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

Gene ID: 51095, updated on 3-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (3126940..3153435)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (3121237..3147781)
105.20220307 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. TRNT-1 Deficiency Is Associated with Loss of tRNA Integrity and Imbalance of Distinct Proteins. Fatica T, et al. Genes (Basel), 2023 May 5. PMID 37239403, Free PMC Article
  2. A phenotypic expansion of TRNT1 associated sideroblastic anemia with immunodeficiency, fevers, and developmental delay. Odom J, et al. Am J Med Genet A, 2022 Jan. PMID 34510712
  3. 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. Wang J, et al. Clin Chim Acta, 2021 Oct. PMID 34310935
  4. Mechanistic insights into mitochondrial tRNA(Ala) 3'-end metabolism deficiency. Ji Y, et al. J Biol Chem, 2021 Jul. PMID 34023389, Free PMC Article
  5. Exploration of CCA-added RNAs revealed the expression of mitochondrial non-coding RNAs regulated by CCA-adding enzyme. Pawar K, et al. RNA Biol, 2019 Dec. PMID 31512554, Free PMC Article

See all (58) 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)

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

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 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
  
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_2023_10

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

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

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

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

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

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

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