b	CLIP-seq
MIRT1265378	hsa-miR-4646-3p	CLIP-seq
MIRT1265379	hsa-miR-4685-3p	CLIP-seq
MIRT1265380	hsa-miR-4709-3p	CLIP-seq
MIRT1265381	hsa-miR-4713-5p	CLIP-seq
MIRT1265382	hsa-miR-4733-3p	CLIP-seq
MIRT1265383	hsa-miR-4739	CLIP-seq
MIRT1265384	hsa-miR-4740-5p	CLIP-seq
MIRT1265385	hsa-miR-4756-5p	CLIP-seq
MIRT1265386	hsa-miR-4768-3p	CLIP-seq
MIRT1265387	hsa-miR-4779	CLIP-seq
MIRT1265388	hsa-miR-4784	CLIP-seq
MIRT1265389	hsa-miR-510	CLIP-seq
MIRT1265390	hsa-miR-548an	CLIP-seq
MIRT1265391	hsa-miR-632	CLIP-seq
MIRT1265392	hsa-miR-765	CLIP-seq
MIRT1265393	hsa-miR-939	CLIP-seq
MIRT1265394	hsa-miR-96	CLIP-seq
MIRT1265352	hsa-miR-1321	CLIP-seq
MIRT2078022	hsa-miR-3121-3p	CLIP-seq
MIRT2078023	hsa-miR-3153	CLIP-seq
MIRT1265359	hsa-miR-3169	CLIP-seq
MIRT2078024	hsa-miR-3689a-3p	CLIP-seq
MIRT2078025	hsa-miR-3689c	CLIP-seq
MIRT2078026	hsa-miR-4425	CLIP-seq
MIRT2078027	hsa-miR-4668-5p	CLIP-seq
MIRT1265380	hsa-miR-4709-3p	CLIP-seq
MIRT2078028	hsa-miR-4728-5p	CLIP-seq
MIRT1265383	hsa-miR-4739	CLIP-seq
MIRT1265384	hsa-miR-4740-5p	CLIP-seq
MIRT1265385	hsa-miR-4756-5p	CLIP-seq
MIRT1265390	hsa-miR-548an	CLIP-seq
MIRT1265363	hsa-miR-3664-3p	CLIP-seq
MIRT2304529	hsa-miR-3936	CLIP-seq
MIRT1265373	hsa-miR-4433	CLIP-seq
MIRT1265374	hsa-miR-4459	CLIP-seq
MIRT1265377	hsa-miR-451b	CLIP-seq
MIRT1265386	hsa-miR-4768-3p	CLIP-seq
MIRT1265387	hsa-miR-4779	CLIP-seq
MIRT2304530	hsa-miR-501-3p	CLIP-seq
MIRT2304531	hsa-miR-502-3p	CLIP-seq
MIRT1265389	hsa-miR-510	CLIP-seq
MIRT1265393	hsa-miR-939	CLIP-seq
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
MIRT1265356	hsa-miR-211	CLIP-seq
MIRT1265357	hsa-miR-2355-3p	CLIP-seq
MIRT2078022	hsa-miR-3121-3p	CLIP-seq
MIRT2078023	hsa-miR-3153	CLIP-seq
MIRT1265359	hsa-miR-3169	CLIP-seq
MIRT1265361	hsa-miR-346	CLIP-seq
MIRT1265363	hsa-miR-3664-3p	CLIP-seq
MIRT2078024	hsa-miR-3689a-3p	CLIP-seq
MIRT2078025	hsa-miR-3689c	CLIP-seq
MIRT1265364	hsa-miR-377	CLIP-seq
MIRT1265366	hsa-miR-4251	CLIP-seq
MIRT1265367	hsa-miR-4277	CLIP-seq
MIRT1265368	hsa-miR-4287	CLIP-seq
MIRT1265369	hsa-miR-4288	CLIP-seq
MIRT1265370	hsa-miR-4303	CLIP-seq
MIRT1265371	hsa-miR-4329	CLIP-seq
MIRT2078026	hsa-miR-4425	CLIP-seq
MIRT1265373	hsa-miR-4433	CLIP-seq
MIRT1265374	hsa-miR-4459	CLIP-seq
MIRT1265375	hsa-miR-4469	CLIP-seq
MIRT1265377	hsa-miR-451b	CLIP-seq
MIRT1265378	hsa-miR-4646-3p	CLIP-seq
MIRT2078027	hsa-miR-4668-5p	CLIP-seq
MIRT1265379	hsa-miR-4685-3p	CLIP-seq
MIRT1265380	hsa-miR-4709-3p	CLIP-seq
MIRT1265381	hsa-miR-4713-5p	CLIP-seq
MIRT2078028	hsa-miR-4728-5p	CLIP-seq
MIRT1265383	hsa-miR-4739	CLIP-seq
MIRT1265384	hsa-miR-4740-5p	CLIP-seq
MIRT1265385	hsa-miR-4756-5p	CLIP-seq
MIRT1265386	hsa-miR-4768-3p	CLIP-seq
MIRT1265387	hsa-miR-4779	CLIP-seq
MIRT1265389	hsa-miR-510	CLIP-seq
MIRT1265390	hsa-miR-548an	CLIP-seq
MIRT1265391	hsa-miR-632	CLIP-seq
MIRT1265393	hsa-miR-939	CLIP-seq
MIRT1265394	hsa-miR-96	CLIP-seq
MIRT1265351	hsa-miR-1271	CLIP-seq
MIRT1265353	hsa-miR-199a-5p	CLIP-seq
MIRT1265354	hsa-miR-199b-5p	CLIP-seq
MIRT1265355	hsa-miR-204	CLIP-seq
MIRT1265356	hsa-miR-211	CLIP-seq
MIRT1265357	hsa-miR-2355-3p	CLIP-seq
MIRT2078022	hsa-miR-3121-3p	CLIP-seq
MIRT2078023	hsa-miR-3153	CLIP-seq
MIRT1265359	hsa-miR-3169	CLIP-seq
MIRT1265361	hsa-miR-346	CLIP-seq
MIRT1265363	hsa-miR-3664-3p	CLIP-seq
MIRT2078024	hsa-miR-3689a-3p	CLIP-seq
MIRT2078025	hsa-miR-3689c	CLIP-seq
MIRT1265364	hsa-miR-377	CLIP-seq
MIRT1265366	hsa-miR-4251	CLIP-seq
MIRT1265367	hsa-miR-4277	CLIP-seq
MIRT1265368	hsa-miR-4287	CLIP-seq
MIRT1265369	hsa-miR-4288	CLIP-seq
MIRT1265370	hsa-miR-4303	CLIP-seq
MIRT1265371	hsa-miR-4329	CLIP-seq
MIRT2078026	hsa-miR-4425	CLIP-seq
MIRT1265373	hsa-miR-4433	CLIP-seq
MIRT1265374	hsa-miR-4459	CLIP-seq
MIRT1265375	hsa-miR-4469	CLIP-seq
MIRT1265377	hsa-miR-451b	CLIP-seq
MIRT1265378	hsa-miR-4646-3p	CLIP-seq
MIRT2078027	hsa-miR-4668-5p	CLIP-seq
MIRT1265379	hsa-miR-4685-3p	CLIP-seq
MIRT1265381	hsa-miR-4713-5p	CLIP-seq
MIRT2078028	hsa-miR-4728-5p	CLIP-seq
MIRT1265384	hsa-miR-4740-5p	CLIP-seq
MIRT1265386	hsa-miR-4768-3p	CLIP-seq
MIRT1265387	hsa-miR-4779	CLIP-seq
MIRT1265389	hsa-miR-510	CLIP-seq
MIRT1265391	hsa-miR-632	CLIP-seq
MIRT1265393	hsa-miR-939	CLIP-seq
MIRT1265394	hsa-miR-96	CLIP-seq

Show/Hide all (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
GO:0000398	Process	MRNA splicing, via spliceosome	NAS	9328476
GO:0003723	Function	RNA binding	HDA	22681889
GO:0005515	Function	Protein binding	IPI	15314151, 16189514, 16723661, 17332742, 20595234, 21516116, 22365833, 25383878, 25416956, 25910212, 26030138, 28514442, 32296183, 33961781, 35271311, 39251607
GO:0005634	Component	Nucleus	IDA	20595234, 26912367, 28781166
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	9328476
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	NAS	9328476
GO:0005829	Component	Cytosol	IDA
GO:0006397	Process	MRNA processing	IEA
GO:0006397	Process	MRNA processing	TAS	9328476
GO:0008380	Process	RNA splicing	IEA
GO:0008380	Process	RNA splicing	TAS	9328476
GO:0015030	Component	Cajal body	IDA	15257298
GO:0016607	Component	Nuclear speck	IDA
GO:0016607	Component	Nuclear speck	IEA
GO:0032991	Component	Protein-containing complex	IEA
GO:0042802	Function	Identical protein binding	IPI	22365833
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IBA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	26912367
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IEA
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	28781166

MIM	HGNC	e!Ensembl
607301	17348	ENSG00000117360

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

MALSKRELDELKPWIEKTVKRVLGFSEPTVVTAALNCVGKGMDKKKAADHLKPFLDDSTL
RFVDKLFEAVEEGRSSRHSKSSSDRSRKRELKEVFGDDSEISKESSGVKKRRIPRFEEVE
EEPEVIPGPPSESPGMLTKLQIKQMMEAATRQIEERKKQLSFISPPTPQPKTPSSSQPER
LPIGNTIQPSQAATFMNDAIEKARKAAELQARIQAQLALKPGLIGNANMVGLANLHAMGI
APPKVELKDQTKPTPLILDEQGRTVDATGKEIELTHRMPTLKANIRAVKREQFKQQLKEK
PSEDMESNTFFDPRVSIAPSQRQRRTFKFHDKGKFEKIAQRLRTKAQLEKLQAEISQAAR
KTGIHTSTRLALIAPKKELKEGDIPEIEWWDSYIIPNGFDLTEENPKREDYFGITNLVEH
PAQLNPPVDNDTPVTLGVYLTKKEQKKLRRQTRREAQKELQEKVRLGLMPPPEPKVRISN
LMRVLGTEAVQDPTKVEAHVRAQMAKRQKAHEEANAARKLTAEQRKVKKIKKLKEDISQG
VHISVYRVRNLSNPAKKFKIEANAGQLYLTGVVVLHKDVNVVVVEGGPKAQKKFKRLMLH
RIKWDEQTSNTKGDDDEESDEEAVKKTNKCVLVWEGTAKDRSFGEMKFKQCPTENMAREH
FKKHGAEHYWDLALSESVLESTD

Sequence length

683

Interactions

View interactions

	KEGG		Reactome
	Spliceosome		mRNA Splicing - Major Pathway

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Retinal dystrophy	Pathogenic; Likely pathogenic	rs121434241, rs121434242, rs1657981991, rs1658082808	RCV001074785 RCV004814816 RCV001075175 RCV001074516
Retinitis pigmentosa	Pathogenic	rs121434241, rs1658062720	RCV001003129 RCV001199729
Retinitis pigmentosa 18	Pathogenic; Likely pathogenic	rs121434241, rs121434242, rs121434243, rs1572263404, rs1658063448	RCV000003516 RCV000003517 RCV000003518 RCV001002720 RCV001261958

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Uncertain significance	rs782747350	RCV005912133
Familial cancer of breast	Uncertain significance	rs782747350	RCV005912132
Ovarian serous cystadenocarcinoma	Uncertain significance	rs782747350	RCV005912134
PRPF3-related disorder	Conflicting classifications of pathogenicity; Likely benign; Benign	rs143350315, rs782160046, rs587647917, rs782790176, rs146995242, rs199721048, rs80201355	RCV003952514 RCV003946202 RCV004758807 RCV003933499 RCV004758664 RCV003927690 RCV003920179
Retinitis Pigmentosa, Dominant	Uncertain significance; Likely benign	rs886045257, rs3767630, rs886045259, rs886045264, rs868986702	RCV000267788 RCV000363628 RCV000265899 RCV000401178 RCV000325243
Uterine corpus endometrial carcinoma	Uncertain significance	rs782747350	RCV005912135

Show/Hide Text Mining Associations (21)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenoma Islet Cell	Associate	33154504
Atrophy	Associate	20309403
Carcinogenesis	Associate	31926109
Carcinoma Hepatocellular	Associate	31926109
Carcinoma Squamous Cell	Associate	32483193
Death	Associate	15944448
Diabetes Mellitus Type 1	Associate	33154504
Eye Diseases	Associate	15944448
Keratosis Actinic	Stimulate	32483193
Myopia	Associate	20309403
Neoplasm Metastasis	Stimulate	32483193
Neoplasms	Associate	31926109, 32483193
Night Blindness	Associate	20309403
Pancreatic Neoplasms	Associate	35260078
Refsum Disease Infantile	Associate	27898983
Retinal Degeneration	Associate	17517693
Retinal Diseases	Associate	39795970
Retinal Dystrophies	Associate	39596324
Retinitis Pigmentosa	Associate	15944448, 16799052, 17517693, 17932117, 20309403, 23049240, 23559859, 23950152, 27886254, 35138024, 35814500
Retinitis Pigmentosa 18	Associate	17932117
Stomach Neoplasms	Associate	26840027

PRPF3 (pre-mRNA processing factor 3)