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    ALKBH8 alkB homolog 8, tRNA methyltransferase [ Homo sapiens (human) ]

    Gene ID: 91801, updated on 2-Nov-2024

    Summary

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    Official Symbol
    ALKBH8provided by HGNC
    Official Full Name
    alkB homolog 8, tRNA methyltransferaseprovided by HGNC
    Primary source
    HGNC:HGNC:25189
    See related
    Ensembl:ENSG00000137760 MIM:613306; AllianceGenome:HGNC:25189
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ABH8; TRM9; MRT71; TRMT9; TRMT9A
    Summary
    Enables tRNA (uridine) methyltransferase activity; tRNA binding activity; and zinc ion binding activity. Involved in DNA damage response; tRNA methylation; and tRNA wobble uridine modification. Located in cytosol and nucleoplasm. Implicated in autosomal recessive intellectual developmental disorder 71. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 3.3), lymph node (RPKM 3.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ALKBH8 in Genome Data Viewer
    Location:
    11q22.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (107502727..107565735, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (107509865..107572838, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (107373453..107436461, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105369477 Neighboring gene uncharacterized LOC124902745 Neighboring gene NANOG hESC enhancer GRCh37_chr11:107143023-107143770 Neighboring gene CWF19 like cell cycle control factor 2 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:107232171-107233370 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:107267561-107268760 Neighboring gene SMARCE1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:107328330-107328835 Neighboring gene H3K27ac hESC enhancers GRCh37_chr11:107435812-107436330 and GRCh37_chr11:107436331-107436847 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5471 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3870 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3871 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5472 Neighboring gene SUCLG2 pseudogene 3 Neighboring gene METTL5 pseudogene 4 Neighboring gene ELMO domain containing 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 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 first Turkish family with a novel biallelic missense variant of the ALKBH8 gene: A study on the clinical and variant spectrum of ALKBH8-related intellectual developmental disorders. Yılmaz M, et al. Am J Med Genet A, 2024 May. PMID 38189198
    2. HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs. Cavallin I, et al. RNA, 2022 Dec. PMID 36192131, Free PMC Article
    3. A novel human AlkB homologue, ALKBH8, contributes to human bladder cancer progression. Shimada K, et al. Cancer Res, 2009 Apr 1. PMID 19293182
    4. Insight into ALKBH8-related intellectual developmental disability based on the first pathogenic missense variant. Maddirevula S, et al. Hum Genet, 2022 Feb. PMID 34757492
    5. Neurodevelopmental disorder in an Egyptian family with a biallelic ALKBH8 variant. Saad AK, et al. Am J Med Genet A, 2021 Apr. PMID 33544954, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The first Turkish family with a novel biallelic missense variant of the ALKBH8 gene: A study on the clinical and variant spectrum of ALKBH8-related intellectual developmental disorders.
      Title: The first Turkish family with a novel biallelic missense variant of the ALKBH8 gene: A study on the clinical and variant spectrum of ALKBH8-related intellectual developmental disorders.
    2. HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs.
      Title: HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs.
    3. Insight into ALKBH8-related intellectual developmental disability based on the first pathogenic missense variant.
      Title: Insight into ALKBH8-related intellectual developmental disability based on the first pathogenic missense variant.
    4. Neurodevelopmental disorder in an Egyptian family with a biallelic ALKBH8 variant.
      Title: Neurodevelopmental disorder in an Egyptian family with a biallelic ALKBH8 variant.
    5. Loss of epitranscriptomic control of selenocysteine utilization engages senescence and mitochondrial reprogramming().
      Title: Loss of epitranscriptomic control of selenocysteine utilization engages senescence and mitochondrial reprogramming(☆).
    6. Recessive Truncating Mutations in ALKBH8 Cause Intellectual Disability and Severe Impairment of Wobble Uridine Modification.
      Title: Recessive Truncating Mutations in ALKBH8 Cause Intellectual Disability and Severe Impairment of Wobble Uridine Modification.
    7. findings suggest that the high expression of ALKBH8 is critical for the growth and progression of bladder cancer
      Title: ALKBH8 promotes bladder cancer growth and progression through regulating the expression of survivin.
    8. Many eukaryotic tRNAs contain the wobble modification 5-methoxycarbonylmethyl-uridine (mcm5U). It is demonstrated that (R)- and (S)-5-methoxycarbonylhydroxymethyluridine (mchm5U), hydroxylated forms of mcm(5)U, are present in mammalian tRNA-Arg(UCG), and tRNA-Gly(UCC), respectively. It is shown that the hydroxylation reaction leading to the formation of (S)-mchm5U is catalyzed by the oxygenase (AlkB) domain of ALKBH8.
      Title: ALKBH8-mediated formation of a novel diastereomeric pair of wobble nucleosides in mammalian tRNA.
    9. The methyltransferase domain of ALKBH8 is demonstrated to be a functional homologue of the Saccharomyces cerevisiae Trm9 protein, mediating the last step in the formation of the wobble uridine modification 5-methoxycarbonylmethyl-uridine in tRNA. This modification is shown to be important for efficient selenoprotein synthesis. ALKBH8 knock-out mice are generated and described.
      Title: Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding.
    10. Data show that human AlkB homolog 8 (ABH8) catalyzes tRNA methylation to generate 5-methylcarboxymethyl uridine (mcm(5)U) at the wobble position of certain tRNAs, a critical anticodon loop modification linked to DNA damage survival.
      Title: Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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 developmental disorder, autosomal recessive 71
    MedGen: C5193133 OMIM: 618504 GeneReviews: Not available
    		not available

    EBI GWAS Catalog

    Description
    Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
    EBI GWAS Catalog

    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

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of alkB, alkylation repair homolog 8 (ALKBH8) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • FLJ38204, MGC10235

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 2-oxoglutarate-dependent dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables S-adenosylmethionine-dependent methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables iron ion binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA (5-carboxymethyluridine(34)-5-O)-methyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tRNA (uridine) methyltransferase 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 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA methylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tRNA wobble uridine modification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA wobble uridine modification IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in tRNA wobble uridine modification IMP
    Inferred from Mutant Phenotype
    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
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    alkylated DNA repair protein alkB homolog 8
    Names
    AlkB homologue 8
    S-adenosyl-L-methionine-dependent tRNA methyltransferase ABH8
    alkB, alkylation repair homolog 8
    probable alpha-ketoglutarate-dependent dioxygenase ABH8
    tRNA (carboxymethyluridine(34)-5-O)-methyltransferase ABH8
    tRNA methyltransferase 9 homolog
    tRNA methyltransferase 9 related
    NP_001287939.2
    NP_001365062.1
    NP_620130.2
    XP_016874046.1
    XP_047283826.1
    XP_047283827.1
    XP_054226479.1
    XP_054226480.1
    XP_054226481.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    mRNA and Protein(s)

    1. NM_001301010.3 → NP_001287939.2  alkylated DNA repair protein alkB homolog 8 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 2. Variants 1 and 2 both encode the same isoform (1).
      Source sequence(s)
      AP001823
      Consensus CDS
      CCDS8337.2
      UniProtKB/Swiss-Prot
      B1Q2M0, B4DEF6, Q8N989, Q96BT7
      Related
      ENSP00000397673.3, ENST00000417449.6
      Conserved Domains (4) summary
      pfam09004
      Location:1 → 37
      DUF1891; Domain of unknown function (DUF1891)
      pfam13649
      Location:410 → 497
      Methyltransf_25; Methyltransferase domain
      cd12431
      Location:42 → 122
      RRM_ALKBH8; RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins
      cl21496
      Location:152 → 334
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

    2. NM_001378133.1 → NP_001365062.1  alkylated DNA repair protein alkB homolog 8 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AP001823
      Conserved Domains (3) summary
      pfam09004
      Location:1 → 37
      DUF1891; Domain of unknown function (DUF1891)
      cd12431
      Location:42 → 122
      RRM_ALKBH8; RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins
      cl21496
      Location:152 → 334
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

    3. NM_138775.3 → NP_620130.2  alkylated DNA repair protein alkB homolog 8 isoform 1

      See identical proteins and their annotated locations for NP_620130.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longer isoform (1). Variants 1 and 2 both encode the same isoform (1).
      Source sequence(s)
      AB218768, AP001823, BX649085
      Consensus CDS
      CCDS8337.2
      UniProtKB/Swiss-Prot
      B1Q2M0, B4DEF6, Q8N989, Q96BT7
      Related
      ENSP00000415885.2, ENST00000428149.7
      Conserved Domains (4) summary
      pfam09004
      Location:1 → 37
      DUF1891; Domain of unknown function (DUF1891)
      pfam13649
      Location:410 → 497
      Methyltransf_25; Methyltransferase domain
      cd12431
      Location:42 → 122
      RRM_ALKBH8; RNA recognition motif (RRM) found in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins
      cl21496
      Location:152 → 334
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

    RNA

    1. NR_165421.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AP001823

    2. NR_165422.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AP001823

    3. NR_165423.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AP001823

    4. NR_165424.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AP001823

    5. NR_165425.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AP001823

    6. NR_165426.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AP001823

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      107502727..107565735 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427870.1 → XP_047283826.1  alkylated DNA repair protein alkB homolog 8 isoform X1

    2. XM_047427871.1 → XP_047283827.1  alkylated DNA repair protein alkB homolog 8 isoform X3

    3. XM_017018557.2 → XP_016874046.1  alkylated DNA repair protein alkB homolog 8 isoform X2

      Conserved Domains (3) summary
      pfam09004
      Location:4 → 40
      DUF1891; Domain of unknown function (DUF1891)
      cd12431
      Location:45 → 125
      RRM_ALKBH8; RNA recognition motif in alkylated DNA repair protein alkB homolog 8 (ALKBH8) and similar proteins
      cl21496
      Location:155 → 337
      2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      107509865..107572838 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370504.1 → XP_054226479.1  alkylated DNA repair protein alkB homolog 8 isoform X1

    2. XM_054370506.1 → XP_054226481.1  alkylated DNA repair protein alkB homolog 8 isoform X3

    3. XM_054370505.1 → XP_054226480.1  alkylated DNA repair protein alkB homolog 8 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96BT7.2 GenPept UniProtKB/Swiss-Prot:Q96BT7

    Gene LinkOut

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

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