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    VARS2 valyl-tRNA synthetase 2, mitochondrial [ Homo sapiens (human) ]

    Gene ID: 57176, updated on 23-Nov-2023

    Summary

    Official Symbol
    VARS2provided by HGNC
    Official Full Name
    valyl-tRNA synthetase 2, mitochondrialprovided by HGNC
    Primary source
    HGNC:HGNC:21642
    See related
    Ensembl:ENSG00000137411 MIM:612802; AllianceGenome:HGNC:21642
    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
    VALRS; VARSL; VARS2L; COXPD20
    Summary
    This gene encodes a mitochondrial aminoacyl-tRNA synthetase, which catalyzes the attachment of valine to tRNA(Val) for mitochondrial translation. Mutations in this gene cause combined oxidative phosphorylation deficiency-20, and are also associated with early-onset mitochondrial encephalopathies. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Aug 2014]
    Expression
    Ubiquitous expression in brain (RPKM 7.4), esophagus (RPKM 6.1) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See VARS2 in Genome Data Viewer
    Location:
    6p21.33
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30914238..30926459)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (30778904..30791138)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30882015..30894236)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene discoidin domain receptor tyrosine kinase 1 Neighboring gene microRNA 4640 Neighboring gene general transcription factor IIH subunit 4 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:30889690-30890889 Neighboring gene surfactant associated 2 Neighboring gene uncharacterized LOC124901299 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:30905665-30906166

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Combined oxidative phosphorylation defect type 20
    MedGen: C4014660 OMIM: 615917 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Common genetic variation and the control of HIV-1 in humans.
    EBI GWAS Catalog
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    EBI GWAS Catalog
    Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: GTF2H4

    Clone Names

    • KIAA1885, MGC138259, MGC142165

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables valine-tRNA ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables valine-tRNA ligase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in aminoacyl-tRNA metabolism involved in translational fidelity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in valyl-tRNA aminoacylation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in mitochondrion IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    valine--tRNA ligase, mitochondrial
    Names
    valine tRNA ligase 2, mitochondrial (putative)
    valyl-tRNA synthetase like
    NP_001161205.1
    NP_001161206.1
    NP_065175.4

    NCBI Reference Sequences (RefSeq)

    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_034224.1 RefSeqGene

      Range
      5031..17252
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001167733.3NP_001161205.1  valine--tRNA ligase, mitochondrial isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains alternate 5' exon structure, and it thus differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AK293780, AK303415, BC073838
      Consensus CDS
      CCDS54981.1
      UniProtKB/TrEMBL
      A0A140T8Y0
      Related
      ENSP00000485818.1, ENST00000625423.2
      Conserved Domains (3) summary
      cd07962
      Location:594728
      Anticodon_Ia_Val; Anticodon-binding domain of valyl tRNA synthetases
      cd00817
      Location:1594
      ValRS_core; catalytic core domain of valyl-tRNA synthetases
      PTZ00419
      Location:1911
      PTZ00419; valyl-tRNA synthetase-like protein; Provisional
    2. NM_001167734.2NP_001161206.1  valine--tRNA ligase, mitochondrial isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK304807, AL669830, BC073838, BC112054
      UniProtKB/TrEMBL
      A0A140TA35, A0A1U9X992, A0A1U9X9A8, A0A1U9X9B3
      Conserved Domains (1) summary
      cl26128
      Location:1161081
      tRNA-synt_1g; tRNA synthetases class I (M)
    3. NM_020442.6NP_065175.4  valine--tRNA ligase, mitochondrial isoform 2 precursor

      See identical proteins and their annotated locations for NP_065175.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains alternate 5' exon structure, and it thus differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.
      Source sequence(s)
      AK294451, AK303415, BC073838
      Consensus CDS
      CCDS34387.1
      UniProtKB/Swiss-Prot
      A2ABL7, B4DET4, B4E3P5, F5GXJ0, F5H323, Q2M2A0, Q59FI1, Q5SQ96, Q5SS98, Q5ST30, Q6DKJ5, Q6ZV24, Q96GN2, Q96H77, Q96Q02, Q9H6R2, Q9UFH7
      UniProtKB/TrEMBL
      A0A140T8Y0
      Related
      ENSP00000502585.1, ENST00000676266.1
      Conserved Domains (3) summary
      cd07962
      Location:734868
      Anticodon_Ia_Val; Anticodon-binding domain of valyl tRNA synthetases
      cd00817
      Location:137734
      ValRS_core; catalytic core domain of valyl-tRNA synthetases
      PTZ00419
      Location:861051
      PTZ00419; valyl-tRNA synthetase-like protein; Provisional

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      30914238..30926459
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      2393984..2406057
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      2170542..2182776
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      2224474..2236697
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      2258385..2270615
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      2169404..2181636
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      30778904..30791138
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)