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    TRNT1 tRNA nucleotidyl transferase 1 [ Homo sapiens (human) ]

    Gene ID: 51095, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TRNT1provided by HGNC
    Official Full Name
    tRNA nucleotidyl transferase 1provided by HGNC
    Primary source
    HGNC:HGNC:17341
    See related
    Ensembl:ENSG00000072756 MIM:612907; AllianceGenome:HGNC:17341
    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
    CCA1; RPEM; SIFD; MtCCA; CGI-47
    Summary
    The protein encoded by this gene is a CCA-adding enzyme which belongs to the tRNA nucleotidyltransferase/poly(A) polymerase family. This essential enzyme functions by catalyzing the addition of the conserved nucleotide triplet CCA to the 3' terminus of tRNA molecules. Mutations in this gene result in sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
    Expression
    Ubiquitous expression in prostate (RPKM 8.6), testis (RPKM 7.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TRNT1 in Genome Data Viewer
    Location:
    3p26.2
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (3126940..3153435)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (3121237..3147781)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (3168624..3195119)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19343 Neighboring gene uncharacterized LOC124909339 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14009 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:3168955-3169685 Neighboring gene interleukin 5 receptor subunit alpha Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14010 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19345 Neighboring gene cereblon Neighboring gene ReSE screen-validated silencer GRCh37_chr3:3310572-3310785 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69928 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69934 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_69968 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:3600748-3601947 Neighboring gene uncharacterized LOC100130207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14011 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14013 Neighboring gene Sharpr-MPRA regulatory region 107 Neighboring gene leucine rich repeat neuronal 1 Neighboring gene polyribonucleotide nucleotidyltransferase 1 pseudogene 1

    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. The 3' addition of CCA to mitochondrial tRNASer(AGY) is specifically impaired in patients with mutations in the tRNA nucleotidyl transferase TRNT1. Sasarman F, et al. Hum Mol Genet, 2015 May 15. PMID 25652405, Free PMC Article
    2. Patient-specific induced pluripotent stem cells to evaluate the pathophysiology of TRNT1-associated Retinitis pigmentosa. Sharma TP, et al. Stem Cell Res, 2017 May. PMID 28390992
    3. Expanding the Phenotype of TRNT1-Related Immunodeficiency to Include Childhood Cataract and Inner Retinal Dysfunction. Hull S, et al. JAMA Ophthalmol, 2016 Sep 1. PMID 27389523
    4. In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity. Leibovitch M, et al. Biochim Biophys Acta Proteins Proteom, 2018 Apr. PMID 29454993
    5. Impaired activity of CCA-adding enzyme TRNT1 impacts OXPHOS complexes and cellular respiration in SIFD patient-derived fibroblasts. Liwak-Muir U, et al. Orphanet J Rare Dis, 2016 Jun 18. PMID 27317422, Free PMC Article

    See all (62) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TRNT-1 Deficiency Is Associated with Loss of tRNA Integrity and Imbalance of Distinct Proteins.
      Title: TRNT-1 Deficiency Is Associated with Loss of tRNA Integrity and Imbalance of Distinct Proteins.
    2. A phenotypic expansion of TRNT1 associated sideroblastic anemia with immunodeficiency, fevers, and developmental delay.
      Title: A phenotypic expansion of TRNT1 associated sideroblastic anemia with immunodeficiency, fevers, and developmental delay.
    3. Genes for tRNA recycling are upregulated in response to infection with Theiler's mouse encephalitis virus.
      Title: Genes for tRNA recycling are upregulated in response to infection with Theiler's mouse encephalitis virus.
    4. Two cases of sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) syndrome in Chinese Han children caused by novel compound heterozygous variants of the TRNT1 gene.
      Title: Two cases of sideroblastic anemia with B-cell immunodeficiency, periodic fevers, and developmental delay (SIFD) syndrome in Chinese Han children caused by novel compound heterozygous variants of the TRNT1 gene.
    5. The expression of mitochondrial non-coding RNAs regulated by TRNT1 has been described.
      Title: Exploration of CCA-added RNAs revealed the expression of mitochondrial non-coding RNAs regulated by CCA-adding enzyme.
    6. In vitro analysis revealed that the I326T substitution decreases the thermal stability of TRNT1 and causes a ten-fold reduction in enzyme activity. These data suggest that the structural changes in the I326T variant result from a rearrangement of helices within the body domain of the protein which can be probed by the inability of the monomeric enzyme to form a covalent dimer in vitro.
      Title: Analysis of the pathogenic I326T variant of human tRNA nucleotidyltransferase reveals reduced catalytic activity and thermal stability in vitro linked to a conformational change.
    7. Peripheral B-cell deficiency of TRNT1 deficiency may be associated with augmented ER stress in immature B cells in the bone marrow.
      Title: Atypical SIFD with novel TRNT1 mutations: a case study on the pathogenesis of B-cell deficiency.
    8. We studied nine patients with biallelic mutations in TRNT1 and the syndrome of congenital sideroblastic anaemia with immunodeficiency, fevers and developmental delay. Mutations of TRNT1 lead to a severe and often fatal syndrome, linking protein homeostasis and autoinflammation.
      Title: Aberrant tRNA processing causes an autoinflammatory syndrome responsive to TNF inhibitors.
    9. In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity.
      Title: In vitro studies of disease-linked variants of human tRNA nucleotidyltransferase reveal decreased thermal stability and altered catalytic activity.
    10. patient-specific induced pluripotent stem cells (iPSCs) and iPSC-derived retinal organoids from dermal fibroblasts of patients with molecularly confirmed TRNT1-associated retinitis pigmentosa.
      Title: Patient-specific induced pluripotent stem cells to evaluate the pathophysiology of TRNT1-associated Retinitis pigmentosa.
    Submit: New GeneRIF Correction See all GeneRIFs (23)

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-3' RNA polymerase activity TAS
    Traceable Author Statement
    more info
    		  
    enables ATP binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables CCA tRNA nucleotidyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables CCACCA tRNA nucleotidyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mitochondrial tRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitochondrial tRNA 3'-end processing IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrial tRNA 3'-end processing TAS
    Traceable Author Statement
    more info
    		  
    involved_in rescue of stalled ribosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA 3'-end processing TAS
    Traceable Author Statement
    more info
    		  
    involved_in tRNA 3'-terminal CCA addition IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA 3'-terminal CCA addition IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA surveillance IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    CCA tRNA nucleotidyltransferase 1, mitochondrial
    Names
    ATP(CTP):tRNA nucleotidyltransferase
    CCA-adding enzyme
    mitochondrial CCA-adding tRNA-nucleotidyltransferase
    mt CCA-adding enzyme
    mt tRNA CCA-diphosphorylase
    mt tRNA CCA-pyrophosphorylase
    mt tRNA adenylyltransferase
    tRNA CCA nucleotidyl transferase 1
    tRNA nucleotidyl transferase, CCA-adding, 1
    tRNA-nucleotidyltransferase 1, mitochondrial
    NP_001289875.2
    NP_001354250.1
    NP_001354251.1
    NP_001354252.1
    NP_886552.3
    XP_047304196.1
    XP_047304197.1
    XP_054202692.1
    XP_054202693.1

    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_041800.2 RefSeqGene

      Range
      5025..27108
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1314

    mRNA and Protein(s)

    1. NM_001302946.2 → NP_001289875.2  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC024060, AL834397
      Consensus CDS
      CCDS77691.1
      UniProtKB/TrEMBL
      A0A8V8TM71
      Related
      ENSP00000280591.6, ENST00000280591.10
      Conserved Domains (1) summary
      COG0617
      Location:40 → 316
      PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]

    2. NM_001367321.1 → NP_001354250.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC024060
      Consensus CDS
      CCDS2561.2
      UniProtKB/Swiss-Prot
      A8K2Z6, B7WP13, C9JKA2, Q8ND57, Q96Q11, Q9BS97, Q9Y362
      UniProtKB/TrEMBL
      A0A8V8TM71
      Related
      ENSP00000513700.1, ENST00000698406.1
      Conserved Domains (1) summary
      COG0617
      Location:40 → 417
      PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]

    3. NM_001367322.1 → NP_001354251.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC024060
      Consensus CDS
      CCDS2561.2
      UniProtKB/Swiss-Prot
      A8K2Z6, B7WP13, C9JKA2, Q8ND57, Q96Q11, Q9BS97, Q9Y362
      UniProtKB/TrEMBL
      A0A8V8TM71
      Related
      ENSP00000513706.1, ENST00000698413.1
      Conserved Domains (1) summary
      COG0617
      Location:40 → 417
      PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]

    4. NM_001367323.1 → NP_001354252.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC024060
      Consensus CDS
      CCDS2561.2
      UniProtKB/Swiss-Prot
      A8K2Z6, B7WP13, C9JKA2, Q8ND57, Q96Q11, Q9BS97, Q9Y362
      UniProtKB/TrEMBL
      A0A8V8TM71
      Related
      ENSP00000513705.1, ENST00000698412.1
      Conserved Domains (1) summary
      COG0617
      Location:40 → 417
      PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]

    5. NM_182916.3 → NP_886552.3  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AB063105, AC024060, AL834397, BQ722111, DA884423, DB032432, DB525237
      Consensus CDS
      CCDS2561.2
      UniProtKB/Swiss-Prot
      A8K2Z6, B7WP13, C9JKA2, Q8ND57, Q96Q11, Q9BS97, Q9Y362
      UniProtKB/TrEMBL
      A0A8V8TM71
      Related
      ENSP00000251607.6, ENST00000251607.11
      Conserved Domains (1) summary
      COG0617
      Location:40 → 417
      PcnB; tRNA nucleotidyltransferase/poly(A) polymerase [Translation, ribosomal structure and biogenesis]

    RNA

    1. NR_159934.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060

    2. NR_159935.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060

    3. NR_159936.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060

    4. NR_159937.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060

    5. NR_159938.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060
      Related
      ENST00000651591.1

    6. NR_159939.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060

    7. NR_159940.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060
      Related
      ENST00000650839.1

    8. NR_159941.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060

    9. NR_159942.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060
      Related
      ENST00000339437.11

    10. NR_159943.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060
      Related
      ENST00000402675.5

    11. NR_159944.3 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC024060

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      3126940..3153435
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047448240.1 → XP_047304196.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K2Z6, B7WP13, C9JKA2, Q8ND57, Q96Q11, Q9BS97, Q9Y362
      UniProtKB/TrEMBL
      A0A8V8TM71

    2. XM_047448241.1 → XP_047304197.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K2Z6, B7WP13, C9JKA2, Q8ND57, Q96Q11, Q9BS97, Q9Y362
      UniProtKB/TrEMBL
      A0A8V8TM71

    RNA

    1. XR_007095683.1 RNA Sequence

      Related
      ENST00000698410.1

    2. XR_007095685.1 RNA Sequence

    3. XR_007095687.1 RNA Sequence

    4. XR_007095684.1 RNA Sequence

    5. XR_007095686.1 RNA Sequence

    6. XR_007095688.1 RNA Sequence

    7. XR_001740168.3 RNA Sequence

    8. XR_001740169.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      3121237..3147781
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346717.1 → XP_054202692.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform X1

      UniProtKB/TrEMBL
      A0A8V8TM71

    2. XM_054346718.1 → XP_054202693.1  CCA tRNA nucleotidyltransferase 1, mitochondrial isoform X1

      UniProtKB/TrEMBL
      A0A8V8TM71

    RNA

    1. XR_008486721.1 RNA Sequence

    2. XR_008486724.1 RNA Sequence

    3. XR_008486726.1 RNA Sequence

    4. XR_008486722.1 RNA Sequence

    5. XR_008486725.1 RNA Sequence

    6. XR_008486727.1 RNA Sequence

    7. XR_008486720.1 RNA Sequence

    8. XR_008486723.1 RNA Sequence

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_016000.3: Suppressed sequence

      Description
      NM_016000.3: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96Q11.2 GenPept UniProtKB/Swiss-Prot:Q96Q11

    Gene LinkOut

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

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