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

    Gene ID: 113179, updated on 10-Dec-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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    See ADAT3 in Genome Data Viewer
    Location:
    19p13.3
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (1905399..1913447)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (1876716..1884760)
    RS_2024_09 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. Mutation in ADAT3, encoding adenosine deaminase acting on transfer RNA, causes intellectual disability and strabismus. Alazami AM, et al. J Med Genet, 2013 Jul. PMID 23620220
    4. ADAT3-related intellectual disability: Further delineation of the phenotype. El-Hattab AW, et al. Am J Med Genet A, 2016 May. PMID 26842963
    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
    		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)

    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_2024_08

    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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