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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	26121
Gene name Gene Name - the full gene name approved by the HGNC.	Pre-mRNA processing factor 31
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PRPF31
Synonyms (NCBI Gene) Gene synonyms aliases	NY-BR-99, PRP31, RP11, SNRNP61
Chromosome Chromosome number	19
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	19q13.42
Summary Summary of gene provided in NCBI Entrez Gene.	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

Protein

UniProt ID

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

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
retinal dystrophy	Retinal dystrophy	rs869312187, rs2073855020, rs2073970450, rs2073873693, rs2074043162, rs2073971858, rs587776590, rs878853331, rs2073875313, rs764232082, rs2073798309, rs878853335, rs2073876392, rs2073701307, rs1600340117 View all (19 more)	N/A
Retinitis Pigmentosa	retinitis pigmentosa, retinitis pigmentosa 11	rs1600337158, rs2073702243, rs1555793207, rs587776590, rs2073970897, rs1600360338, rs869312187, rs764232082, rs2073704298, rs1555794302, rs2073971805, rs1600360654, rs2073708638, rs1555794509, rs2073842959 View all (44 more)	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Diabetes	Change in HbA1c levels in response to metformin treatment in type 2 diabetes	N/A	N/A	GWAS
Leber Congenital Amaurosis	leber congenital amaurosis	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (26)

Disease Name	Relationship Type	References
Associations from Text Mining Disease 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)