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ADAT3 adenosine deaminase tRNA specific 3 [ Homo sapiens (human) ]

Gene ID: 113179, updated on 5-Mar-2024

Summary

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Official Symbol
ADAT3provided by HGNC
Official Full Name
adenosine deaminase tRNA specific 3provided by HGNC
Primary source
HGNC:HGNC:25151
See related
Ensembl:ENSG00000213638 MIM:615302; AllianceGenome:HGNC:25151
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
TAD3; MRT36; FWP005; MST121; NEDBGF; S863-5; MSTP121
Summary
This gene encodes a subunit of a tRNA-specific adenosine deaminase. This heterodimeric enzyme converts adenosine to inosine in the tRNA anticodon. A mutation in this gene causes a syndrome characterized by intellectual disability and strabismus. This gene shares its 5' exon with the overlapping gene, secretory carrier membrane protein 4 (Gene ID: 113178). [provided by RefSeq, Jul 2016]
Expression
Broad expression in colon (RPKM 2.1), stomach (RPKM 1.3) and 22 other tissues See more
Orthologs
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Genomic context

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Location:
19p13.3
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (1905399..1913447)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (1876716..1884760)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (1905398..1913446)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1853940-1854496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1854497-1855054 Neighboring gene Sharpr-MPRA regulatory region 8340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13629 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1861121-1862006 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9748 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9749 Neighboring gene KLF16 promoter region Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1865114-1865668 Neighboring gene KLF transcription factor 16 Neighboring gene KLF16-I enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:1873541-1874256 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:1875445-1876145 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1876146-1876845 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1876846-1877546 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1884760-1884907 Neighboring gene abhydrolase domain containing 17A, depalmitoylase Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1887074-1887578 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1887579-1888084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13632 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1897455-1898150 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1898955-1899127 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13633 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13634 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9753 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13635 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1907977-1908788 Neighboring gene secretory carrier membrane protein 4 Neighboring gene Sharpr-MPRA regulatory region 4132 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13636 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:1938387-1938587 Neighboring gene uncharacterized LOC105372238 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9755 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9756 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13637 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13638 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:1946998-1947718 Neighboring gene casein kinase 1 gamma 2 Neighboring gene CSNK1G2 antisense RNA 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. Formation of tRNA Wobble Inosine in Humans Is Disrupted by a Millennia-Old Mutation Causing Intellectual Disability. Ramos J, et al. Mol Cell Biol, 2019 Oct 1. PMID 31263000, Free PMC Article
  2. A new case confirming and expanding the phenotype spectrum of ADAT3-related intellectual disability syndrome. Sharkia R, et al. Eur J Med Genet, 2019 Nov. PMID 30296593
  3. ADAT3-related intellectual disability: Further delineation of the phenotype. El-Hattab AW, et al. Am J Med Genet A, 2016 May. PMID 26842963
  4. Inosine modifications in human tRNAs are incorporated at the precursor tRNA level. Torres AG, et al. Nucleic Acids Res, 2015 May 26. PMID 25916855, Free PMC Article
  5. A-to-I editing on tRNAs: biochemical, biological and evolutionary implications. Torres AG, et al. FEBS Lett, 2014 Nov 28. PMID 25263703

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic diagnosis in Sudanese and Tunisian families with syndromic intellectual disability through exome sequencing.
    Title: Genetic diagnosis in Sudanese and Tunisian families with syndromic intellectual disability through exome sequencing.
  2. Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder.
    Title: Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder.
  3. We conclude that the ADAT3 gene mutation is responsible for ADAT3-related intellectual disability syndrome, which induces the variety clinical manifestations exhibited by our patients.
    Title: A new case confirming and expanding the phenotype spectrum of ADAT3-related intellectual disability syndrome.
  4. Study demonstrates that cells isolated from intellectual disability patients with homozygous for the ADAT3-V144M mutation contain diminished levels of wobble inosine in several tRNA isoacceptors. V144M mutation compromises the adenosine deaminase activity of ADAT2/3 complexes, increases the propensity of ADAT3 to oligomerize, and alters the subcellular localization properties of ADAT3.
    Title: Formation of tRNA Wobble Inosine in Humans Is Disrupted by a Millennia-Old Mutation Causing Intellectual Disability.
  5. ADAT3-related intellectual disability is an important recognizable cause of intellectual disability in Arabia
    Title: ADAT3-related intellectual disability: Further delineation of the phenotype.
  6. A single missense mutation was identified in ADAT3 in all studied families on an ancient ancestral haplotype.
    Title: Mutation in ADAT3, encoding adenosine deaminase acting on transfer RNA, causes intellectual disability and strabismus.
Submit: New GeneRIF Correction

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
Intellectual disability-strabismus syndrome
MedGen: C4750838 OMIM: 615286 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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Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to tRNA-specific adenosine-34 deaminase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in tRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
probable inactive tRNA-specific adenosine deaminase-like protein 3
Names
adenosine deaminase, tRNA-specific 3, TAD3 homolog
tRNA-specific adenosine-34 deaminase subunit ADAT3

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_051211.1 RefSeqGene

    Range
    5186..13234
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001329533.2 → NP_001316462.1  probable inactive tRNA-specific adenosine deaminase-like protein 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and uses a downstream translation start site compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    BC011824, HY023983
    UniProtKB/Swiss-Prot
    Q96EY9
    Conserved Domains (1) summary
    COG0590
    Location:195 → 345
    TadA; tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]

  2. NM_138422.4 → NP_612431.2  probable inactive tRNA-specific adenosine deaminase-like protein 3 isoform 1

    See identical proteins and their annotated locations for NP_612431.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC011824, DB127534
    Consensus CDS
    CCDS12076.2
    UniProtKB/TrEMBL
    D6W601, D6W602
    Related
    ENSP00000332448.2, ENST00000329478.4
    Conserved Domains (1) summary
    COG0590
    Location:211 → 361
    TadA; tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    1905399..1913447
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    1876716..1884760
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96EY9.1 GenPept UniProtKB/Swiss-Prot:Q96EY9

Gene LinkOut

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

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