NT5C3A (5'-nucleotidase, cytosolic IIIA)

Gene

• Entrez ID: 51251
• Gene name: 5'-nucleotidase, cytosolic IIIA
• Gene symbol: NT5C3A
• Synonyms (NCBI Gene): CNSHA8, NT5C3, P5'N-1, P5N-1, PN-I, POMP, PSN1, UMPH, UMPH1, cN-III, hUMP1, p36
• 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

SNPs

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

miRNA

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

Gene ontology (GO)

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

Other IDs

• MIM: 606224
• HGNC: 17820
• e!Ensembl: ENSG00000122643

Protein

• UniProt ID: 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

Pathways

KEGG:

Pyrimidine metabolism
Metabolic pathways
Nucleotide metabolism

Reactome:

Pyrimidine catabolism

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
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
CHLORACNE	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ 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

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adult Acute Myeloblastic Leukemia	Myeloblastic Leukemia	BEFREE	16330448		★☆☆☆☆ Found in Text Mining only
Alzheimer Disease, Early Onset	Alzheimer disease	BEFREE	15272895		★☆☆☆☆ Found in Text Mining only
Anemia Hemolytic	Hemolytic anemia	Pubtator	36434495	Associate	★☆☆☆☆ Found in Text Mining only
Anemia Hemolytic Congenital Nonspherocytic	Hemolytic anemia	Pubtator	15604219	Associate	★☆☆☆☆ Found in Text Mining only
Anemia, Hemolytic	Anemia	BEFREE	15571242, 16461318		★☆☆☆☆ Found in Text Mining only
Anemia, Hemolytic	Anemia	LHGDN	18499901		★☆☆☆☆ Found in Text Mining only
Anemia, Hemolytic	Anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anemia, Hemolytic, Congenital	Anemia	BEFREE	16956825		★☆☆☆☆ Found in Text Mining only
Anemia, Hemolytic, Congenital Nonspherocytic	Anemia	CTD_human_DG	16672222		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aneurysm, Posterior Communicating Artery	Posterior communicating artery aneurysm	BEFREE	28862551		★☆☆☆☆ Found in Text Mining only
Bare Lymphocyte Syndrome	Bare Lymphocyte Syndrome	BEFREE	9190936		★☆☆☆☆ Found in Text Mining only
Bare lymphocyte syndrome 2	Bare Lymphocyte Syndrome	BEFREE	9190936		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain Neoplasms	BEFREE	11461077, 11536309		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain neoplasms	Pubtator	11461077	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	28827004		★☆☆☆☆ Found in Text Mining only
Carcinogenesis	Carcinogenesis	Pubtator	10838189	Associate	★☆☆☆☆ Found in Text Mining only
Central Nervous System Neoplasms	Central Nervous System Neoplasms	BEFREE	11536309		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	10838189	Associate	★☆☆☆☆ Found in Text Mining only
Crohn Disease	Crohn Disease	BEFREE	10398839, 11118734		★☆☆☆☆ Found in Text Mining only
Diabetes	Diabetes	BEFREE	10567346		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes Mellitus	BEFREE	10567346		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	28012244, 30347229		★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down Syndrome	BEFREE	15308304		★☆☆☆☆ Found in Text Mining only
Ductal Breast Carcinoma	Breast Carcinoma	BEFREE	14553951		★☆☆☆☆ Found in Text Mining only
Enzymopathy	Enzymopathy	BEFREE	16956825		★☆☆☆☆ Found in Text Mining only
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	12119563		★☆☆☆☆ Found in Text Mining only
Esophageal Neoplasms	Esophagus Neoplasm	BEFREE	12119563		★☆☆☆☆ Found in Text Mining only
Exophthalmos	Proptosis	BEFREE	30771770		★☆☆☆☆ Found in Text Mining only
Gerstmann-Straussler-Scheinker Disease	Gerstmann-Straussler-Scheinker syndrome	BEFREE	10712583		★☆☆☆☆ Found in Text Mining only
Gilbert Disease (disorder)	Gilbert Disease	BEFREE	25153905		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	30395843		★☆☆☆☆ Found in Text Mining only
Glycogen Storage Disease	Glycogen Storage Disease	BEFREE	10712583		★☆☆☆☆ Found in Text Mining only
Harlequin Fetus	Harlequin Ichthyosis	BEFREE	28196356		★☆☆☆☆ Found in Text Mining only
Hemolytic anemia due to pyrimidine 5` nucleotidase deficiency	Hemolytic Anemia	Orphanet			★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	31615064		★☆☆☆☆ Found in Text Mining only
Hyperinsulinism	Hyperinsulinism	BEFREE	28443026		★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	10398839		★☆☆☆☆ Found in Text Mining only
Intracranial Aneurysm	Intracranial Aneurysm	BEFREE	28862551		★☆☆☆☆ Found in Text Mining only
Leprosy	Leprosy	BEFREE	8862592		★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	12547161, 16330448, 25000516		★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	2160596, 7542850		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus	Lupus Erythematosus	BEFREE	8557639		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Discoid	Lupus Erythematosus	BEFREE	8557639		★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	8557639		★☆☆☆☆ Found in Text Mining only
Lupus Vulgaris	Lupus Vulgaris	BEFREE	8557639		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of brain	Brain Neoplasms	BEFREE	11536309		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	28827004		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of esophagus	Esophagus Neoplasm	BEFREE	12119563		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	12060845, 12841682, 16969121, 28827004		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of prostate	Prostate cancer	BEFREE	11536309		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	11522620, 12547161, 29447983		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	28494188		★☆☆☆☆ Found in Text Mining only
Meningioma	Meningioma	Pubtator	11461077	Associate	★☆☆☆☆ Found in Text Mining only
Myotonic Dystrophy	Myotonic dystrophy	Pubtator	32902349	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	10616197, 11461077, 11536309, 12547161, 7700633		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	10616197, 7700633		★☆☆☆☆ Found in Text Mining only
Neuroectodermal Tumor, Primitive	Neuroectodermal Tumors	BEFREE	7738588		★☆☆☆☆ Found in Text Mining only
Osteosarcoma	Osteosarcoma	BEFREE	11672768		★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	12060845, 12841682, 16969121, 28827004		★☆☆☆☆ Found in Text Mining only
Paratuberculosis	Paratuberculosis	BEFREE	10398839, 11118734		★☆☆☆☆ Found in Text Mining only
Prostate carcinoma	Prostate cancer	BEFREE	11536309		★☆☆☆☆ Found in Text Mining only
Sarcoidosis	Sarcoidosis	BEFREE	8862592		★☆☆☆☆ Found in Text Mining only
Secondary malignant neoplasm of colon and/or rectum	Colorectal Neoplasms	BEFREE	30838483		★☆☆☆☆ Found in Text Mining only
Ulcerative Colitis	Ulcerative colitis	BEFREE	10398839		★☆☆☆☆ Found in Text Mining only
Uridine 5-Prime Monophosphate Hydrolase Deficiency, Hemolytic Anemia due to	Hemolytic Anemia	UNIPROT_DG	11369620, 12930399, 15238149, 15604219, 15968458, 16461318, 18499901, 25153905		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uridine 5-Prime Monophosphate Hydrolase Deficiency, Hemolytic Anemia due to	Hemolytic Anemia	ORPHANET_DG	11369620, 12714505		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uridine 5-Prime Monophosphate Hydrolase Deficiency, Hemolytic Anemia due to	Hemolytic Anemia	GENOMICS_ENGLAND_DG	11369620, 27604308		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uridine 5-Prime Monophosphate Hydrolase Deficiency, Hemolytic Anemia due to	Hemolytic Anemia	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uridine 5-Prime Monophosphate Hydrolase Deficiency, Hemolytic Anemia due to	Hemolytic Anemia	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations