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

Gene ID: 57176, updated on 26-May-2016
Official Symbol
VARS2provided by HGNC
Official Full Name
valyl-tRNA synthetase 2, mitochondrialprovided by HGNC
Primary source
HGNC:HGNC:21642
See related
Ensembl:ENSG00000137411 HPRD:11670; MIM:612802; Vega:OTTHUMG00000031263
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]
Orthologs
Location:
6p21.33
Exon count:
30
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 6 NC_000006.12 (30914208..30926459)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30881982..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 surfactant associated 2 Neighboring gene diffuse panbronchiolitis critical region 1 Neighboring gene HLA complex group 21 (non-protein coding)

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Combined oxidative phosphorylation deficiency 20
MedGen: CN219640 OMIM: 615917 GeneReviews: Not available
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NHGRI GWAS Catalog

Description
Common genetic variation and the control of HIV-1 in humans.
NHGRI GWA Catalog
Genetic predictors of medically refractory ulcerative colitis.
NHGRI GWA Catalog
Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.
NHGRI GWA Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Potential readthrough

Included gene: GTF2H4

Homology

Clone Names

  • KIAA1885, MGC138259, MGC142165

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
aminoacyl-tRNA editing activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
valine-tRNA ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
Process Evidence Code Pubs
regulation of translational fidelity IEA
Inferred from Electronic Annotation
more info
 
valyl-tRNA aminoacylation IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
NOT cytosol IBA
Inferred from Biological aspect of Ancestor
more info
 
mitochondrion IEA
Inferred from Electronic Annotation
more info
 
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

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
    5001..17252
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001167733.2NP_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, DC307585
    Consensus CDS
    CCDS54981.1
    UniProtKB/Swiss-Prot
    Q5ST30
    UniProtKB/TrEMBL
    B4E0K6
    Related
    ENSP00000485818, OTTHUMP00000279370, ENST00000625423, OTTHUMT00000484413
    Conserved Domains (4) 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
    pfam12318
    Location:809918
    FAD-SLDH; Membrane bound FAD containing D-sorbitol dehydrogenase
  2. NM_001167734.1NP_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
    Consensus CDS
    CCDS54980.1
    UniProtKB/Swiss-Prot
    Q5ST30
    Related
    ENSP00000441000, OTTHUMP00000279371, ENST00000541562, OTTHUMT00000484414
    Conserved Domains (4) summary
    cd07962
    Location:764898
    Anticodon_Ia_Val; Anticodon-binding domain of valyl tRNA synthetases
    cd00817
    Location:167764
    ValRS_core; catalytic core domain of valyl-tRNA synthetases
    PTZ00419
    Location:1161081
    PTZ00419; valyl-tRNA synthetase-like protein; Provisional
    pfam12318
    Location:9791088
    FAD-SLDH; Membrane bound FAD containing D-sorbitol dehydrogenase
  3. NM_020442.5NP_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, DC307585
    Consensus CDS
    CCDS34387.1
    UniProtKB/Swiss-Prot
    Q5ST30
    UniProtKB/TrEMBL
    B4DG77, B4E0K6
    Related
    ENSP00000316092, OTTHUMP00000029388, ENST00000321897, OTTHUMT00000076566
    Conserved Domains (4) 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
    pfam12318
    Location:9491058
    FAD-SLDH; Membrane bound FAD containing D-sorbitol dehydrogenase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p2 Primary Assembly

    Range
    30914208..30926459
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p2 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p2 ALT_REF_LOCI_2

    Range
    2393954..2406057
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p2 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p2 ALT_REF_LOCI_3

    Range
    2170512..2182776
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p2 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p2 ALT_REF_LOCI_4

    Range
    2224444..2236697
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p2 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p2 ALT_REF_LOCI_5

    Range
    2258355..2270615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p2 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p2 ALT_REF_LOCI_6

    Range
    2169374..2181636
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018917.2 Alternate CHM1_1.1

    Range
    30884171..30896411
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)