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Aliases for VARS Gene

Aliases for VARS Gene

  • Valyl-TRNA Synthetase 2 3 4 5
  • Valine TRNA Ligase 1, Cytoplasmic 2 3
  • Valyl-TRNA Synthetase 2 2 3
  • Protein G7a 3 4
  • EC 6.1.1.9 4 56
  • ValRS 3 4
  • VARS2 3 4
  • G7A 3 4
  • Valine--TRNA Ligase 3
  • EC 6.1.1 56
  • NDMSCA 3
  • VARS1 3

External Ids for VARS Gene

Previous HGNC Symbols for VARS Gene

  • VARS2

Previous GeneCards Identifiers for VARS Gene

  • GC06M031855
  • GC06M031745
  • GC06M031531
  • GC06M031780
  • GC06M031782
  • GC06M031785
  • GC06M031801
  • GC06M031842
  • GC06M031883
  • GC06M031904

Summaries for VARS Gene

Entrez Gene Summary for VARS Gene

  • Aminoacyl-tRNA synthetases catalyze the aminoacylation of tRNA by their cognate amino acid. Because of their central role in linking amino acids with nucleotide triplets contained in tRNAs, aminoacyl-tRNA synthetases are thought to be among the first proteins that appeared in evolution. The protein encoded by this gene belongs to class-I aminoacyl-tRNA synthetase family and is located in the class III region of the major histocompatibility complex. [provided by RefSeq, Jul 2008]

GeneCards Summary for VARS Gene

VARS (Valyl-TRNA Synthetase) is a Protein Coding gene. Diseases associated with VARS include Neurodevelopmental Disorder With Microcephaly, Seizures, And Cortical Atrophy. Among its related pathways are Gene Expression and tRNA Aminoacylation. Gene Ontology (GO) annotations related to this gene include nucleotide binding and aminoacyl-tRNA editing activity. An important paralog of this gene is VARS2.

Gene Wiki entry for VARS Gene

Additional gene information for VARS Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for VARS Gene

Genomics for VARS Gene

GeneHancer (GH) Regulatory Elements for VARS Gene

Promoters and enhancers for VARS Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I031792 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 550.8 +0.3 258 6.7 DMAP1 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC MEF2D SSRP1 ZNF610 VARS2 VARS MSH5 SKIV2L C4A LSM2 ATF6B BAG6 LY6G5B HLA-DRB5
GH06I031733 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 47.5 +58.5 58498 8.5 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 MSH5 CLIC1 DDX39B LY6G5B ATF6B LSM2 CSNK2B SKIV2L GPANK1 BAG6
GH06I031813 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 45.7 -29.9 -29923 25.6 CLOCK ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 C6orf48 HSPA1B HSPA1A HSPA1L GC06P032039 ATF6B DDX39B LY6G5B LSM2 BAG6
GH06I032175 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 36 -381.8 -381807 5.1 DMAP1 YBX1 YY1 E2F8 ZNF143 ZNF548 SP3 NFYC GLIS1 NR2C1 RNF5 AGPAT1 BRD2 LSM2 LY6G5B DDX39B ATF6B GPANK1 VARS BAG6
GH06I031725 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 21.3 +67.4 67372 5.6 HDGF HNRNPUL1 PKNOX1 CLOCK ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 DDAH2 DDX39B LY6G5B ATF6B LSM2 SKIV2L PBX2 NFKBIL1 CSNK2B MSH5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around VARS on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the VARS gene promoter:

Genomic Locations for VARS Gene

Genomic Locations for VARS Gene
chr6:31,777,518-31,795,953
(GRCh38/hg38)
Size:
18,436 bases
Orientation:
Minus strand
chr6:31,745,295-31,763,730
(GRCh37/hg19)

Genomic View for VARS Gene

Genes around VARS on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
VARS Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for VARS Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for VARS Gene

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

    Protein Symbol:
    P26640-SYVC_HUMAN
    Recommended name:
    Valine--tRNA ligase
    Protein Accession:
    P26640
    Secondary Accessions:
    • B0V1N1
    • B4DZ61
    • Q5JQ90
    • Q96E77
    • Q9UQM2

    Protein attributes for VARS Gene

    Size:
    1264 amino acids
    Molecular mass:
    140476 Da
    Quaternary structure:
    • Forms high-molecular-mass aggregates with elongation factor 1.
    SequenceCaution:
    • Sequence=CAA41990.1; Type=Frameshift; Positions=620, 640; Evidence={ECO:0000305};

    Alternative splice isoforms for VARS Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for VARS Gene

Selected DME Specific Peptides for VARS Gene

P26640:
  • KITPAHD
  • PPPNVTG
  • GRKMSKS
  • GNVIDPL
  • FWLYELCDVY
  • IYRSTRLVNW
  • WCISRQL
  • YVEAAWYPWW
  • GRDINLD
  • DHAGIATQ
  • LDTWFSS
  • RFEARKAV
  • ISRQLWWGH
  • GFFKPEY
  • AQLKKEAKKREKLEKFQQK
  • GNVIDPLD
  • DILFFWV
  • FCNKLWNA
  • MSKSLGN
  • GTDALRF
  • DVLDTWFS
  • GEKKDVS
  • SAISDIEV
  • AVTEAFVR
  • WWGHRIP
  • EKGDRIYHQLKKLGSSLDWDRACFTMDPKLS
  • EAFVRLHE
  • SDEEVVVATTRIETMLGD

Post-translational modifications for VARS Gene

  • Ubiquitination at posLast=320320, isoforms=2418, isoforms=952, posLast=966966, and isoforms=1262

Other Protein References for VARS Gene

Domains & Families for VARS Gene

Gene Families for VARS Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

P26640

UniProtKB/Swiss-Prot:

SYVC_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 VARS: view

Function for VARS Gene

Molecular function for VARS Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val).
UniProtKB/Swiss-Prot EnzymeRegulation:
Can be regulated by protein kinase C-dependent phosphorylation.

Enzyme Numbers (IUBMB) for VARS Gene

Phenotypes From GWAS Catalog for VARS Gene

Gene Ontology (GO) - Molecular Function for VARS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002161 aminoacyl-tRNA editing activity IEA --
GO:0004812 aminoacyl-tRNA ligase activity IEA --
GO:0004832 valine-tRNA ligase activity TAS,IEA --
GO:0005515 protein binding IPI 24965446
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with VARS: view
genes like me logo Genes that share phenotypes with VARS: view

Inhibitory RNA Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for VARS Gene

Localization for VARS Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for VARS gene
Compartment Confidence
cytosol 5
mitochondrion 3
peroxisome 1
nucleus 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for VARS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IEA --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with VARS: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for VARS Gene

Pathways & Interactions for VARS Gene

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

Pathways by source for VARS Gene

1 BioSystems pathway for VARS Gene
1 KEGG pathway for VARS Gene

Gene Ontology (GO) - Biological Process for VARS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006412 translation IEA --
GO:0006418 tRNA aminoacylation for protein translation TAS,IEA --
GO:0006438 valyl-tRNA aminoacylation IEA,IBA --
GO:0006450 regulation of translational fidelity IEA --
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity IEA --
genes like me logo Genes that share ontologies with VARS: view

No data available for SIGNOR curated interactions for VARS Gene

Drugs & Compounds for VARS Gene

(9) Drugs for VARS Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
L-Valine Approved Nutra Target, Enzyme, substrate 0
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved, Investigational Nutra 0
ATP Investigational Nutra Agonist 0

(5) Additional Compounds for VARS Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with VARS: view

Transcripts for VARS Gene

Unigene Clusters for VARS Gene

Valyl-tRNA synthetase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for VARS Gene

GeneLoc Exon Structure for
VARS
ECgene alternative splicing isoforms for
VARS

Expression for VARS Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for VARS Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for VARS Gene

This gene is overexpressed in Lymph node (8.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for VARS Gene



Protein tissue co-expression partners for VARS Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of VARS Gene:

VARS

SOURCE GeneReport for Unigene cluster for VARS Gene:

Hs.520026

Evidence on tissue expression from TISSUES for VARS Gene

  • Liver(4.5)
  • Nervous system(4.5)
  • Muscle(4.1)
  • Skin(3.4)
  • Intestine(3.3)
  • Eye(2.5)
  • Pancreas(2.5)
  • Adrenal gland(2.1)
  • Heart(2.1)
genes like me logo Genes that share expression patterns with VARS: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for VARS Gene

Orthologs for VARS Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for VARS Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia VARS 33 34
  • 99.53 (n)
cow
(Bos Taurus)
Mammalia VARS 33 34
  • 90.33 (n)
dog
(Canis familiaris)
Mammalia VARS 33 34
  • 89.77 (n)
rat
(Rattus norvegicus)
Mammalia Vars 33
  • 87.55 (n)
mouse
(Mus musculus)
Mammalia Vars 33 16 34
  • 87.23 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 86 (a)
OneToMany
-- 34
  • 63 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia VARS 34
  • 79 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 70 (a)
OneToMany
-- 34
  • 62 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia vars 33
  • 63.38 (n)
Str.11856 33
zebrafish
(Danio rerio)
Actinopterygii vars 33 34
  • 64.74 (n)
vars2 33
fruit fly
(Drosophila melanogaster)
Insecta Aats-val 33 34
  • 61.25 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010420 33
  • 59.37 (n)
worm
(Caenorhabditis elegans)
Secernentea vars-2 33 34
  • 55.07 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR034W 33
  • 55.03 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D14971g 33
  • 53.2 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VAS1 33 34
  • 52.65 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons TWN2 33
  • 54.03 (n)
soybean
(Glycine max)
eudicotyledons Gma.16767 33
rice
(Oryza sativa)
Liliopsida Os03g0694900 33
  • 54.02 (n)
barley
(Hordeum vulgare)
Liliopsida Hv.3064 33
wheat
(Triticum aestivum)
Liliopsida Ta.2835 33
bread mold
(Neurospora crassa)
Ascomycetes NCU01965 33
  • 56.16 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes vrs1 33
  • 53.62 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3304 33
Species where no ortholog for VARS was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for VARS Gene

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

Paralogs for VARS Gene

Paralogs for VARS Gene

(2) SIMAP similar genes for VARS Gene using alignment to 4 proteins:

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

Variants for VARS Gene

Sequence variations from dbSNP and Humsavar for VARS Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1060499734 likely-pathogenic, pathogenic, Abnormality of brain morphology, NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, SEIZURES, AND CORTICAL ATROPHY 31,780,935(-) G/A coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs769369302 likely-pathogenic, pathogenic, Abnormality of brain morphology, NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, SEIZURES, AND CORTICAL ATROPHY 31,779,723(-) C/T coding_sequence_variant, downstream_transcript_variant, genic_downstream_transcript_variant, missense_variant
rs1000311185 -- 31,795,737(-) G/T 5_prime_UTR_variant, genic_upstream_transcript_variant, non_coding_transcript_variant
rs1000403325 -- 31,793,828(-) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000411178 -- 31,788,147(-) G/A intron_variant

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

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
esv3370799 CNV duplication 20981092
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv601943 CNV loss 21841781
nsv601944 CNV loss 21841781

Variation tolerance for VARS Gene

Residual Variation Intolerance Score: 27.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 16.30; 97.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for VARS Gene

Human Gene Mutation Database (HGMD)
VARS
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VARS

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

Disorders for VARS Gene

MalaCards: The human disease database

(1) MalaCards diseases for VARS Gene - From: OMIM

- elite association - COSMIC cancer census association via MalaCards
Search VARS in MalaCards View complete list of genes associated with diseases

Additional Disease Information for VARS

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with VARS: view

No data available for UniProtKB/Swiss-Prot and Genatlas for VARS Gene

Publications for VARS Gene

  1. Evidence that gene G7a in the human major histocompatibility complex encodes valyl-tRNA synthetase. (PMID: 1898367) Hsieh SL … Campbell RD (The Biochemical journal 1991) 3 4 22 58
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  3. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 44 58
  4. Toward the full set of human mitochondrial aminoacyl-tRNA synthetases: characterization of AspRS and TyrRS. (PMID: 15779907) Bonnefond L … Sissler M (Biochemistry 2005) 2 3 58
  5. Three-dimensional reconstruction of the valyl-tRNA synthetase/elongation factor-1H complex and localization of the delta subunit. (PMID: 16229838) Jiang S … Norcum MT (FEBS letters 2005) 3 22 58

Products for VARS Gene

Sources for VARS Gene

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