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.	5631
Gene name Gene Name - the full gene name approved by the HGNC.	Phosphoribosyl pyrophosphate synthetase 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PRPS1
Synonyms (NCBI Gene) Gene synonyms aliases	ARTS, CMTX5, DFN2, DFNX1, PPRibP, PRS-I, PRSI
Chromosome Chromosome number	X
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	Xq22.3
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes an enzyme that catalyzes the phosphoribosylation of ribose 5-phosphate to 5-phosphoribosyl-1-pyrophosphate, which is necessary for purine metabolism and nucleotide biosynthesis. Defects in this gene are a cause of phosphoribosylpyrophosp

Show/Hide all(30)

SNP ID	Visualize variation	Clinical significance	Consequence
rs80338675	A>C	Pathogenic	Coding sequence variant, intron variant, missense variant
rs80338676	T>C	Pathogenic, uncertain-significance	Coding sequence variant, intron variant, missense variant
rs80338731	A>C	Pathogenic	Coding sequence variant, intron variant, missense variant
rs80338732	T>C	Pathogenic, likely-pathogenic	Coding sequence variant, intron variant, missense variant
rs137852540	A>G	Pathogenic, likely-pathogenic	Coding sequence variant, intron variant, missense variant
rs137852541	G>C	Pathogenic	Coding sequence variant, 5 prime UTR variant, missense variant
rs137852542	G>C	Pathogenic	Coding sequence variant, intron variant, missense variant
rs137852543	C>A	Pathogenic	Coding sequence variant, intron variant, missense variant
rs137852544	C>T	Pathogenic	Coding sequence variant, 5 prime UTR variant, missense variant
rs137852545	C>G	Pathogenic	Coding sequence variant, 5 prime UTR variant, missense variant
rs180177151	G>A	Pathogenic	Intron variant, missense variant, coding sequence variant
rs180177152	G>A	Pathogenic	Intron variant, missense variant, coding sequence variant
rs180177153	T>C	Pathogenic	Missense variant, coding sequence variant
rs180177154	G>A	Pathogenic	Missense variant, coding sequence variant
rs398122855	G>C	Pathogenic	Missense variant, intron variant, coding sequence variant
rs587777150	C>G	Pathogenic	Missense variant, intron variant, coding sequence variant
rs587781261	G>T	Pathogenic	Missense variant, intron variant, coding sequence variant
rs587781262	A>G	Pathogenic	Missense variant, intron variant, coding sequence variant
rs587781263	G>T	Pathogenic	Missense variant, coding sequence variant
rs768454424	T>C,G	Likely-pathogenic	Intron variant, coding sequence variant, synonymous variant, missense variant
rs867288458	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs869025593	A>C	Pathogenic	Missense variant, coding sequence variant
rs869025594	T>C	Pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant
rs879253970	G>A	Likely-pathogenic	Intron variant, missense variant, coding sequence variant
rs1556297584	C>T	Likely-pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant
rs1556299881	A>G	Pathogenic	Intron variant, splice acceptor variant
rs1556300610	C>T	Likely-pathogenic	Missense variant, 5 prime UTR variant, coding sequence variant
rs1556300621	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs1602893221	G>C	Likely-pathogenic	Coding sequence variant, 5 prime UTR variant, missense variant
rs1602901832	G>T	Likely-pathogenic	Coding sequence variant, missense variant, intron variant

Show/Hide all(79)

miRTarBase ID	miRNA	Experiments	Reference
MIRT001856	hsa-miR-376a-5p	Luciferase reporter assay	17322061
MIRT001856	hsa-miR-376a-5p	Luciferase reporter assay	17322061
MIRT022908	hsa-miR-124-3p	Microarray	18668037
MIRT032397	hsa-let-7b-5p	Proteomics	18668040
MIRT046478	hsa-miR-15b-5p	CLASH	23622248
MIRT042233	hsa-miR-484	CLASH	23622248
MIRT1265988	hsa-miR-3668	CLIP-seq
MIRT1265989	hsa-miR-1238	CLIP-seq
MIRT1265990	hsa-miR-124	CLIP-seq
MIRT1265991	hsa-miR-1283	CLIP-seq
MIRT1265992	hsa-miR-216a	CLIP-seq
MIRT1265993	hsa-miR-3671	CLIP-seq
MIRT1265994	hsa-miR-376c	CLIP-seq
MIRT1265995	hsa-miR-3908	CLIP-seq
MIRT1265996	hsa-miR-3942-5p	CLIP-seq
MIRT1265997	hsa-miR-4261	CLIP-seq
MIRT1265998	hsa-miR-4264	CLIP-seq
MIRT1265999	hsa-miR-4275	CLIP-seq
MIRT1266000	hsa-miR-4277	CLIP-seq
MIRT1266001	hsa-miR-4690-5p	CLIP-seq
MIRT1266002	hsa-miR-4703-5p	CLIP-seq
MIRT1266003	hsa-miR-4766-3p	CLIP-seq
MIRT1266004	hsa-miR-4797-3p	CLIP-seq
MIRT1266005	hsa-miR-506	CLIP-seq
MIRT1266006	hsa-miR-548aa	CLIP-seq
MIRT1266007	hsa-miR-548an	CLIP-seq
MIRT1266008	hsa-miR-579	CLIP-seq
MIRT2078177	hsa-miR-1206	CLIP-seq
MIRT2078178	hsa-miR-1290	CLIP-seq
MIRT2078179	hsa-miR-2355-5p	CLIP-seq
MIRT2078180	hsa-miR-3160-5p	CLIP-seq
MIRT2078181	hsa-miR-3165	CLIP-seq
MIRT2078182	hsa-miR-3167	CLIP-seq
MIRT2078183	hsa-miR-3180-5p	CLIP-seq
MIRT2078184	hsa-miR-342-5p	CLIP-seq
MIRT1265997	hsa-miR-4261	CLIP-seq
MIRT2078185	hsa-miR-4651	CLIP-seq
MIRT2078186	hsa-miR-4664-5p	CLIP-seq
MIRT2078187	hsa-miR-520a-5p	CLIP-seq
MIRT2078188	hsa-miR-525-5p	CLIP-seq
MIRT1266006	hsa-miR-548aa	CLIP-seq
MIRT1266008	hsa-miR-579	CLIP-seq
MIRT2078189	hsa-miR-608	CLIP-seq
MIRT2078190	hsa-miR-876-5p	CLIP-seq
MIRT2304638	hsa-miR-150	CLIP-seq
MIRT1265992	hsa-miR-216a	CLIP-seq
MIRT2304639	hsa-miR-221	CLIP-seq
MIRT2304640	hsa-miR-222	CLIP-seq
MIRT2304641	hsa-miR-3134	CLIP-seq
MIRT2304642	hsa-miR-3155	CLIP-seq
MIRT2304643	hsa-miR-3155b	CLIP-seq
MIRT2078180	hsa-miR-3160-5p	CLIP-seq
MIRT2078183	hsa-miR-3180-5p	CLIP-seq
MIRT2304644	hsa-miR-320a	CLIP-seq
MIRT2304645	hsa-miR-320b	CLIP-seq
MIRT2304646	hsa-miR-320c	CLIP-seq
MIRT2304647	hsa-miR-320d	CLIP-seq
MIRT2304648	hsa-miR-329	CLIP-seq
MIRT2304649	hsa-miR-362-3p	CLIP-seq
MIRT1265993	hsa-miR-3671	CLIP-seq
MIRT1265994	hsa-miR-376c	CLIP-seq
MIRT2304650	hsa-miR-377	CLIP-seq
MIRT2304651	hsa-miR-3926	CLIP-seq
MIRT2304652	hsa-miR-3941	CLIP-seq
MIRT1265997	hsa-miR-4261	CLIP-seq
MIRT1266000	hsa-miR-4277	CLIP-seq
MIRT2304653	hsa-miR-4429	CLIP-seq
MIRT2304654	hsa-miR-4534	CLIP-seq
MIRT2304655	hsa-miR-4691-5p	CLIP-seq
MIRT2304656	hsa-miR-4772-5p	CLIP-seq
MIRT2304657	hsa-miR-4778-3p	CLIP-seq
MIRT2078187	hsa-miR-520a-5p	CLIP-seq
MIRT2304658	hsa-miR-520d-5p	CLIP-seq
MIRT2304659	hsa-miR-524-5p	CLIP-seq
MIRT2078188	hsa-miR-525-5p	CLIP-seq
MIRT1266006	hsa-miR-548aa	CLIP-seq
MIRT1266008	hsa-miR-579	CLIP-seq
MIRT2304660	hsa-miR-603	CLIP-seq
MIRT1266006	hsa-miR-548aa	CLIP-seq

Show/Hide all(29)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000287	Function	Magnesium ion binding	IEA
GO:0002189	Component	Ribose phosphate diphosphokinase complex	IBA
GO:0004749	Function	Ribose phosphate diphosphokinase activity	IBA
GO:0004749	Function	Ribose phosphate diphosphokinase activity	IDA	16939420, 17701900
GO:0004749	Function	Ribose phosphate diphosphokinase activity	IEA
GO:0004749	Function	Ribose phosphate diphosphokinase activity	IMP	12847698, 17701896
GO:0005515	Function	Protein binding	IPI	16189514, 25416956, 25910212, 26496610, 27088854, 28514442, 29892012, 31515488, 32296183, 32814053, 33961781
GO:0005524	Function	ATP binding	IDA	16939420
GO:0005524	Function	ATP binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005829	Component	Cytosol	TAS
GO:0006015	Process	5-phosphoribose 1-diphosphate biosynthetic process	IBA
GO:0006015	Process	5-phosphoribose 1-diphosphate biosynthetic process	IEA
GO:0006139	Process	Nucleobase-containing compound metabolic process	IEA
GO:0006144	Process	Purine nucleobase metabolic process	IMP	8253776
GO:0006164	Process	Purine nucleotide biosynthetic process	IBA
GO:0006164	Process	Purine nucleotide biosynthetic process	IMP	12847698
GO:0006221	Process	Pyrimidine nucleotide biosynthetic process	NAS	17701896
GO:0007399	Process	Nervous system development	IMP	8253776, 17701900
GO:0009156	Process	Ribonucleoside monophosphate biosynthetic process	IEA
GO:0009165	Process	Nucleotide biosynthetic process	IEA
GO:0016301	Function	Kinase activity	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0034418	Process	Urate biosynthetic process	IMP	12847698
GO:0042802	Function	Identical protein binding	IPI	16189514, 25416956, 25502805, 25910212, 31515488, 32296183
GO:0042803	Function	Protein homodimerization activity	IPI	16939420
GO:0046101	Process	Hypoxanthine biosynthetic process	IMP	17701896
GO:0046872	Function	Metal ion binding	IEA

MIM	HGNC	e!Ensembl
311850	9462	ENSG00000147224

Protein

UniProt ID

P60891

Protein name

Ribose-phosphate pyrophosphokinase 1 (EC 2.7.6.1) (PPRibP) (Phosphoribosyl pyrophosphate synthase I) (PRS-I)

Protein function

Catalyzes the synthesis of phosphoribosylpyrophosphate (PRPP) that is essential for nucleotide synthesis.

PDB

2H06 , 2H07 , 2H08 , 2HCR , 3EFH , 3S5J , 4F8E , 4LYG , 4LZN , 4LZO , 4M0P , 4M0U , 8DBC , 8DBD , 8DBE , 8DBF , 8DBG , 8DBH , 8DBI , 8DBJ , 8DBK , 8DBL , 8DBM , 8DBN , 8DBO

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13793	Pribosyltran_N	4 → 120	N-terminal domain of ribose phosphate pyrophosphokinase	Domain
PF14572	Pribosyl_synth	198 → 314	Phosphoribosyl synthetase-associated domain	Domain

Sequence

MPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGC
GEINDNLMELLIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAG
ADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTS
IADRLNVDFALIHKERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAG
ATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISMILAEAI
RRTHNGESVSYLFSHVPL

Sequence length

318

Interactions

View interactions

	KEGG		Reactome
	Pentose phosphate pathway Purine metabolism Metabolic pathways Carbon metabolism Biosynthesis of amino acids		5-Phosphoribose 1-diphosphate biosynthesis

Show/Hide Causal Diseases (6)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
arts syndrome	Arts syndrome	rs398122855, rs137852540, rs1556300621, rs137852541, rs1556299881, rs80338675, rs869025593	N/A
Charcot-Marie-Tooth disease	Charcot-Marie-Tooth Neuropathy X	rs879253919, rs1556300610, rs1556300621, rs80338732	N/A
Hearing Loss	Hearing loss, X-linked 1	rs180177151, rs180177154, rs180177153, rs587781261, rs587781262, rs869025593	N/A
Phosphoribosylpyrophosphate Synthetase Superactivity	phosphoribosylpyrophosphate synthetase superactivity	rs137852540, rs137852541, rs1556300621, rs768454424	N/A
Charcot-Marie-Tooth Disease, X-Linked	Charcot-Marie-Tooth disease X-linked recessive 5	rs869025594, rs587777150, rs80338731, rs587781262, rs80338732, rs587781263	N/A
retinal dystrophy	Retinal dystrophy	rs1925733148, rs1556297584, rs1556300610, rs1556300621	N/A

Show/Hide Unknown Diseases (1)

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.
Nephronophthisis	Nephrolithiasis/nephrocalcinosis	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (47)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Arts syndrome	Associate	17701896, 24961627, 25182139, 25491489, 34803094, 37308732
Ataxia	Associate	31443513
Burkitt Lymphoma	Associate	32391636
Carbamoyl Phosphate Synthase I Deficiency Disease	Associate	25491489
Carcinogenesis	Associate	37308732, 40028213
Carcinoma Hepatocellular	Associate	27088854
Charcot Marie Tooth Disease	Associate	31338985
Charcot Marie Tooth disease Type 2B	Associate	17701900
Charcot Marie Tooth disease X linked 1	Associate	25491489
Chondrocalcinosis 2	Associate	34803094
Deafness	Associate	25182139
Deafness X Linked 1	Associate	24961627, 25182139, 25491489, 34803094
Fetal Growth Retardation	Associate	24961627
Gout	Associate	30423175
Hearing Disorders	Associate	39684270
Hearing Loss	Associate	17701900, 25182139, 25491489, 31338985, 31443513, 34021019
Hearing Loss Noise Induced	Associate	25484013
Hearing Loss Sensorineural	Associate	17701900, 27886419, 29986705, 31338985
Hypertensive Retinopathy	Associate	25491489
Inherited Peripheral Neuropathy	Associate	17701900
Lesch Nyhan Syndrome	Stimulate	6423640
Leukemia Biphenotypic Acute	Associate	25962120
Lung Neoplasms	Associate	37308732
Melanoma	Stimulate	36203561
Muscle Hypotonia	Associate	31443513
Muscle Spasticity	Associate	24961627
Neoplasm Metastasis	Associate	36203561
Neoplasms	Associate	28811348, 31443513
Neoplastic Syndromes Hereditary	Associate	17701900, 39272213
Nervous System Diseases	Associate	25491489
Neuroblastoma	Associate	31443513
Nonsyndromic sensorineural hearing loss	Associate	25182139
Optic Atrophy	Associate	25491489, 31338985
Optic atrophy polyneuropathy deafness	Associate	17701900, 24961627, 25182139, 25491489, 31338985, 34803094
Optic Nerve Diseases	Associate	17701900, 31338985
Peripheral Nervous System Diseases	Associate	17701900, 25182139
Phosphoribosylpyrophosphate synthetase deficiency	Associate	10066814, 12847698
Phosphoribosylpyrophosphate Synthetase Superactivity	Associate	24961627
Polyneuropathies	Associate	31338985
Precursor T Cell Lymphoblastic Leukemia Lymphoma	Associate	34636169
Progressive hearing loss stapes fixation	Associate	25182139, 32795431
Retinal Diseases	Associate	34021019
Retinal Dystrophies	Associate	24961627
Retinitis Pigmentosa	Associate	25491489, 32795431
Tetra amelia with ectodermal dysplasia and lacrimal duct abnormalities	Associate	31697823
Vision Disorders	Associate	17701900
Voice Disorders	Associate	17701900

PRPS1 (phosphoribosyl pyrophosphate synthetase 1)