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    LARS2 leucyl-tRNA synthetase 2, mitochondrial [ Homo sapiens (human) ]

    Gene ID: 23395, updated on 28-Oct-2024

    Summary

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    Official Symbol
    LARS2provided by HGNC
    Official Full Name
    leucyl-tRNA synthetase 2, mitochondrialprovided by HGNC
    Primary source
    HGNC:HGNC:17095
    See related
    Ensembl:ENSG00000011376 MIM:604544; AllianceGenome:HGNC:17095
    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
    HLASA; LEURS; PRLTS4; mtLeuRS
    Summary
    This gene encodes a class 1 aminoacyl-tRNA synthetase, mitochondrial leucyl-tRNA synthetase. Each of the twenty aminoacyl-tRNA synthetases catalyzes the aminoacylation of a specific tRNA or tRNA isoaccepting family with the cognate amino acid. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in kidney (RPKM 6.2), brain (RPKM 5.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LARS2 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (45388576..45549407)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (45404942..45565766)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45430068..45590899)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA U3 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:45314637-45315836 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45348077-45348577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45347576-45348076 Neighboring gene uncharacterized LOC105377061 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:45353385-45353948 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:45353949-45354510 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:45354511-45355074 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:45355075-45355636 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45363491-45363991 Neighboring gene uncharacterized LOC105377062 Neighboring gene NANOG hESC enhancer GRCh37_chr3:45387482-45388007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14282 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:45430895-45431470 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:45434289-45435488 Neighboring gene MPRA-validated peak4627 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45534631-45534827 Neighboring gene LARS2 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:45549416-45550282 Neighboring gene Sharpr-MPRA regulatory region 486 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45585473-45585699 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45586492-45586702 Neighboring gene Sharpr-MPRA regulatory region 4333 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr3:45592715-45593914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19776 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19778 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45608597-45609123 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14283 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14284 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19779 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45638615-45639114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45649345-45649845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19781 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14285 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45671459-45671960 Neighboring gene LIM domain containing 1 Neighboring gene Sharpr-MPRA regulatory region 10324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:45688585-45689086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19782 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19783 Neighboring gene tRNA-Arg (anticodon ACG) 2-1 Neighboring gene LIMD1 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 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. Overexpressed mitochondrial leucyl-tRNA synthetase suppresses the A3243G mutation in the mitochondrial tRNA(Leu(UUR)) gene. Park H, et al. RNA, 2008 Nov. PMID 18796578, Free PMC Article
    2. The expanding LARS2 phenotypic spectrum: HLASA, Perrault syndrome with leukodystrophy, and mitochondrial myopathy. Riley LG, et al. Hum Mutat, 2020 Aug. PMID 32442335
    3. Knockdown of IARS2 suppressed growth of gastric cancer cells by regulating the phosphorylation of cell cycle-related proteins. Fang Z, et al. Mol Cell Biochem, 2018 Jun. PMID 29071539
    4. First independent replication of the involvement of LARS2 in Perrault syndrome by whole-exome sequencing of an Italian family. Soldà G, et al. J Hum Genet, 2016 Apr. PMID 26657938, Free PMC Article
    5. Degenerate connective polypeptide 1 (CP1) domain from human mitochondrial leucyl-tRNA synthetase. Ye Q, et al. J Biol Chem, 2015 Oct 2. PMID 26272616, Free PMC Article

    See all (77) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Exome sequencing reveals pathogenic mutations in the LARS2 and HSD17B4 genes associated with Perrault syndrome and D-bifunctional protein deficiency in Moroccan families.
      Title: Exome sequencing reveals pathogenic mutations in the LARS2 and HSD17B4 genes associated with Perrault syndrome and D-bifunctional protein deficiency in Moroccan families.
    2. [Analysis of perrault syndrome caused by pathogenic variants in LARS2 and HARS2 genes].
      Title: [Analysis of perrault syndrome caused by pathogenic variants in LARS2 and HARS2 genes].
    3. Neonatal lactic acidosis explained by LARS2 defect.
      Title: Neonatal lactic acidosis explained by LARS2 defect.
    4. Lin28a induced mitochondrial dysfunction in human granulosa cells via suppressing LARS2 expression.
      Title: Lin28a induced mitochondrial dysfunction in human granulosa cells via suppressing LARS2 expression.
    5. Leucine-tRNA-synthase-2-expressing B cells contribute to colorectal cancer immunoevasion.
      Title: Leucine-tRNA-synthase-2-expressing B cells contribute to colorectal cancer immunoevasion.
    6. LARS2 Regulates Apoptosis via ROS-Mediated Mitochondrial Dysfunction and Endoplasmic Reticulum Stress in Ovarian Granulosa Cells.
      Title: LARS2 Regulates Apoptosis via ROS-Mediated Mitochondrial Dysfunction and Endoplasmic Reticulum Stress in Ovarian Granulosa Cells.
    7. The expanding LARS2 phenotypic spectrum: HLASA, Perrault syndrome with leukodystrophy, and mitochondrial myopathy.
      Title: The expanding LARS2 phenotypic spectrum: HLASA, Perrault syndrome with leukodystrophy, and mitochondrial myopathy.
    8. This study adds LARS2 and KARS pathogenic variants as gene defects that may underlie deafness, ovarian failure, and leukodystrophy with mitochondrial signature.
      Title: Biallelic variants in LARS2 and KARS cause deafness and (ovario)leukodystrophy.
    9. We report novel associations between methylation at MSI2 and LARS2 and obesity-related traits. These results provide further insight into mechanisms underlying obesity-related traits, which can enable identification of new biomarkers in obesity-related chronic diseases.
      Title: An Epigenome-Wide Association Study of Obesity-Related Traits.
    10. We concluded that Perrault syndrome patients with LARS2 mutations are at risk for neurologic problems, despite previous notions otherwise.
      Title: Biallelic mutations in LARS2 can cause Perrault syndrome type 2 with neurologic symptoms.
    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

    Associated conditions

    Description Tests
    Hydrops-lactic acidosis-sideroblastic anemia-multisystemic failure syndrome
    MedGen: C4310761 OMIM: 617021 GeneReviews: Not available
    		Compare labs
    Perrault syndrome 4
    MedGen: C3809105 OMIM: 615300 GeneReviews: Perrault Syndrome
    		Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
    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

    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

    • KIAA0028, MGC26121

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables aminoacyl-tRNA editing activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables leucine-tRNA ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables leucine-tRNA ligase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables leucine-tRNA ligase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in aminoacyl-tRNA metabolism involved in translational fidelity IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in leucyl-tRNA aminoacylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in leucyl-tRNA aminoacylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mitochondrial translation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA aminoacylation for protein translation TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    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
    		  

    General protein information

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    Preferred Names
    leucine--tRNA ligase, mitochondrial
    Names
    leucine tRNA ligase 2, mitochondrial
    leucine tRNA ligase 2, mitocondrial
    leucine translase
    probable leucine--tRNA ligase, mitochondrial
    probable leucyl-tRNA synthetase, mitochondrial
    NP_001355192.1
    NP_056155.1
    XP_011531856.1
    XP_016861531.1
    XP_047303785.1
    XP_047303786.1
    XP_054201876.1
    XP_054201877.1
    XP_054201878.1
    XP_054201879.1

    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.

    Genomic

    1. NG_033907.3 RefSeqGene

      Range
      5013..165844
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1353

    mRNA and Protein(s)

    1. NM_001368263.1 → NP_001355192.1  leucine--tRNA ligase, mitochondrial

      Status: REVIEWED

      Source sequence(s)
      AC006515, AC092500, AC099539
      Consensus CDS
      CCDS2728.1
      UniProtKB/Swiss-Prot
      Q15031
      UniProtKB/TrEMBL
      E9PHM2
      Related
      ENSP00000498867.1, ENST00000650792.2

    2. NM_015340.4 → NP_056155.1  leucine--tRNA ligase, mitochondrial

      See identical proteins and their annotated locations for NP_056155.1

      Status: REVIEWED

      Source sequence(s)
      AC006515, AC099539, BI463427, D21851
      Consensus CDS
      CCDS2728.1
      UniProtKB/Swiss-Prot
      Q15031
      UniProtKB/TrEMBL
      E9PHM2
      Related
      ENSP00000495093.1, ENST00000645846.2
      Conserved Domains (1) summary
      PRK00390
      Location:57 → 901
      leuS; leucyl-tRNA synthetase; Validated

    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
      45388576..45549407
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017006042.2 → XP_016861531.1  leucine--tRNA ligase, mitochondrial isoform X2

      UniProtKB/TrEMBL
      E9PHM2
      Conserved Domains (1) summary
      PRK00390
      Location:57 → 801
      leuS; leucyl-tRNA synthetase; Validated

    2. XM_047447830.1 → XP_047303786.1  leucine--tRNA ligase, mitochondrial isoform X2

    3. XM_011533554.3 → XP_011531856.1  leucine--tRNA ligase, mitochondrial isoform X1

      UniProtKB/TrEMBL
      E9PHM2
      Conserved Domains (4) summary
      cd07958
      Location:678 → 803
      Anticodon_Ia_Leu_BEm; Anticodon-binding domain of bacterial and eukaryotic mitochondrial leucyl tRNA synthetases
      cd00812
      Location:83 → 678
      LeuRS_core; catalytic core domain of leucyl-tRNA synthetases
      pfam00133
      Location:61 → 679
      tRNA-synt_1; tRNA synthetases class I (I, L, M and V)
      pfam13603
      Location:271 → 430
      tRNA-synt_1_2; Leucyl-tRNA synthetase, Domain 2

    4. XM_047447829.1 → XP_047303785.1  leucine--tRNA ligase, mitochondrial isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      45404942..45565766
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345903.1 → XP_054201878.1  leucine--tRNA ligase, mitochondrial isoform X2

    2. XM_054345904.1 → XP_054201879.1  leucine--tRNA ligase, mitochondrial isoform X2

    3. XM_054345902.1 → XP_054201877.1  leucine--tRNA ligase, mitochondrial isoform X1

    4. XM_054345901.1 → XP_054201876.1  leucine--tRNA ligase, mitochondrial isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15031.2 GenPept UniProtKB/Swiss-Prot:Q15031

    Gene LinkOut

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

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