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

Gene Gene information from NCBI Gene database. Gene SNPs Other IDs Associated diseases
Entrez ID	5631
Gene name	Phosphoribosyl pyrophosphate synthetase 1
Gene symbol	PRPS1
Synonyms (NCBI Gene)	ARTSCMTX5DFN2DFNX1PPRibPPRS-IPRSI
Chromosome	X
Chromosome location	Xq22.3
Summary	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

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

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)

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Arts syndrome	Likely pathogenic; Pathogenic	rs2147681381, rs869025593, rs879253919, rs137852540, rs137852541, rs80338675, rs398122855, rs1556300621, rs1556299881	RCV004556094 RCV000208743 RCV005409639 RCV001328985 RCV003147280 View all (4 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Charcot-Marie-Tooth disease X-linked recessive 5	Pathogenic; Likely pathogenic	rs587777150, rs587781262, rs587781263, rs2521349816, rs869025594, rs879253919, rs80338731, rs80338732	RCV000087131 RCV000143859 RCV000143860 RCV002291147 RCV000208733 RCV005409639 RCV000010612 RCV000010613 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Charcot-Marie-Tooth Neuropathy X	Pathogenic; Likely pathogenic	rs2147681484, rs2147684810, rs2521342044, rs2521345872, rs879253919, rs80338732, rs2521342152, rs1556300610, rs1556300621	RCV001866068 RCV001941661 RCV002828153 RCV003053906 RCV001319152 View all (4 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hearing loss	Likely pathogenic; Pathogenic	rs1556300621, rs867288458	RCV000590916 RCV000590950	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hearing loss, X-linked 1	Pathogenic; Likely pathogenic	rs587781261, rs587781262, rs869025593, rs180177151, rs180177154, rs180177153, rs2521345889	RCV000143857 RCV000143858 RCV000208721 RCV000010616 RCV000010618 RCV000010619 RCV003991165 View all (2 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Phosphoribosylpyrophosphate synthetase superactivity	Likely pathogenic; Pathogenic	rs137852540, rs137852541, rs1556300621, rs768454424	RCV000010606 RCV000010607 RCV001196872 RCV000995614	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PRPS1-related disorder	Likely pathogenic; Pathogenic	rs180177154	RCV004757102	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Retinal dystrophy	Likely pathogenic; Pathogenic	rs1556297584, rs1556300610, rs1556300621, rs867288458, rs1925733148	RCV000590944 RCV000590871 RCV001075877 RCV000590950 RCV001075223	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (29)

Phenotype Name	Clinical Significance	Source	Evidence Score
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.
ARTHRITIS, GOUTY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ATAXIA, FATAL X-LINKED, WITH DEAFNESS AND LOSS OF VISION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHARCOT-MARIE-TOOTH DISEASE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CHARCOT-MARIE-TOOTH DISEASE, X-LINKED RECESSIVE, 5	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Charcot-Marie-Tooth, X-linked	Likely benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, X-LINKED 1	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEJERINE-SOTTAS DISEASE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY MOTOR AND SENSORY NEUROPATHIES	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY MOTOR AND SENSORY NEUROPATHY, TYPES I-IV	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
History of neurodevelopmental disorder	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPERTROPHIC NEUROPATHY OF INFANCY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MILD PHOSPHORIBOSYLPYROPHOSPHATE SYNTHETASE SUPERACTIVITY	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MILD PRPP SYNTHETASE SUPERACTIVITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nephrolithiasis/nephrocalcinosis	Conflicting classifications of pathogenicity; Uncertain significance; Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OPTIC ATROPHY POLYNEUROPATHY DEAFNESS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PERONEAL MUSCULAR ATROPHY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRPS1 deficiency disorder	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ROUSSY-LEVY SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance; no classifications from unflagged records	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED CHARCOT-MARIE-TOOTH DISEASE TYPE 5	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED INTELLECTUAL DISABILITY, LIMB SPASTICITY, RETINAL DYSTROPHY, ARGININE VASOPRESSIN DEFICIENCY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED INTELLECTUAL DISABILITY-LIMB SPASTICITY-RETINAL DYSTROPHY-ARGININE VASOPRESSIN DEFICIENCY	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED INTELLECTUAL DISABILITY-LIMB SPASTICITY-RETINAL DYSTROPHY-DIABETES INSIPIDUS SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED ISOLATED SENSORINEURAL HEARING LOSS TYPE DFN	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-linked nonsyndromic hearing loss	Likely benign; Uncertain significance	ClinVar GWAS catalog	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)

PRPS1 (phosphoribosyl pyrophosphate synthetase 1)