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	51251
Gene name	5'-nucleotidase, cytosolic IIIA
Gene symbol	NT5C3A
Synonyms (NCBI Gene)	CNSHA8NT5C3P5'N-1P5N-1PN-IPOMPPSN1UMPHUMPH1cN-IIIhUMP1p36
Chromosome	7
Chromosome location	7p14.3
Summary	This gene encodes a member of the 5`-nucleotidase family of enzymes that catalyze the dephosphorylation of nucleoside 5`-monophosphates. The encoded protein is the type 1 isozyme of pyrimidine 5` nucleotidase and catalyzes the dephosphorylation of pyrimid

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs104894025	T>A	Pathogenic	Missense variant, coding sequence variant
rs104894026	G>A	Pathogenic	Coding sequence variant, stop gained
rs104894027	A>C	Pathogenic	Coding sequence variant, stop gained
rs104894028	T>C	Pathogenic	Missense variant, coding sequence variant
rs104894029	C>G	Pathogenic	Missense variant, intron variant, coding sequence variant
rs397518435	C>A,G	Pathogenic	Splice acceptor variant, intron variant
rs397518436	->CC	Pathogenic	Frameshift variant, coding sequence variant, intron variant
rs397518437	->T	Pathogenic	Frameshift variant, coding sequence variant
rs397518438	C>-	Pathogenic	Frameshift variant, coding sequence variant
rs1583884979	T>C	Likely-pathogenic	Splice acceptor variant

Show/Hide all (24)

miRTarBase ID	miRNA	Experiments	Reference
MIRT005184	hsa-miR-30a-5p	pSILAC	18668040
MIRT007081	hsa-miR-122-5p	Luciferase reporter assay	23055569
MIRT007081	hsa-miR-122-5p	Luciferase reporter assay	23055569
MIRT005184	hsa-miR-30a-5p	Proteomics;Other	18668040
MIRT031382	hsa-miR-16-5p	Proteomics	18668040
MIRT044479	hsa-miR-320a	CLASH	23622248
MIRT555439	hsa-miR-101-3p	PAR-CLIP	21572407
MIRT555445	hsa-miR-144-3p	PAR-CLIP	21572407
MIRT555444	hsa-miR-499a-3p	PAR-CLIP	21572407
MIRT555443	hsa-miR-499b-3p	PAR-CLIP	21572407
MIRT555442	hsa-miR-6504-3p	PAR-CLIP	21572407
MIRT555441	hsa-miR-520d-5p	PAR-CLIP	21572407
MIRT555440	hsa-miR-524-5p	PAR-CLIP	21572407
MIRT555439	hsa-miR-101-3p	PAR-CLIP	21572407
MIRT555438	hsa-miR-582-5p	PAR-CLIP	21572407
MIRT555439	hsa-miR-101-3p	PAR-CLIP	21572407
MIRT555445	hsa-miR-144-3p	PAR-CLIP	21572407
MIRT555444	hsa-miR-499a-3p	PAR-CLIP	21572407
MIRT555443	hsa-miR-499b-3p	PAR-CLIP	21572407
MIRT555442	hsa-miR-6504-3p	PAR-CLIP	21572407
MIRT555441	hsa-miR-520d-5p	PAR-CLIP	21572407
MIRT555440	hsa-miR-524-5p	PAR-CLIP	21572407
MIRT555439	hsa-miR-101-3p	PAR-CLIP	21572407
MIRT555438	hsa-miR-582-5p	PAR-CLIP	21572407

Show/Hide all (26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000215	Function	TRNA 2'-phosphotransferase activity	NAS	9428647
GO:0000215	Function	TRNA 2'-phosphotransferase activity	TAS	10942414
GO:0000287	Function	Magnesium ion binding	IEA
GO:0000287	Function	Magnesium ion binding	NAS	11795870
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	8557639
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005783	Component	Endoplasmic reticulum	IDA	8557639
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0006213	Process	Pyrimidine nucleoside metabolic process	NAS	10942414
GO:0008253	Function	5'-nucleotidase activity	IBA
GO:0008253	Function	5'-nucleotidase activity	IDA	10942414
GO:0008253	Function	5'-nucleotidase activity	IEA
GO:0008253	Function	5'-nucleotidase activity	NAS	12930399
GO:0009117	Process	Nucleotide metabolic process	IEA
GO:0016604	Component	Nuclear body	IDA
GO:0016740	Function	Transferase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051607	Process	Defense response to virus	IDA	21478870

MIM	HGNC	e!Ensembl
606224	17820	ENSG00000122643

Q9H0P0

Protein name

Cytosolic 5'-nucleotidase 3A (EC 3.1.3.5) (7-methylguanosine phosphate-specific 5'-nucleotidase) (7-methylguanosine nucleotidase) (EC 3.1.3.91) (Cytosolic 5'-nucleotidase 3) (Cytosolic 5'-nucleotidase III) (cN-III) (Pyrimidine 5'-nucleotidase 1) (P5'N-1)

Protein function

Nucleotidase which shows specific activity towards cytidine monophosphate (CMP) and 7-methylguanosine monophosphate (m(7)GMP) (PubMed:24603684). CMP seems to be the preferred substrate (PubMed:15968458). {ECO:0000269|PubMed:15968458, ECO:0000269

PDB

2CN1 , 2JGA , 2VKQ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05822	UMPH-1	91 → 336		Family

Tissue specificity

TISSUE SPECIFICITY: Isoforms 1, 3 and 4 are expressed in reticulocytes. Isoform 4 is hardly detectable in bone marrow and fetal liver. {ECO:0000269|PubMed:11369620, ECO:0000269|PubMed:15238149}.

Sequence

MRAPSMDRAAVARVGAVASASVCALVAGVVLAQYIFTLKRKTGRKTKIIEMMPEFQKSSV
RIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYKGKRCPTCHNIIDNCKLVTDEC
RKKLLQLKEKYYAIEVDPVLTVEEKYPYMVEWYTKSHGLLVQQALPKAKLKEIVAESDVM
LKEGYENFFDKLQQHSIPVFIFSAGIGDVLEEVIRQAGVYHPNVKVVSNFMDFDETGVLK
GFKGELIHVFNKHDGALRNTEYFNQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYL
NDRVDELLEKYMDSYDIVLVQDESLEVANSILQKIL

Sequence length

336

Interactions

View interactions

	KEGG		Reactome
	Pyrimidine metabolism Metabolic pathways Nucleotide metabolism		Pyrimidine 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 (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency	Likely pathogenic; Pathogenic	rs2127996432, rs925502732, rs104894025, rs104894026, rs397518435, rs397518436, rs104894027, rs397518437, rs104894028, rs397518438, rs104894029, rs753346459	RCV001728169 RCV002251182 RCV000004736 RCV000004737 RCV000004738 RCV000004739 RCV000004740 RCV000004741 RCV000004742 RCV000004743 RCV000004744 RCV000004745 RCV001534612	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (15)

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.
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANEMIA, CONGENITAL, NONSPHEROCYTIC HEMOLYTIC, 8	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ANEMIA, HEMOLYTIC, CONGENITAL NONSPHEROCYTIC	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NT5C3A-related disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
URIDINE 5-PRIME MONOPHOSPHATE HYDROLASE DEFICIENCY, HEMOLYTIC ANEMIA DUE TO	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
5 Nucleotidase syndrome	Associate	15604219	★★★★★ ★☆☆☆☆ Found in Text Mining only
Anemia Hemolytic	Associate	36434495	★★★★★ ★☆☆☆☆ Found in Text Mining only
Anemia Hemolytic Congenital Nonspherocytic	Associate	15604219	★★★★★ ★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Associate	11461077	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Associate	10838189	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Associate	10838189	★★★★★ ★☆☆☆☆ Found in Text Mining only
Meningioma	Associate	11461077	★★★★★ ★☆☆☆☆ Found in Text Mining only
Myotonic Dystrophy	Associate	32902349	★★★★★ ★☆☆☆☆ Found in Text Mining only
N acetyltransferase deficiency	Associate	11369620	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	11461077, 18757419	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uridine 5 Prime Monophosphate Hydrolase Deficiency Hemolytic Anemia due to	Inhibit	11369620	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uridine 5 Prime Monophosphate Hydrolase Deficiency Hemolytic Anemia due to	Associate	11369620, 12930399, 36434495	★★★★★ ★☆☆☆☆ Found in Text Mining only

NT5C3A (5'-nucleotidase, cytosolic IIIA)