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	26121
Gene name	Pre-mRNA processing factor 31
Gene symbol	PRPF31
Synonyms (NCBI Gene)	NY-BR-99PRP31RP11SNRNP61
Chromosome	19
Chromosome location	19q13.42
Summary	This gene encodes a component of the spliceosome complex and is one of several retinitis pigmentosa-causing genes. When the gene product is added to the spliceosome complex, activation occurs.[provided by RefSeq, Jan 2009]

Show/Hide all (53)

SNP ID	Visualize variation	Clinical significance	Consequence
rs119475042	G>A,C	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs119475043	C>A,T	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs144738703	C>A,G,T	Likely-pathogenic, pathogenic	Non coding transcript variant, synonymous variant, stop gained, coding sequence variant
rs527236094	G>A,T	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant, missense variant
rs527236095	A>T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs587776589	GGAAGCAGGCC>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs587776590	A>G	Pathogenic	Intron variant
rs587776591	C>G	Pathogenic	Intron variant
rs727504107	C>T	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs764232082	C>A,T	Pathogenic	Synonymous variant, coding sequence variant, non coding transcript variant, stop gained
rs794727001	G>A	Pathogenic	Splice donor variant
rs868538598	C>T	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs869312187	C>A,T	Likely-pathogenic, pathogenic	Stop gained, missense variant, coding sequence variant, non coding transcript variant
rs878853331	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs878853334	C>T	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs878853335	G>T	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs886041773	G>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1057517982	G>T	Pathogenic	Splice donor variant
rs1057520752	G>A,T	Pathogenic, likely-pathogenic	Splice donor variant
rs1064797250	->A	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1184467860	G>C,T	Pathogenic	Non coding transcript variant, stop gained, missense variant, coding sequence variant
rs1389305246	C>G,T	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, missense variant
rs1439576531	G>A,T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant, stop gained
rs1555791188	A>T	Likely-pathogenic	Non coding transcript variant, missense variant, initiator codon variant
rs1555792415	A>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1555792879	GC>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1555793170	GGGCCCAGCG>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1555793207	->GTGC	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1555793828	G>-	Pathogenic, likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1555794201	G>T	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1555794205	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1555794302	C>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1555794509	AGGCCTCAGCCGGGCCGAGTGGGTACCGGAGCAGGTGCCCGTGGGACCGGCCGGCTGGTGACCGCTGGGCTTCGGGCTGGTGGAGGGGGTGCCTCGGTGGCTGGAGGGCAGGGCCTGGTCGCTGAACTGCAGGGCGCCTCCTCTCCCCCCTAGATCGAGGAGGACGCCTACCAGGAGGACCTGGGATTCAGCCTGGGCCACCT>-	Likely-pathogenic	Intron variant, coding sequence variant, non coding transcript variant, splice acceptor variant
rs1568600184	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs1600324262	G>A	Likely-pathogenic	Initiator codon variant, non coding transcript variant, missense variant
rs1600324442	CAGC>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1600334904	A>G	Likely-pathogenic	Splice acceptor variant
rs1600335148	->C	Likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1600335289	G>A	Pathogenic	Splice donor variant
rs1600337143	ATAAGTTCATCC>-	Pathogenic	Inframe deletion, coding sequence variant, non coding transcript variant
rs1600337158	A>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1600340117	A>G	Likely-pathogenic	Splice acceptor variant
rs1600341902	TAT>-	Likely-pathogenic	Inframe deletion, coding sequence variant, non coding transcript variant
rs1600341931	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1600342032	A>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1600342050	G>A	Pathogenic	Splice donor variant
rs1600344451	->A	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1600350656	G>A	Pathogenic	Splice acceptor variant, non coding transcript variant
rs1600355373	A>T	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs1600355502	G>-	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1600356790	GATCCGGA>-	Likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1600360338	->G	Likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs1600360654	G>-	Likely-pathogenic	Stop gained, coding sequence variant, non coding transcript variant

Show/Hide all (7)

miRTarBase ID	miRNA	Experiments	Reference
MIRT041831	hsa-miR-484	CLASH	23622248
MIRT041299	hsa-miR-193b-3p	CLASH	23622248
MIRT2432283	hsa-miR-3657	CLIP-seq
MIRT2432284	hsa-miR-4276	CLIP-seq
MIRT2432285	hsa-miR-4535	CLIP-seq
MIRT2432286	hsa-miR-4669	CLIP-seq
MIRT2432287	hsa-miR-492	CLIP-seq

Show/Hide all (47)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000244	Process	Spliceosomal tri-snRNP complex assembly	IDA	11867543
GO:0000244	Process	Spliceosomal tri-snRNP complex assembly	IDA	20118938
GO:0000244	Process	Spliceosomal tri-snRNP complex assembly	IEA
GO:0000244	Process	Spliceosomal tri-snRNP complex assembly	IMP	15257298
GO:0000398	Process	MRNA splicing, via spliceosome	IBA
GO:0000398	Process	MRNA splicing, via spliceosome	IC	15257298
GO:0000398	Process	MRNA splicing, via spliceosome	IDA	11867543
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	30975767
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	16723661, 21385873, 22365833, 23793891, 25416956, 25910212, 27107012, 31515488, 32296183, 32814053, 33961781
GO:0005634	Component	Nucleus	IDA	26912367, 28781166
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	30975767
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005681	Component	Spliceosomal complex	IEA
GO:0005681	Component	Spliceosomal complex	IPI	30975767
GO:0005684	Component	U2-type spliceosomal complex	IC	17412961
GO:0005687	Component	U4 snRNP	IBA
GO:0005687	Component	U4 snRNP	IDA	17412961
GO:0005690	Component	U4atac snRNP	IDA	21784869
GO:0005690	Component	U4atac snRNP	TAS	17412961
GO:0006397	Process	MRNA processing	IEA
GO:0008380	Process	RNA splicing	IEA
GO:0015030	Component	Cajal body	IDA	11867543
GO:0015030	Component	Cajal body	IEA
GO:0016607	Component	Nuclear speck	IDA	11867543
GO:0016607	Component	Nuclear speck	IEA
GO:0030621	Function	U4 snRNA binding	IDA	16857676
GO:0030622	Function	U4atac snRNA binding	IDA	16857676, 21784869
GO:0030674	Function	Protein-macromolecule adaptor activity	IDA	20118938
GO:0042802	Function	Identical protein binding	IPI	32296183
GO:0043021	Function	Ribonucleoprotein complex binding	IDA	11867543
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IDA	11867543, 23793891, 26912367
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IEA
GO:0046540	Component	U4/U6 x U5 tri-snRNP complex	IPI	30975767
GO:0048254	Process	SnoRNA localization	IMP	17636026
GO:0070990	Function	SnRNP binding	IPI	17412961
GO:0071005	Component	U2-type precatalytic spliceosome	IDA	28781166
GO:0071011	Component	Precatalytic spliceosome	IBA
GO:0071166	Process	Ribonucleoprotein complex localization	IMP	17636026
GO:0071339	Component	MLL1 complex	IDA	15960975
GO:0097526	Component	Spliceosomal tri-snRNP complex	IBA
GO:1990904	Component	Ribonucleoprotein complex	IEA

MIM	HGNC	e!Ensembl
606419	15446	ENSG00000105618

Q8WWY3

Protein name

U4/U6 small nuclear ribonucleoprotein Prp31 (Pre-mRNA-processing factor 31) (Serologically defined breast cancer antigen NY-BR-99) (U4/U6 snRNP 61 kDa protein) (Protein 61K) (hPrp31)

Protein function

Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11867543, PubMed:20118938, PubMed:28781166). Required for the assembly of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome (PubMed:11867543). {ECO

PDB

2OZB , 3JCR , 3SIU , 3SIV , 5O9Z , 6AH0 , 6AHD , 6QW6 , 6QX9 , 8H6E , 8H6J , 8H6K , 8H6L , 8Q7N , 8QO9 , 8QOZ , 8QP8 , 8QP9 , 8QPA , 8QPB , 8QPE , 8QPK , 8QXD , 8QZS , 8R08 , 8R09 , 8R0A , 8R0B , 8RM5 , 8Y6O

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01798	Nop	99 → 330	snoRNA binding domain, fibrillarin	Family
PF09785	Prp31_C	337 → 465	Prp31 C terminal domain	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitously expressed. {ECO:0000269|PubMed:11545739}.

Sequence

MSLADELLADLEEAAEEEEGGSYGEEEEEPAIEDVQEETQLDLSGDSVKTIAKLWDSKMF
AEIMMKIEEYISKQAKASEVMGPVEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSK
RFPELESLVPNALDYIRTVKELGNSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLS
EEELERLEEACDMALELNASKHRIYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTN
LSKMPACNIMLLGAQRKTLSGFSSTSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCT
LAARVDSFHESTEGKVGYELKDEIERKFDKWQEPPPVKQVKPLPAPLDGQRKKRGGRRYR
KMKERLGLTEIRKQANRMSFGEIEEDAYQEDLGFSLGHLGKSGSGRVRQTQVNEATKARI
SKTLQRTLQKQSVVYGGKSTIRDRSSGTASSVAFTPLQGLEIVNPQAAEKKVAEANQKYF
SSMAEFLKVKGEKSGLMST

Sequence length

499

Interactions

View interactions

	KEGG		Reactome
	Spliceosome		mRNA Splicing - Major Pathway

362

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
PRPF31-related disorder	Pathogenic; Likely pathogenic	rs1555792415, rs2516206637, rs868538598, rs2073926924	RCV004731213 RCV003916550 RCV004757175 RCV003906174
Retinal dystrophy	Likely pathogenic; Pathogenic	rs2146418999, rs2146445865, rs1555792415, rs2146413215, rs2146420160, rs779270349, rs794727001, rs587776590, rs2516077994, rs869312187, rs878853331, rs878853335, rs878853334, rs868538598, rs2516206256 View all (36 more)	RCV004815500 RCV004815566 RCV004816819 RCV003888348 RCV004816825 RCV004817225 RCV001074798 RCV001073395 RCV004817129 RCV000210312 RCV000225511 RCV000225424 RCV000225503 RCV000225648 RCV004818396 RCV003889347 RCV003890376 RCV003890377 RCV003890378 RCV003890385 RCV003890387 RCV003890388 RCV003890391 RCV004818462 RCV001075617 RCV000504670 RCV004818010 RCV001075718 RCV004818122 RCV004818149 RCV004818150 RCV001074667 RCV001075682 RCV001073888 RCV001074826 RCV001073856 RCV001075077 RCV001073229 RCV001073552 RCV001073228 RCV001074712 RCV001073622 RCV001074599 RCV001074012 RCV001075755 RCV001073823 RCV001074471 RCV001074296 RCV001073949 RCV001073925 RCV001074295 RCV001075636 RCV001075047 RCV001073298 RCV004813750 RCV004814056
Retinitis pigmentosa	Likely pathogenic; Pathogenic	rs2146420485, rs2146445593, rs527236094, rs144738703, rs527236095, rs868538598, rs886041773, rs1555791188, rs1555793207, rs1555794302, rs1555794509, rs1555792879, rs1555794205, rs1600341902, rs1600341931 View all (32 more)	RCV001724807 RCV001724809 RCV000132673 RCV000132674 RCV000132675 RCV001723811 RCV001723870 RCV000505066 RCV000504828 RCV000504840 RCV000504852 RCV001199739 RCV000991057 RCV000787655 RCV000787656 RCV000787658 RCV000787659 RCV000787652 RCV000787653 RCV000787654 RCV000787657 RCV000991048 RCV000991049 RCV000991050 RCV000991054 RCV000991055 RCV000991056 RCV000991310 RCV001199735 RCV001003130 RCV001003132 RCV001003131 RCV001199740 RCV001199511 RCV001199734 RCV001199512 RCV001199736 RCV001199738 RCV001199509 RCV001199510 RCV001199513 RCV001199514 RCV001199731 RCV001199732 RCV001724240 RCV001724229 RCV001249885
Retinitis pigmentosa 11	Likely pathogenic; Pathogenic	rs2146392668, rs2146393019, rs2146394271, rs2146418999, rs2146420554, rs2146421305, rs2146450161, rs2146450721, rs2146393245, rs2146453060, rs2146380786, rs2146409568, rs2146420160, rs2146436400, rs2146437002 View all (27 more)	RCV001376476 RCV001376223 RCV001376355 RCV001376265 RCV001376222 RCV001376353 RCV001376224 RCV001376423 RCV001526734 RCV001542615 RCV001591825 RCV001809203 RCV002295356 RCV005253906 RCV002246221 RCV002250266 RCV005254698 RCV000004606 RCV000004607 RCV000004608 RCV000004610 RCV000004612 RCV000004613 RCV000004614 RCV001542614 RCV003224916 RCV003448825 RCV004566468 RCV004555473 RCV005870642 RCV001376220 RCV000678604 RCV005253120 RCV005863324 RCV001029844 RCV002497486 RCV004796363 RCV001376221 RCV002497488 RCV002471034 RCV005866803 RCV005253718 RCV001197522 RCV001280917
See cases	Pathogenic	rs1057517982	RCV003231471

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Hepatocellular carcinoma	Likely benign	rs776690225	RCV005924062
Leber congenital amaurosis	Uncertain significance	rs1600361737	RCV000787864
Ovarian serous cystadenocarcinoma	Likely benign	rs587594853	RCV005894839
Retinal disorder	Conflicting classifications of pathogenicity	rs759589041	RCV006254157
Retinitis Pigmentosa, Dominant	Uncertain significance; Conflicting classifications of pathogenicity; Likely benign	rs587674748, rs45619231, rs75629461, rs587601857, rs587763567, rs17526361, rs117225554	RCV000268343 RCV000302480 RCV000360744 RCV000359738 RCV000340511 RCV000272031 RCV000390160

Show/Hide Text Mining Associations (26)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alopecia Areata	Associate	33525114
Blindness	Associate	23144630, 26781568
Chromosome 21 monosomy	Associate	23031812
Cluster Headache	Associate	34180076
Cone Rod Dystrophies	Associate	40220513
Diabetes Mellitus Type 2	Associate	29650774
Hypertensive Retinopathy	Associate	34680937
Monosomy	Associate	21791309
Neoplasms	Associate	20111712
Night Blindness	Associate	30030392
Osteosarcoma	Associate	31146489
Ovarian Neoplasms	Associate	20111712, 26152742
Pancreatic Neoplasms	Associate	31917448, 34238114
Paraneoplastic Syndromes Ocular	Associate	34198599
Refsum Disease Infantile	Associate	27898983, 36811936
Retinal Degeneration	Associate	18317597, 27212874
Retinal Diseases	Associate	32423767, 36524988, 36811936, 38184646
Retinal Dystrophies	Associate	26197217, 27391102, 36084042
Retinitis	Associate	12923864
Retinitis Pigmentosa	Associate	11867543, 12923864, 15162096, 16636657, 16799052, 16917484, 17003455, 18177735, 18317597, 18431455, 18552984, 19050727, 19584904, 19618371, 20238024 View all (36 more)
Retinitis Pigmentosa 11	Associate	30611018, 34680937, 36833363, 40220513
Retinoschisis	Associate	33851411
Schizophrenia	Associate	33046718
Squamous Cell Carcinoma of Head and Neck	Associate	31815689
Venous Thromboembolism	Associate	31420334
Vision Disorders	Associate	23288994

PRPF31 (pre-mRNA processing factor 31)