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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
    mouse all
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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
    		Compare labs

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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