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Aliases for VARS2 Gene

Aliases for VARS2 Gene

  • Valyl-TRNA Synthetase 2, Mitochondrial 2 3
  • Valyl-TRNA Synthetase Like 2 3
  • EC 6.1.1.9 4 63
  • KIAA1885 4 6
  • VARS2L 3 4
  • ValRS 3 4
  • VARSL 3 4
  • Valyl-TRNA Synthetase 2, Mitochondrial (Putative) 2
  • Valine TRNA Ligase 2, Mitochondrial (Putative) 3
  • Valine--TRNA Ligase, Mitochondrial 3
  • Valyl-TRNA Synthetase 2-Like 2
  • Valyl-TRNA Synthetase-Like 4
  • Valyl-TRNA Synthetase 4
  • Valine TRNA Ligase 2 2
  • Mitochondrial 2
  • EC 6.1.1 63
  • COXPD20 3

External Ids for VARS2 Gene

Previous HGNC Symbols for VARS2 Gene

  • VARS2L
  • VARSL

Previous GeneCards Identifiers for VARS2 Gene

  • GC06M031816
  • GC06M031516
  • GC06M031851
  • GC06M031852
  • GC06M031853
  • GC06Pc31014
  • GC06P030992
  • GC06P030876
  • GC06P030682

Summaries for VARS2 Gene

Entrez Gene Summary for VARS2 Gene

  • 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]

GeneCards Summary for VARS2 Gene

VARS2 (Valyl-TRNA Synthetase 2, Mitochondrial) is a Protein Coding gene. Diseases associated with VARS2 include combined oxidative phosphorylation deficiency 20. Among its related pathways are Gene Expression and tRNA Aminoacylation. GO annotations related to this gene include aminoacyl-tRNA editing activity and valine-tRNA ligase activity. An important paralog of this gene is VARS.

No data available for UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VARS2 Gene

Genomics for VARS2 Gene

Regulatory Elements for VARS2 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for VARS2 Gene

Start:
30,908,242 bp from pter
End:
30,926,459 bp from pter
Size:
18,218 bases
Orientation:
Plus strand

Genomic View for VARS2 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for VARS2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for VARS2 Gene

  • Protein details for VARS2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q5ST30-SYVM_HUMAN
    Recommended name:
    Valine--tRNA ligase, mitochondrial
    Protein Accession:
    Q5ST30
    Secondary Accessions:
    • A2ABL7
    • B4DET4
    • B4E3P5
    • F5GXJ0
    • F5H323
    • Q2M2A0
    • Q59FI1
    • Q5SQ96
    • Q5SS98
    • Q6DKJ5
    • Q6ZV24
    • Q96GN2
    • Q96H77
    • Q96Q02
    • Q9H6R2
    • Q9UFH7

    Protein attributes for VARS2 Gene

    Size:
    1063 amino acids
    Molecular mass:
    118490 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB15191.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAB67778.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=BAD92716.1; Type=Miscellaneous discrepancy; Note=The sequence differs from that shown because it seems to be derived from a pre-mRNA.; Evidence={ECO:0000305}; Sequence=CAM24842.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAM25404.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAQ06763.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAQ09774.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAQ10925.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for VARS2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VARS2 Gene

Proteomics data for VARS2 Gene at MOPED

Post-translational modifications for VARS2 Gene

  • Ubiquitination at Lys54, Lys74, Lys477, and Lys684
  • Modification sites at PhosphoSitePlus

Other Protein References for VARS2 Gene

Domains for VARS2 Gene

Gene Families for VARS2 Gene

HGNC:
  • aaRS1 :Aminoacyl tRNA synthetases / Class I

Graphical View of Domain Structure for InterPro Entry

Q5ST30

UniProtKB/Swiss-Prot:

SYVM_HUMAN :
  • Q5ST30
Family:
  • Belongs to the class-I aminoacyl-tRNA synthetase family.
genes like me logo Genes that share domains with VARS2: view

Function for VARS2 Gene

Molecular function for VARS2 Gene

GENATLAS Biochemistry: valyl-tRNA synthetase 2,same as G7a,see HTFAG@
UniProtKB/Swiss-Prot CatalyticActivity: ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val)

Enzyme Numbers (IUBMB) for VARS2 Gene

Gene Ontology (GO) - Molecular Function for VARS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding --
GO:0002161 aminoacyl-tRNA editing activity IEA --
GO:0004812 aminoacyl-tRNA ligase activity --
GO:0004832 valine-tRNA ligase activity IBA --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with VARS2: view

Phenotypes for VARS2 Gene

GenomeRNAi human phenotypes for VARS2:
genes like me logo Genes that share phenotypes with VARS2: view

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VARS2

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , miRNA , Transcription Factor Targeting and HOMER Transcription for VARS2 Gene

Localization for VARS2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for VARS2 Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for VARS2 Gene COMPARTMENTS Subcellular localization image for VARS2 gene
Compartment Confidence
mitochondrion 3
cytosol 1
nucleus 1

Gene Ontology (GO) - Cellular Components for VARS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005829 NOT cytosol IBA --
genes like me logo Genes that share ontologies with VARS2: view

Pathways for VARS2 Gene

genes like me logo Genes that share pathways with VARS2: view

Pathways by source for VARS2 Gene

1 KEGG pathway for VARS2 Gene

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for VARS2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006418 tRNA aminoacylation for protein translation TAS --
GO:0006438 valyl-tRNA aminoacylation IBA --
GO:0006450 regulation of translational fidelity IEA --
GO:0010467 gene expression TAS --
genes like me logo Genes that share ontologies with VARS2: view

Compounds for VARS2 Gene

(5) HMDB Compounds for VARS2 Gene

Compound Synonyms Cas Number PubMed IDs
Adenosine monophosphate
  • 5'-AMP
61-19-8
Adenosine triphosphate
  • 5'-(tetrahydrogen triphosphate) Adenosine
56-65-5
L-Valine
  • (2S)-2-Amino-3-methylbutanoate
72-18-4
Phosphoric acid
  • acide phosphorique (FRENCH)
7664-38-2
Pyrophosphate
  • (4-)Diphosphoric acid ion
14000-31-8
genes like me logo Genes that share compounds with VARS2: view

Transcripts for VARS2 Gene

Unigene Clusters for VARS2 Gene

Valyl-tRNA synthetase 2, mitochondrial:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for VARS2

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for VARS2 Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b · 5c ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13a · 13b · 13c ^ 14a ·
SP1: - - - - - -
SP2: -
SP3: - - - - - - - - - - - - - - - - -
SP4: - -
SP5: - - -
SP6:
SP7: -
SP8:
SP9: -
SP10:

ExUns: 14b · 14c
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:

Relevant External Links for VARS2 Gene

GeneLoc Exon Structure for
VARS2
ECgene alternative splicing isoforms for
VARS2

Expression for VARS2 Gene

mRNA expression in normal human tissues for VARS2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for VARS2 Gene

SOURCE GeneReport for Unigene cluster for VARS2 Gene Hs.597526

genes like me logo Genes that share expressions with VARS2: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for VARS2 Gene

Orthologs for VARS2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for VARS2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VARS2 36
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VARS2 35
  • 88.2 (n)
  • 89.85 (a)
VARS2 36
  • 88 (a)
OneToOne
dog
(Canis familiaris)
Mammalia VARS2 35
  • 86.48 (n)
  • 85.63 (a)
VARS2 36
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vars2 35
  • 84.36 (n)
  • 84.17 (a)
Vars2 16
Vars2 36
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia VARS2 36
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VARS2 36
  • 67 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Vars2 35
  • 84.22 (n)
  • 84.16 (a)
lizard
(Anolis carolinensis)
Reptilia VARS2 36
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100493727 35
  • 57.92 (n)
  • 56.08 (a)
zebrafish
(Danio rerio)
Actinopterygii vars2 35
  • 57.4 (n)
  • 54.1 (a)
vars2 36
  • 50 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG5660 36
  • 37 (a)
OneToOne
Aats-val 37
  • 61 (a)
CG5660 37
  • 39 (a)
worm
(Caenorhabditis elegans)
Secernentea vars-1 36
  • 34 (a)
OneToOne
vrs-2 37
  • 53 (a)
vrs-1 37
  • 38 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VAS1 36
  • 38 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 37 (a)
OneToOne
Species with no ortholog for VARS2:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for VARS2 Gene

ENSEMBL:
Gene Tree for VARS2 (if available)
TreeFam:
Gene Tree for VARS2 (if available)

Paralogs for VARS2 Gene

Paralogs for VARS2 Gene

Selected SIMAP similar genes for VARS2 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with VARS2: view

Variants for VARS2 Gene

Sequence variations from dbSNP and Humsavar for VARS2 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type MAF
rs4678 - 30,926,164(-) GCTGC(C/T)GGAGG missense, reference
rs753725 -- 30,923,094(-) AAGGG(A/G)AGAAT intron-variant
rs753726 -- 30,922,792(-) GGGGG(A/C)AGGCA intron-variant
rs885905 -- 30,922,654(-) CTCTA(C/T)AAGGG intron-variant
rs887381 -- 30,922,429(-) GGTCA(A/G)CAGAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for VARS2 Gene

Variant ID Type Subtype PubMed ID
esv2731791 CNV Deletion 23290073
esv2670269 CNV Deletion 23128226
nsv525438 CNV Gain 19592680
nsv523346 CNV Loss 19592680
esv2088436 CNV Deletion 18987734
nsv884126 CNV Loss 21882294
esv2677874 CNV Deletion 23128226

Relevant External Links for VARS2 Gene

HapMap Linkage Disequilibrium report
VARS2
Human Gene Mutation Database (HGMD)
VARS2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for VARS2 Gene

Disorders for VARS2 Gene

MalaCards: The human disease database

MalaCards: The human disease database. (1) Diseases for VARS2 Gene including...

Search for VARS2 Gene in MalaCards »

UniProtKB/Swiss-Prot

SYVM_HUMAN
  • Combined oxidative phosphorylation deficiency 20 (COXPD20) [MIM:615917]: A disorder due to mitochondrial respiratory chain complex defects. Clinical features are variable and include muscle weakness with hypotonia, central neurological disease with progressive external ophthalmoplegia, ptosis and ataxia, delayed psychomotor development, cardiomyopathy, abnormal liver function, facial dysmorphism, microcephaly and epilepsy. {ECO:0000269 PubMed:24827421, ECO:0000269 PubMed:25058219}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for VARS2

Genetic Association Database (GAD)
VARS2
Human Genome Epidemiology (HuGE) Navigator
VARS2
genes like me logo Genes that share disorders with VARS2: view

Publications for VARS2 Gene

  1. Prediction of the coding sequences of unidentified human genes. XXI. The complete sequences of 60 new cDNA clones from brain which code for large proteins. (PMID: 11572484) Nagase T. … Ohara O. (DNA Res. 2001) 2 3 4
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  3. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos L.F. … Criswell L.A. (PLoS Genet. 2009) 3 48
  4. Common genetic variation and the control of HIV-1 in humans. (PMID: 20041166) Fellay J. … Goldstein D.B. (PLoS Genet. 2009) 3 48
  5. VARS2 and TARS2 mutations in patients with mitochondrial encephalomyopathies. (PMID: 24827421) Diodato D. … Ghezzi D. (Hum. Mutat. 2014) 3 4

Products for VARS2 Gene

Sources for VARS2 Gene

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