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Aliases for VARS2 Gene

Aliases for VARS2 Gene

  • Valyl-TRNA Synthetase 2, Mitochondrial 2 3 5
  • Valyl-TRNA Synthetase Like 2 3
  • EC 6.1.1.9 4 63
  • VARS2L 3 4
  • ValRS 3 4
  • VARSL 3 4
  • Valyl-TRNA Synthetase 2, Mitochondrial (Putative) 2
  • Valine TRNA Ligase 2, Mitochondrial (Putative) 3
  • Valyl-TRNA Synthetase 2-Like 2
  • Valyl-TRNA Synthetase-Like 4
  • Valyl-TRNA Synthetase 4
  • Valine TRNA Ligase 2 2
  • Mitochondrial 2
  • KIAA1885 4
  • 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 and combined oxidative phosphorylation deficiency. Among its related pathways are Gene Expression and tRNA Aminoacylation. GO annotations related to this gene include nucleotide binding and aminoacyl-tRNA editing 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

Promoters for VARS2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around VARS2 on UCSC Golden Path with GeneCards custom track

Genomic Location for VARS2 Gene

Chromosome:
6
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

Genes around VARS2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VARS2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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 Lys 54, Lys 74, Lys 477, and Lys 684
  • Modification sites at PhosphoSitePlus

Domains & Families for VARS2 Gene

Gene Families for VARS2 Gene

Graphical View of Domain Structure for InterPro Entry

Q5ST30

UniProtKB/Swiss-Prot:

SYVM_HUMAN :
  • Belongs to the class-I aminoacyl-tRNA synthetase family.
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:0004812 aminoacyl-tRNA ligase activity IEA --
genes like me logo Genes that share ontologies with VARS2: view

Phenotypes for VARS2 Gene

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

Human Phenotype Ontology for VARS2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for VARS2

No data available for Animal Models , miRNA , Transcription Factor Targets 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 4
cytosol 1
nucleus 1

No data available for Gene Ontology (GO) - Cellular Components for VARS2 Gene

Pathways & Interactions 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

Gene Ontology (GO) - Biological Process for VARS2 Gene

None

No data available for SIGNOR curated interactions for VARS2 Gene

Drugs & Compounds for VARS2 Gene

(4) Drugs for VARS2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine monophosphate Approved Nutra 0
Adenosine triphosphate Approved Nutra 0
L-Valine Approved Nutra 0
Diphosphate Experimental Pharma 0

(1) Additional Compounds for VARS2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
phosphoric acid
  • Acide phosphorique (FRENCH)
  • Acido fosforico [Italian]
  • Acidum phosphoricum
  • Diphosphate tetrasodium
  • Fosforzuuroplossingen [Dutch]
7664-38-2
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:

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

Protein differential expression in normal tissues from HIPED for VARS2 Gene

This gene is overexpressed in Kidney (17.1) and Lymph node (11.1).

Integrated Proteomics: protein expression in normal tissues and cell lines 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 expression patterns with VARS2: view

Protein tissue co-expression partners for VARS2 Gene

Primer Products

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 36
  • 88 (a)
OneToOne
VARS2 35
  • 88.2 (n)
  • 89.85 (a)
dog
(Canis familiaris)
Mammalia VARS2 35
  • 86.48 (n)
  • 85.63 (a)
VARS2 36
  • 84 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Vars2 16
Vars2 36
  • 83 (a)
OneToOne
Vars2 35
  • 84.36 (n)
  • 84.17 (a)
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 36
  • 50 (a)
OneToOne
vars2 35
  • 57.4 (n)
  • 54.1 (a)
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-1 37
  • 38 (a)
vrs-2 37
  • 53 (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

(1) 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
rs6926723 - 30,915,026(+) TAGCA(A/G)GGGAG intron-variant, reference, missense
rs2249464 - 30,920,384(-) GCCCC(A/G)TTCAC reference, missense
rs2074506 - 30,922,706(-) CAGCA(A/C)CTGGG reference, missense
rs9394021 - 30,925,350(+) TCTCC(A/G)AGCCA reference, missense
rs2252863 - 30,925,651(-) TGCTG(C/T)GCCTG reference, missense

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

Variation tolerance for VARS2 Gene

Residual Variation Intolerance Score: 86.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 17.90; 98.38% of all genes are more intolerant (likely to be disease-causing)

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

(3) MalaCards diseases for VARS2 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
combined oxidative phosphorylation deficiency 20
  • combined oxidative phosphorylation deficiency type 20
combined oxidative phosphorylation deficiency
orchitis
  • inflammation of testis
- elite association - COSMIC cancer census association via MalaCards
Search VARS2 in MalaCards View complete list of genes associated with diseases

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
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
VARS2
genes like me logo Genes that share disorders with VARS2: view

No data available for Genatlas for VARS2 Gene

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 67
  2. Overexpression of human mitochondrial valyl tRNA synthetase can partially restore levels of cognate mt-tRNAVal carrying the pathogenic C25U mutation. (PMID: 18400783) Rorbach J. … Lightowlers R.N. (Nucleic Acids Res. 2008) 2 3
  3. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3
  4. Use of whole-exome sequencing to determine the genetic basis of multiple mitochondrial respiratory chain complex deficiencies. (PMID: 25058219) Taylor R.W. … Chinnery P.F. (JAMA 2014) 3
  5. VARS2 and TARS2 mutations in patients with mitochondrial encephalomyopathies. (PMID: 24827421) Diodato D. … Ghezzi D. (Hum. Mutat. 2014) 3

Products for VARS2 Gene

Sources for VARS2 Gene

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