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

Gene ID: 57176, updated on 8-Aug-2021

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
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
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Genomic context

See VARS2 in Genome Data Viewer
Location:
6p21.33
Exon count:
30
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (30914238..30926459)
105.20201022 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 surfactant associated 2 Neighboring gene mucin like 3 Neighboring gene HLA complex group 21

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 deficiency 20
MedGen: C4014660 OMIM: 615917 GeneReviews: Not available
not available
Common genetic variation and the control of HIV-1 in humans.
GeneReviews: Not available
Genetic predictors of medically refractory ulcerative colitis.
GeneReviews: Not available
Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.
GeneReviews: Not available

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Potential readthrough

Included gene: GTF2H4

Homology

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
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
PubMed 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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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_034224.1 RefSeqGene

    Range
    5001..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/Swiss-Prot
    Q5ST30
    UniProtKB/TrEMBL
    B4E0K6
    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
    Consensus CDS
    CCDS54980.1
    UniProtKB/Swiss-Prot
    Q5ST30
    UniProtKB/TrEMBL
    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
    Q5ST30
    UniProtKB/TrEMBL
    B4DG77, B4E0K6
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

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

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

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

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

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

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

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

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

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

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

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