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	4860
Gene name	Purine nucleoside phosphorylase
Gene symbol	PNP
Synonyms (NCBI Gene)	NPPRO1837PUNP
Chromosome	14
Chromosome location	14q11.2
Summary	This gene encodes an enzyme which reversibly catalyzes the phosphorolysis of purine nucleosides. The enzyme is trimeric, containing three identical subunits. Mutations which result in nucleoside phosphorylase deficiency result in defective T-cell (cell-me

Show/Hide all (12)

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894450	A>G	Pathogenic	Missense variant, coding sequence variant
rs104894451	G>A,C	Likely-pathogenic, pathogenic-likely-pathogenic	Missense variant, coding sequence variant
rs104894452	A>G,T	Pathogenic	Missense variant, coding sequence variant
rs104894453	G>A	Pathogenic	Missense variant, coding sequence variant
rs104894454	G>C,T	Pathogenic	Missense variant, coding sequence variant
rs104894455	C>T	Pathogenic	Stop gained, coding sequence variant
rs104894460	C>T	Pathogenic	Stop gained, coding sequence variant
rs1026474882	G>A,C	Pathogenic-likely-pathogenic	Intron variant
rs1247497521	C>G,T	Uncertain-significance, likely-pathogenic	Missense variant, coding sequence variant
rs1464236744	G>A,T	Likely-pathogenic	Coding sequence variant, stop gained, missense variant
rs1566525400	G>A	Pathogenic	Splice donor variant
rs1594427504	C>T	Likely-pathogenic	Missense variant, coding sequence variant

206

Show/Hide all (206)

miRTarBase ID	miRNA	Experiments	Reference
MIRT003765	hsa-miR-1-3p	Microarray	15685193
MIRT003765	hsa-miR-1-3p	Luciferase reporter assayWestern blot	22068816
MIRT003765	hsa-miR-1-3p	Luciferase reporter assayWestern blot	22068816
MIRT006571	hsa-miR-133a-3p	Luciferase reporter assayWestern blot	22068816
MIRT006571	hsa-miR-133a-3p	Luciferase reporter assayWestern blot	22068816
MIRT021132	hsa-miR-186-5p	Sequencing	20371350
MIRT006571	hsa-miR-133a-3p	Western blot;qRT-PCR;Microarray	21701775
MIRT022705	hsa-miR-124-3p	Microarray	18668037
MIRT003765	hsa-miR-1-3p	Microarray	18668037
MIRT003765	hsa-miR-1-3p	Microarray	15685193
MIRT003765	hsa-miR-1-3p	Proteomics	18668040
MIRT003765	hsa-miR-1-3p	Western blot;qRT-PCR;Microarray	21701775
MIRT026040	hsa-miR-196a-5p	Sequencing	20371350
MIRT031731	hsa-miR-16-5p	Sequencing	20371350
MIRT031731	hsa-miR-16-5p	Proteomics	18668040
MIRT036138	hsa-miR-1296-5p	CLASH	23622248
MIRT1245320	hsa-miR-1	CLIP-seq
MIRT1245321	hsa-miR-1225-3p	CLIP-seq
MIRT1245322	hsa-miR-1228	CLIP-seq
MIRT1245323	hsa-miR-1233	CLIP-seq
MIRT1245324	hsa-miR-124	CLIP-seq
MIRT1245325	hsa-miR-1253	CLIP-seq
MIRT1245326	hsa-miR-1276	CLIP-seq
MIRT1245327	hsa-miR-146a	CLIP-seq
MIRT1245328	hsa-miR-146b-5p	CLIP-seq
MIRT1245329	hsa-miR-15a	CLIP-seq
MIRT1245330	hsa-miR-15b	CLIP-seq
MIRT1245331	hsa-miR-16	CLIP-seq
MIRT1245332	hsa-miR-193a-5p	CLIP-seq
MIRT1245333	hsa-miR-195	CLIP-seq
MIRT1245334	hsa-miR-206	CLIP-seq
MIRT1245335	hsa-miR-221	CLIP-seq
MIRT1245336	hsa-miR-222	CLIP-seq
MIRT1245337	hsa-miR-3126-3p	CLIP-seq
MIRT1245338	hsa-miR-3128	CLIP-seq
MIRT1245339	hsa-miR-3168	CLIP-seq
MIRT1245340	hsa-miR-325	CLIP-seq
MIRT1245341	hsa-miR-338-3p	CLIP-seq
MIRT1245342	hsa-miR-3660	CLIP-seq
MIRT1245343	hsa-miR-3669	CLIP-seq
MIRT1245344	hsa-miR-3674	CLIP-seq
MIRT1245345	hsa-miR-3714	CLIP-seq
MIRT1245346	hsa-miR-371-5p	CLIP-seq
MIRT1245347	hsa-miR-371b-5p	CLIP-seq
MIRT1245348	hsa-miR-3910	CLIP-seq
MIRT1245349	hsa-miR-3926	CLIP-seq
MIRT1245350	hsa-miR-424	CLIP-seq
MIRT1245351	hsa-miR-4256	CLIP-seq
MIRT1245352	hsa-miR-4263	CLIP-seq
MIRT1245353	hsa-miR-4521	CLIP-seq
MIRT1245354	hsa-miR-4524	CLIP-seq
MIRT1245355	hsa-miR-4526	CLIP-seq
MIRT1245356	hsa-miR-4530	CLIP-seq
MIRT1245357	hsa-miR-4709-3p	CLIP-seq
MIRT1245358	hsa-miR-4714-3p	CLIP-seq
MIRT1245359	hsa-miR-4720-5p	CLIP-seq
MIRT1245360	hsa-miR-4749-3p	CLIP-seq
MIRT1245361	hsa-miR-4773	CLIP-seq
MIRT1245362	hsa-miR-4799-3p	CLIP-seq
MIRT1245363	hsa-miR-497	CLIP-seq
MIRT1245364	hsa-miR-503	CLIP-seq
MIRT1245365	hsa-miR-506	CLIP-seq
MIRT1245366	hsa-miR-508-5p	CLIP-seq
MIRT1245367	hsa-miR-518a-5p	CLIP-seq
MIRT1245368	hsa-miR-527	CLIP-seq
MIRT1245369	hsa-miR-544	CLIP-seq
MIRT1245370	hsa-miR-548v	CLIP-seq
MIRT1245371	hsa-miR-580	CLIP-seq
MIRT1245372	hsa-miR-589	CLIP-seq
MIRT1245373	hsa-miR-613	CLIP-seq
MIRT1245374	hsa-miR-646	CLIP-seq
MIRT1245375	hsa-miR-766	CLIP-seq
MIRT1245376	hsa-miR-890	CLIP-seq
MIRT1245342	hsa-miR-3660	CLIP-seq
MIRT1245351	hsa-miR-4256	CLIP-seq
MIRT1245353	hsa-miR-4521	CLIP-seq
MIRT1245355	hsa-miR-4526	CLIP-seq
MIRT1245358	hsa-miR-4714-3p	CLIP-seq
MIRT2072593	hsa-miR-4753-3p	CLIP-seq
MIRT2072594	hsa-miR-4762-5p	CLIP-seq
MIRT2072595	hsa-miR-4768-5p	CLIP-seq
MIRT2072596	hsa-miR-4778-5p	CLIP-seq
MIRT1245366	hsa-miR-508-5p	CLIP-seq
MIRT1245375	hsa-miR-766	CLIP-seq
MIRT1245320	hsa-miR-1	CLIP-seq
MIRT2299692	hsa-miR-122	CLIP-seq
MIRT1245321	hsa-miR-1225-3p	CLIP-seq
MIRT1245323	hsa-miR-1233	CLIP-seq
MIRT2299693	hsa-miR-1285	CLIP-seq
MIRT2299694	hsa-miR-1292	CLIP-seq
MIRT2299695	hsa-miR-147	CLIP-seq
MIRT2299696	hsa-miR-185	CLIP-seq
MIRT1245334	hsa-miR-206	CLIP-seq
MIRT1245335	hsa-miR-221	CLIP-seq
MIRT1245336	hsa-miR-222	CLIP-seq
MIRT2299697	hsa-miR-3133	CLIP-seq
MIRT2299698	hsa-miR-3187-5p	CLIP-seq
MIRT2299699	hsa-miR-3652	CLIP-seq
MIRT1245343	hsa-miR-3669	CLIP-seq
MIRT2299700	hsa-miR-3911	CLIP-seq
MIRT2299701	hsa-miR-3945	CLIP-seq
MIRT2299702	hsa-miR-3975	CLIP-seq
MIRT2299703	hsa-miR-421	CLIP-seq
MIRT2299704	hsa-miR-4253	CLIP-seq
MIRT2299705	hsa-miR-4267	CLIP-seq
MIRT2299706	hsa-miR-4306	CLIP-seq
MIRT2299707	hsa-miR-4430	CLIP-seq
MIRT2299708	hsa-miR-4436b-3p	CLIP-seq
MIRT2299709	hsa-miR-4471	CLIP-seq
MIRT2299710	hsa-miR-4505	CLIP-seq
MIRT1245353	hsa-miR-4521	CLIP-seq
MIRT2299711	hsa-miR-4536	CLIP-seq
MIRT2299712	hsa-miR-4644	CLIP-seq
MIRT2299713	hsa-miR-4709-5p	CLIP-seq
MIRT1245358	hsa-miR-4714-3p	CLIP-seq
MIRT1245360	hsa-miR-4749-3p	CLIP-seq
MIRT2299714	hsa-miR-4760-5p	CLIP-seq
MIRT2299715	hsa-miR-4761-3p	CLIP-seq
MIRT2299716	hsa-miR-505	CLIP-seq
MIRT1245370	hsa-miR-548v	CLIP-seq
MIRT2299717	hsa-miR-564	CLIP-seq
MIRT2299718	hsa-miR-576-3p	CLIP-seq
MIRT2299719	hsa-miR-577	CLIP-seq
MIRT2299720	hsa-miR-581	CLIP-seq
MIRT2299721	hsa-miR-612	CLIP-seq
MIRT1245373	hsa-miR-613	CLIP-seq
MIRT2299722	hsa-miR-644	CLIP-seq
MIRT1245375	hsa-miR-766	CLIP-seq
MIRT2299695	hsa-miR-147	CLIP-seq
MIRT1245329	hsa-miR-15a	CLIP-seq
MIRT1245330	hsa-miR-15b	CLIP-seq
MIRT1245331	hsa-miR-16	CLIP-seq
MIRT1245332	hsa-miR-193a-5p	CLIP-seq
MIRT1245333	hsa-miR-195	CLIP-seq
MIRT2299700	hsa-miR-3911	CLIP-seq
MIRT1245350	hsa-miR-424	CLIP-seq
MIRT2299705	hsa-miR-4267	CLIP-seq
MIRT2392768	hsa-miR-4311	CLIP-seq
MIRT2299708	hsa-miR-4436b-3p	CLIP-seq
MIRT1245354	hsa-miR-4524	CLIP-seq
MIRT2299711	hsa-miR-4536	CLIP-seq
MIRT2299715	hsa-miR-4761-3p	CLIP-seq
MIRT1245363	hsa-miR-497	CLIP-seq
MIRT1245364	hsa-miR-503	CLIP-seq
MIRT2299717	hsa-miR-564	CLIP-seq
MIRT2299720	hsa-miR-581	CLIP-seq
MIRT2299722	hsa-miR-644	CLIP-seq
MIRT1245374	hsa-miR-646	CLIP-seq
MIRT1245375	hsa-miR-766	CLIP-seq
MIRT2392769	hsa-miR-888	CLIP-seq
MIRT1245376	hsa-miR-890	CLIP-seq
MIRT1245320	hsa-miR-1	CLIP-seq
MIRT1245321	hsa-miR-1225-3p	CLIP-seq
MIRT1245322	hsa-miR-1228	CLIP-seq
MIRT1245323	hsa-miR-1233	CLIP-seq
MIRT1245325	hsa-miR-1253	CLIP-seq
MIRT1245326	hsa-miR-1276	CLIP-seq
MIRT2299693	hsa-miR-1285	CLIP-seq
MIRT2596443	hsa-miR-1343	CLIP-seq
MIRT2299695	hsa-miR-147	CLIP-seq
MIRT1245329	hsa-miR-15a	CLIP-seq
MIRT1245330	hsa-miR-15b	CLIP-seq
MIRT1245331	hsa-miR-16	CLIP-seq
MIRT1245333	hsa-miR-195	CLIP-seq
MIRT1245334	hsa-miR-206	CLIP-seq
MIRT1245339	hsa-miR-3168	CLIP-seq
MIRT2299698	hsa-miR-3187-5p	CLIP-seq
MIRT1245340	hsa-miR-325	CLIP-seq
MIRT1245343	hsa-miR-3669	CLIP-seq
MIRT1245346	hsa-miR-371-5p	CLIP-seq
MIRT1245347	hsa-miR-371b-5p	CLIP-seq
MIRT2299700	hsa-miR-3911	CLIP-seq
MIRT2299701	hsa-miR-3945	CLIP-seq
MIRT1245350	hsa-miR-424	CLIP-seq
MIRT2299704	hsa-miR-4253	CLIP-seq
MIRT1245352	hsa-miR-4263	CLIP-seq
MIRT1245353	hsa-miR-4521	CLIP-seq
MIRT1245354	hsa-miR-4524	CLIP-seq
MIRT2299711	hsa-miR-4536	CLIP-seq
MIRT2596444	hsa-miR-4747-3p	CLIP-seq
MIRT1245360	hsa-miR-4749-3p	CLIP-seq
MIRT2596445	hsa-miR-4753-5p	CLIP-seq
MIRT2072594	hsa-miR-4762-5p	CLIP-seq
MIRT1245363	hsa-miR-497	CLIP-seq
MIRT1245364	hsa-miR-503	CLIP-seq
MIRT1245367	hsa-miR-518a-5p	CLIP-seq
MIRT1245368	hsa-miR-527	CLIP-seq
MIRT2299718	hsa-miR-576-3p	CLIP-seq
MIRT1245371	hsa-miR-580	CLIP-seq
MIRT2299721	hsa-miR-612	CLIP-seq
MIRT1245373	hsa-miR-613	CLIP-seq
MIRT2299722	hsa-miR-644	CLIP-seq
MIRT1245374	hsa-miR-646	CLIP-seq
MIRT1245320	hsa-miR-1	CLIP-seq
MIRT1245321	hsa-miR-1225-3p	CLIP-seq
MIRT1245322	hsa-miR-1228	CLIP-seq
MIRT1245323	hsa-miR-1233	CLIP-seq
MIRT1245325	hsa-miR-1253	CLIP-seq
MIRT1245326	hsa-miR-1276	CLIP-seq
MIRT1245334	hsa-miR-206	CLIP-seq
MIRT1245343	hsa-miR-3669	CLIP-seq
MIRT1245346	hsa-miR-371-5p	CLIP-seq
MIRT1245347	hsa-miR-371b-5p	CLIP-seq
MIRT1245360	hsa-miR-4749-3p	CLIP-seq
MIRT1245371	hsa-miR-580	CLIP-seq
MIRT1245373	hsa-miR-613	CLIP-seq

Show/Hide all (42)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000255	Process	Allantoin metabolic process	IDA	6771276
GO:0001882	Function	Nucleoside binding	IDA	9305962
GO:0002060	Function	Purine nucleobase binding	IDA	9305962
GO:0003824	Function	Catalytic activity	IEA
GO:0004731	Function	Purine-nucleoside phosphorylase activity	IBA
GO:0004731	Function	Purine-nucleoside phosphorylase activity	IDA	3029074, 6771276, 9305962, 16930574, 16964310, 18938130, 23438750
GO:0004731	Function	Purine-nucleoside phosphorylase activity	IEA
GO:0005515	Function	Protein binding	IPI	32814053
GO:0005576	Component	Extracellular region	TAS
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	3029074, 16930574
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0006139	Process	Nucleobase-containing compound metabolic process	IDA	3029074
GO:0006139	Process	Nucleobase-containing compound metabolic process	IEA
GO:0006148	Process	Inosine catabolic process	IDA	16964310
GO:0006148	Process	Inosine catabolic process	IDA	23438750
GO:0006149	Process	Deoxyinosine catabolic process	IDA	6771276
GO:0006157	Process	Deoxyadenosine catabolic process	IDA	6771276
GO:0006166	Process	Purine ribonucleoside salvage	IEA
GO:0006204	Process	IMP catabolic process	IDA	6771276
GO:0006738	Process	Nicotinamide riboside catabolic process	IDA	19001417
GO:0006955	Process	Immune response	IMP	16930574
GO:0009116	Process	Nucleoside metabolic process	IEA
GO:0009165	Process	Nucleotide biosynthetic process	IGI	19001417
GO:0009410	Process	Response to xenobiotic stimulus	IMP	15047506
GO:0016740	Function	Transferase activity	IEA
GO:0016757	Function	Glycosyltransferase activity	IEA
GO:0016763	Function	Pentosyltransferase activity	IEA
GO:0032743	Process	Positive regulation of interleukin-2 production	IMP	16930574
GO:0034418	Process	Urate biosynthetic process	IDA	16964310
GO:0034774	Component	Secretory granule lumen	TAS
GO:0042102	Process	Positive regulation of T cell proliferation	IDA	16964310
GO:0042301	Function	Phosphate ion binding	IDA	18938130
GO:0042802	Function	Identical protein binding	IPI	20212140, 25502805, 31515488, 32296183
GO:0043101	Process	Purine-containing compound salvage	IDA	18938130
GO:0046059	Process	DAMP catabolic process	IDA	6771276
GO:0046638	Process	Positive regulation of alpha-beta T cell differentiation	IDA	16964310
GO:0047975	Function	Guanosine phosphorylase activity	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 20458337, 23533145
GO:1904813	Component	Ficolin-1-rich granule lumen	TAS

MIM	HGNC	e!Ensembl
164050	7892	ENSG00000198805

P00491

Protein name

Purine nucleoside phosphorylase (PNP) (EC 2.4.2.1) (Inosine phosphorylase) (Inosine-guanosine phosphorylase)

Protein function

Catalyzes the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate (PubMed:23438750, PubMed:9305964). Preferentially acts

PDB

1M73 , 1PF7 , 1PWY , 1RCT , 1RFG , 1RR6 , 1RSZ , 1RT9 , 1ULA , 1ULB , 1V2H , 1V3Q , 1V41 , 1V45 , 1YRY , 2A0W , 2A0X , 2A0Y , 2OC4 , 2OC9 , 2ON6 , 2Q7O , 3BGS , 3D1V , 3GB9 , 3GGS , 3INY , 3K8O , 3K8Q , 3PHB , 4EAR , 4EB8 , 4ECE , 4GKA , 5ETJ , 5UGF , 7ZSL , 7ZSM , 7ZSN , 7ZSO , 7ZSP

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01048	PNP_UDP_1	26 → 280	Phosphorylase superfamily	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in red blood cells; overexpressed in red blood cells (cytoplasm) of patients with hereditary non-spherocytic hemolytic anemia of unknown etiology. {ECO:0000269|PubMed:22509282}.

Sequence

MENGYTYEDYKNTAEWLLSHTKHRPQVAIICGSGLGGLTDKLTQAQIFDYGEIPNFPRST
VPGHAGRLVFGFLNGRACVMMQGRFHMYEGYPLWKVTFPVRVFHLLGVDTLVVTNAAGGL
NPKFEVGDIMLIRDHINLPGFSGQNPLRGPNDERFGDRFPAMSDAYDRTMRQRALSTWKQ
MGEQRELQEGTYVMVAGPSFETVAECRVLQKLGADAVGMSTVPEVIVARHCGLRVFGFSL
ITNKVIMDYESLEKANHEEVLAAGKQAAQKLEQFVSILMASIPLPDKAS

Sequence length

289

Interactions

View interactions

	KEGG		Reactome
	Purine metabolism Nicotinate and nicotinamide metabolism Metabolic pathways Nucleotide metabolism		Neutrophil degranulation Purine salvage Purine catabolism

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 (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Acute myeloid leukemia	Likely pathogenic; Pathogenic	rs1026474882	RCV005898769	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Purine-nucleoside phosphorylase deficiency	Pathogenic; Likely pathogenic	rs2139335365, rs867750505, rs2139338450, rs2139335095, rs2139331878, rs754734713, rs896550845, rs922257453, rs1368860049, rs1566525641, rs1882052778, rs772212348, rs104894453, rs104894454, rs104894450 View all (13 more)	RCV001384050 RCV001389833 RCV001387692 RCV001782663 RCV003631079 View all (23 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Severe combined immunodeficiency disease	Pathogenic; Likely pathogenic	rs754734713, rs922257453, rs104894453, rs104894454, rs104894450, rs104894451, rs1026474882, rs1247497521	RCV005238007 RCV002469964 RCV005237380 RCV004700237 RCV006263627 RCV002298444 RCV003479170 RCV005438032 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (7)

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.
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEARING LOSS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOPOROSIS	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PNP POLYMORPHISM	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PNP-related disorder	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SEVERE COMBINED IMMUNODEFICIENCY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

PNP (purine nucleoside phosphorylase)