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NT5C3A 5'-nucleotidase, cytosolic IIIA [ Homo sapiens (human) ]

Gene ID: 51251, updated on 5-Mar-2024

Summary

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Official Symbol
NT5C3Aprovided by HGNC
Official Full Name
5'-nucleotidase, cytosolic IIIAprovided by HGNC
Primary source
HGNC:HGNC:17820
See related
Ensembl:ENSG00000122643 MIM:606224; AllianceGenome:HGNC:17820
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p36; PN-I; POMP; PSN1; UMPH; NT5C3; P5N-1; UMPH1; hUMP1; P5'N-1; cN-III
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 pyrimidine 5' monophosphates. Mutations in this gene are a cause of hemolytic anemia due to uridine 5-prime monophosphate hydrolase deficiency. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and pseudogenes of this gene are located on the long arm of chromosomes 3 and 4. [provided by RefSeq, Mar 2012]
Expression
Ubiquitous expression in colon (RPKM 15.3), duodenum (RPKM 10.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
7p14.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (33014113..33062776, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (33153715..33202377, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (33053725..33102388, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:32995899-32996849 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18084 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:33018490-33019689 Neighboring gene ribosomal protein L7a pseudogene 78 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:33038245-33038830 Neighboring gene FKBP prolyl isomerase 9 Neighboring gene RNA, U6 small nuclear 388, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18085 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18088 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25833 Neighboring gene uncharacterized LOC124901610 Neighboring gene ribosomal protein S29 pseudogene 14 Neighboring gene RNA, 7SL, cytoplasmic 505, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18089 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25834 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18091 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25835 Neighboring gene RP9 pre-mRNA splicing factor Neighboring gene Bardet-Biedl syndrome 9 Neighboring gene RNA, 5S ribosomal pseudogene 229

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. [Two novel mutations (c.830A>G, c.252+1G>A) in NT5C3A associated with hereditary pyrimidine 5'-nucleotidase deficiency: two cases report and literature review]. Li Y, et al. Zhonghua Xue Ye Xue Za Zhi, 2021 Aug 14. PMID 34547876, Free PMC Article
  2. A New Homozygous Mutation (c.393-394del TA/c.393-394del TA) in the NT5C3 Gene Associated With Pyrimidine-5'-Nucleotidase Deficiency: A Case Report. Köker SA, et al. J Pediatr Hematol Oncol, 2019 Nov. PMID 30951028
  3. The intracellular pyrimidine 5'-nucleotidase NT5C3A is a negative epigenetic factor in interferon and cytokine signaling. Al-Haj L, et al. Sci Signal, 2018 Feb 20. PMID 29463777
  4. Pyrimidine-5'-nucleotidase Campinas, a new mutation (p.R56G) in the NT5C3 gene associated with pyrimidine-5'-nucleotidase type I deficiency and influence of Gilbert's Syndrome on clinical expression. Santos Ad, et al. Blood Cells Mol Dis, 2014 Dec. PMID 25153905
  5. NT5C3 polymorphisms and outcome of first induction chemotherapy in acute myeloid leukemia. Cheong HS, et al. Pharmacogenet Genomics, 2014 Sep. PMID 25000516

See all (59) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. [Two novel mutations (c.830A>G, c.252+1G>A) in NT5C3A associated with hereditary pyrimidine 5'-nucleotidase deficiency: two cases report and literature review].
    Title: [Two novel mutations (c.830A>G, c.252+1G>A) in NT5C3A associated with hereditary pyrimidine 5'-nucleotidase deficiency: two cases report and literature review].
  2. A New Homozygous Mutation (c.393-394del TA/c.393-394del TA) in the NT5C3 Gene Associated With Pyrimidine-5'-Nucleotidase Deficiency.
    Title: A New Homozygous Mutation (c.393-394del TA/c.393-394del TA) in the NT5C3 Gene Associated With Pyrimidine-5'-Nucleotidase Deficiency: A Case Report.
  3. Data indicate an anti-inflammatory pathway that depends on the catalytic activity of pyrimidine 5'-nucleotidase (NT5C3A) and functions as a negative feedback regulator of inflammatory cytokine signaling.
    Title: The intracellular pyrimidine 5'-nucleotidase NT5C3A is a negative epigenetic factor in interferon and cytokine signaling.
  4. Results from a study on gene expression variability markers in early-stage human embryos shows that NT5C3A is a putative expression variability marker for the 3-day, 8-cell embryo stage.
    Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
  5. reduced expression of transketolase in pyrimidine 5'-nucleotidase deficient patients
    Title: Proteomics reveals reduced expression of transketolase in pyrimidine 5'-nucleotidase deficient patients.
  6. Pyrimidine-5'-nucleotidase Campinas is a new mutation (p.R56G) in the NT5C3 gene associated with pyrimidine-5'-nucleotidase type I deficiency.
    Title: Pyrimidine-5'-nucleotidase Campinas, a new mutation (p.R56G) in the NT5C3 gene associated with pyrimidine-5'-nucleotidase type I deficiency and influence of Gilbert's Syndrome on clinical expression.
  7. Results show that NT5C3 expression levels were significantly increased in patients with risk allele homozygote.
    Title: NT5C3 polymorphisms and outcome of first induction chemotherapy in acute myeloid leukemia.
  8. New missense homozygous mutation (Q270Ter) in the pyrimidine 5' nucleotidase type I-related gene in two Indian families with hereditary non-spherocytic hemolytic anemia.
    Title: New missense homozygous mutation (Q270Ter) in the pyrimidine 5' nucleotidase type I-related gene in two Indian families with hereditary non-spherocytic hemolytic anemia.
  9. analysis of Drosophila and human 7-methyl GMP-specific nucleotidases
    Title: Identification of Drosophila and human 7-methyl GMP-specific nucleotidases.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Hemolytic anemia due to pyrimidine 5' nucleotidase deficiency
MedGen: C1849507 OMIM: 266120 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC27337, MGC87109, MGC87828

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 5'-nucleotidase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 5'-nucleotidase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables 5'-nucleotidase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables XMP 5'-nucleosidase activity IEA
Inferred from Electronic Annotation
more info
  
enables magnesium ion binding NAS
Non-traceable Author Statement
more info
 PubMed 
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tRNA 2'-phosphotransferase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables tRNA 2'-phosphotransferase activity TAS
Traceable Author Statement
more info
 PubMed 
Process Evidence Code Pubs
involved_in defense response to virus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in nucleotide metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in pyrimidine nucleoside metabolic process NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
cytosolic 5'-nucleotidase 3A
Names
5'-nucleotidase, cytosolic III
7-methylguanosine phosphate-specific 5'-nucleotidase
cytosolic 5'-nucleotidase 3
lupin
pyrimidine 5'-nucleotidase 1
uridine 5'-monophosphate hydrolase 1
NP_001002009.1
NP_001002010.2
NP_001159590.1
NP_001343925.1
NP_001361264.1
NP_001361265.1
NP_001361266.1
NP_001361267.1
NP_001361268.1
NP_057573.2
XP_047276395.1
XP_054214304.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_015800.1 RefSeqGene

    Range
    5022..53668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001002009.3 → NP_001002009.1  cytosolic 5'-nucleotidase 3A isoform 2

    See identical proteins and their annotated locations for NP_001002009.1

    Status: REVIEWED

    Source sequence(s)
    AC074338, AC083863
    Conserved Domains (1) summary
    cd07504
    Location:25 → 297
    HAD_5NT; haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB

  2. NM_001002010.5 → NP_001002010.2  cytosolic 5'-nucleotidase 3A isoform 1

    Status: REVIEWED

    Source sequence(s)
    AA482595, AF151067, AK290118, HY012697
    Consensus CDS
    CCDS34616.2
    UniProtKB/TrEMBL
    X6RM59
    Related
    ENSP00000476480.2, ENST00000610140.7
    Conserved Domains (1) summary
    cd07504
    Location:59 → 331
    HAD_5NT; haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB

  3. NM_001166118.3 → NP_001159590.1  cytosolic 5'-nucleotidase 3A isoform 3

    See identical proteins and their annotated locations for NP_001159590.1

    Status: REVIEWED

    Source sequence(s)
    AC074338, AC083863
    Consensus CDS
    CCDS55101.1
    UniProtKB/TrEMBL
    A0A090N7U2
    Conserved Domains (1) summary
    cd07504
    Location:13 → 285
    HAD_5NT; haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB

  4. NM_001356996.3 → NP_001343925.1  cytosolic 5'-nucleotidase 3A isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC074338, AC083863, DA975244
    Consensus CDS
    CCDS55101.1
    UniProtKB/TrEMBL
    A0A090N7U2
    Related
    ENSP00000387166.1, ENST00000409467.6
    Conserved Domains (1) summary
    cd07504
    Location:13 → 285
    HAD_5NT; haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB

  5. NM_001374335.1 → NP_001361264.1  cytosolic 5'-nucleotidase 3A isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC074338, AC083863
    Conserved Domains (1) summary
    cd07504
    Location:46 → 298
    HAD_5NT; haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB

  6. NM_001374336.1 → NP_001361265.1  cytosolic 5'-nucleotidase 3A isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC074338, AC083863
    Consensus CDS
    CCDS55101.1
    UniProtKB/TrEMBL
    A0A090N7U2
    Conserved Domains (1) summary
    cd07504
    Location:13 → 285
    HAD_5NT; haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB

  7. NM_001374337.1 → NP_001361266.1  cytosolic 5'-nucleotidase 3A isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC074338, AC083863
    Consensus CDS
    CCDS55101.1
    UniProtKB/TrEMBL
    A0A090N7U2
    Conserved Domains (1) summary
    cd07504
    Location:13 → 285
    HAD_5NT; haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB

  8. NM_001374338.1 → NP_001361267.1  cytosolic 5'-nucleotidase 3A isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC074338, AC083863
    Conserved Domains (1) summary
    cl21460
    Location:59 → 264
    HAD_like; Haloacid Dehalogenase-like Hydrolases

  9. NM_001374339.1 → NP_001361268.1  cytosolic 5'-nucleotidase 3A isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC074338, AC083863
    Conserved Domains (1) summary
    cd07504
    Location:12 → 264
    HAD_5NT; haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB

  10. NM_016489.14 → NP_057573.2  cytosolic 5'-nucleotidase 3A isoform 2

    See identical proteins and their annotated locations for NP_057573.2

    Status: REVIEWED

    Source sequence(s)
    AA482595, BC015856, BC071652, DB346026
    Consensus CDS
    CCDS34617.1
    Related
    ENSP00000496364.1, ENST00000643244.1
    Conserved Domains (1) summary
    cd07504
    Location:25 → 297
    HAD_5NT; haloacid dehalogenase (HAD)-like 5'-nucleotidases similar to human cytosolic IIIA and IIIB

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    33014113..33062776 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047420439.1 → XP_047276395.1  cytosolic 5'-nucleotidase 3A isoform X1

    UniProtKB/TrEMBL
    A0A090N7U2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    33153715..33202377 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358329.1 → XP_054214304.1  cytosolic 5'-nucleotidase 3A isoform X1

    UniProtKB/TrEMBL
    A0A090N7U2
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H0P0.3 GenPept UniProtKB/Swiss-Prot:Q9H0P0

Gene LinkOut

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