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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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NT5C3A
5'-nucleotidase, cytosolic IIIA
Chromosome 7 Β· 7p14.3
NCBI Gene: 51251Ensembl: ENSG00000122643.24HGNC: HGNC:17820UniProt: A0A090N7U2
64PubMed Papers
21Diseases
0Drugs
19Pathogenic Variants
FUNCTIONAL ROLE
Hub Gene
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cytosolmitochondrionendoplasmic reticulum5'-nucleotidase activityhemolytic anemia due to pyrimidine 5' nucleotidase deficiencyacute myeloid leukemiahemolytic anemiakidney disease
✦AI Summary

NT5C3A (5'-nucleotidase, cytosolic IIIA) is a pyrimidine-metabolizing enzyme that catalyzes the dephosphorylation of cytidine monophosphate (CMP) and other nucleoside monophosphates 1. Beyond nucleotide catabolism, NT5C3A functions as a negative regulator of inflammatory signaling. Type I interferon induces NT5C3A expression through IRF1-dependent mechanisms, and the enzyme suppresses NF-ΞΊB-mediated cytokine production by increasing NAD+ levels and activating the NAD+-dependent deacetylases SIRT1 and SIRT6, which deacetylate histone H3 and the NF-ΞΊB subunit RelA 2. This pathway represents an anti-inflammatory feedback mechanism during immune responses 3. NT5C3A is also part of the antiviral response, with expression upregulated during influenza A virus infection 4. Clinically, NT5C3A deficiency causes pyrimidine 5'-nucleotidase (P5N) deficiency, a rare erythrocyte enzymopathy presenting as nonspherocytic hemolytic anemia 56. Loss-of-function mutations in NT5C3A result in accumulation of pyrimidine nucleotides and hemolysis. Additionally, NT5C3A has emerged as a candidate biomarker for disease activity monitoring in chr7 inflammatory demyelinating polyneuropathy 7, and altered NT5C3A methylation is associated with maternal atopy in neonatal cord blood 8.

Sources cited
1
NT5C3A shows specific nucleotidase activity toward CMP and m(7)GMP substrates
PMID: 24603684
2
NT5C3A is induced by type I interferons and suppresses cytokine production through NF-ΞΊB inhibition via sirtuin activation and NAD+ metabolism
PMID: 29463777
3
NT5C3A translation is mTOR-sensitive during interferon stimulation due to IFN-induced changes in transcription start site
PMID: 26207988
4
NT5C3A expression is upregulated during antiviral responses to influenza A virus infection
PMID: 27451344
5
NT5C3A mutations cause pyrimidine 5'-nucleotidase deficiency presenting as hemolytic anemia in erythrocytes
PMID: 36434495
6
NT5C3A homozygous mutations cause P5N deficiency manifesting as nonspherocytic hemolytic anemia
PMID: 39967523
7
NT5C3A is a candidate biomarker for disease activity in chronic inflammatory demyelinating polyneuropathy
PMID: 37879899
8
NT5C3A methylation patterns are associated with maternal atopy in neonatal cord blood
PMID: 32902349
Disease Associationsβ“˜21
hemolytic anemia due to pyrimidine 5' nucleotidase deficiencyOpen Targets
0.81Strong
acute myeloid leukemiaOpen Targets
0.37Weak
hemolytic anemiaOpen Targets
0.37Weak
kidney diseaseOpen Targets
0.31Weak
Abruptio PlacentaeOpen Targets
0.28Weak
liver diseaseOpen Targets
0.27Weak
connective tissue neoplasmOpen Targets
0.27Weak
Abnormality of the skeletal systemOpen Targets
0.26Weak
glaucomaOpen Targets
0.14Weak
Respiratory insufficiencyOpen Targets
0.11Weak
neoplasmOpen Targets
0.07Suggestive
hemoglobin D diseaseOpen Targets
0.04Suggestive
hemoglobin E diseaseOpen Targets
0.04Suggestive
overhydrated hereditary stomatocytosisOpen Targets
0.04Suggestive
hemolytic anemia due to glutathione reductase deficiencyOpen Targets
0.03Suggestive
Hallux valgusOpen Targets
0.03Suggestive
Familial ocular anterior segment mesenchymal dysgenesisOpen Targets
0.03Suggestive
galactokinase deficiencyOpen Targets
0.03Suggestive
exfoliation syndromeOpen Targets
0.03Suggestive
dehydrated hereditary stomatocytosisOpen Targets
0.03Suggestive
P5N deficiencyUniProt
Pathogenic Variants19
NM_001002010.5(NT5C3A):c.395A>T (p.Asp132Val)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 132
NM_001002010.5(NT5C3A):c.631C>T (p.Gln211Ter)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency|not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 211
NM_001002010.5(NT5C3A):c.579del (p.Val194fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 194
NM_001002010.5(NT5C3A):c.499_502del (p.Glu167fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 167
NM_001002010.5(NT5C3A):c.844_845dup (p.Val283fs)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency|not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 283
NM_001002010.5(NT5C3A):c.139-9021dupPathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_001002010.5(NT5C3A):c.333del (p.Thr112fs)Likely pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜…β˜†β˜†β˜†2024β†’ Residue 112
NM_001002010.5(NT5C3A):c.440G>A (p.Trp147Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 147
NM_001002010.5(NT5C3A):c.693+1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2022
NM_001002010.5(NT5C3A):c.718G>T (p.Glu240Ter)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜…β˜†β˜†β˜†2022β†’ Residue 240
NM_001002010.5(NT5C3A):c.166C>T (p.Arg56Ter)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜…β˜†β˜†β˜†2019β†’ Residue 56
NM_001002010.5(NT5C3A):c.342dup (p.Cys115fs)Likely pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜†β˜†β˜†β˜†2021β†’ Residue 115
NM_001002010.5(NT5C3A):c.823G>C (p.Gly275Arg)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜†β˜†β˜†β˜†2004β†’ Residue 275
NM_001002010.5(NT5C3A):c.679del (p.Asp227fs)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜†β˜†β˜†β˜†2003β†’ Residue 227
NM_001002010.5(NT5C3A):c.671A>G (p.Asn224Ser)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜†β˜†β˜†β˜†2003β†’ Residue 224
NM_001002010.5(NT5C3A):c.694-1G>CPathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜†β˜†β˜†β˜†2003
NM_001002010.5(NT5C3A):c.486dup (p.Ala163fs)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜†β˜†β˜†β˜†2003β†’ Residue 163
NM_001002010.5(NT5C3A):c.645T>G (p.Tyr215Ter)Pathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜†β˜†β˜†β˜†2003β†’ Residue 215
NM_001002010.5(NT5C3A):c.694-1G>TPathogenic
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
β˜†β˜†β˜†β˜†2001
View on ClinVar β†—
Related Genes
UPRTProtein interaction97%PRPS1L1Protein interaction97%ADAProtein interaction96%ADKProtein interaction96%ADSLProtein interaction96%ADSS2Protein interaction96%
Tissue Expression6 tissues
Brain
100%
Bone Marrow
81%
Lung
74%
Ovary
59%
Heart
57%
Liver
43%
Gene Interaction Network
Click a node to explore
NT5C3AUPRTPRPS1L1ADAADKADSLADSS2
PROTEIN STRUCTURE
Preparing viewer…
PDB2VKQ Β· 2.50 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.14LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.70 [0.45–1.14]
RankingsWhere NT5C3A stands among ~20K protein-coding genes
  • #7,298of 20,598
    Most Researched64
  • #2,240of 5,498
    Most Pathogenic Variants19
  • #11,776of 17,882
    Most Constrained (LOEUF)1.14
Genes detectedNT5C3A
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
The plasma peptides of Alzheimer's disease.
PMID: 34182925
Clin Proteomics Β· 2021
1.00
2
The intracellular pyrimidine 5'-nucleotidase NT5C3A is a negative epigenetic factor in interferon and cytokine signaling.
PMID: 29463777
Sci Signal Β· 2018
0.90
3
A rare mutation (p.F149del) of the NT5C3A gene is associated with pyrimidine 5'-nucleotidase deficiency.
PMID: 36434495
Cell Mol Biol Lett Β· 2022
0.80
4
Pyrimidine-5'-Nucleotidase Deficiency: a New Homozygous NT5C3A Mutation (c.693+1G>A variant).
PMID: 39967523
Clin Lab Β· 2025
0.70
5
Assessment of mTOR-Dependent Translational Regulation of Interferon Stimulated Genes.
PMID: 26207988
PLoS One Β· 2015
0.60