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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 58
  • 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 2, Mitochondrial 2
  • Valine--TRNA Ligase, Mitochondrial 3
  • Valyl-TRNA Synthetase 2-Like 2
  • Valyl-TRNA Synthetase-Like 4
  • Valyl-TRNA Synthetase 4
  • KIAA1885 4
  • EC 6.1.1 58
  • 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
  • GC06P030910
  • GC06P030912
  • GC06P031041

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 tRNA Aminoacylation and Gene Expression. GO annotations related to this gene include nucleotide binding and aminoacyl-tRNA editing activity. An important paralog of this gene is VARS.

Additional gene information for VARS2 Gene

No data available for CIViC summary , 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

Enhancers for VARS2 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H030875 1.7 FANTOM5 ENCODE dbSUPER 59.9 -31.4 -31423 3 HDGF PKNOX1 FOXA2 ARNT ARID4B ZNF2 YY1 ZNF766 ZNF143 DEK VARS2 ABCF1 LSM2 VARS TRIM39 PPP1R10 TRIM26 MDC1 DDX39B LY6G5B
GH06H030913 1.4 ENCODE dbSUPER 48.2 +6.4 6420 2 HNRNPUL1 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 VARS2 LSM2 NRM TRIM39 DDX39B LY6G5B DHX16 ZNRD1 TCF19 HLA-C
GH06H030777 2.1 FANTOM5 Ensembl ENCODE dbSUPER 31.6 -125.9 -125877 10 MLX ZFP64 DMAP1 YY1 SLC30A9 SP3 NFYC PPARGC1A MEF2D SSRP1 IER3 VARS2 PPP1R10 MDC1 DDX39B GTF2H4 ENSG00000233892 LY6G5B ETF1P1 TRIM39
GH06H030843 1.3 Ensembl ENCODE dbSUPER 47.3 -63.5 -63498 2 HDAC1 CTCF PKNOX1 MAX RAD21 YY1 TEAD3 GATA3 EGR1 SMC3 VARS2 HLA-C ENSG00000272501 ATP6V1G2 ZNRD1 LINC02570 LINC00243
GH06H030955 1.3 FANTOM5 ENCODE 47.3 +47.6 47603 0 PKNOX1 ATF1 SIN3A ELK1 ZNF143 ATF7 RUNX3 NCOA1 ZC3H11A REST VARS2 DDR1 DDR1-AS1 MICD GNL1 CCHCR1 HCG21 NAPGP2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around VARS2 on UCSC Golden Path with GeneCards custom track

Promoters for VARS2 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000195469 -142 1401 DMAP1 YBX1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC ZC3H11A MEF2D

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

Selected DME Specific Peptides for VARS2 Gene

Q5ST30:
  • GTGAVKVTPAH
  • DWCVSRQ
  • AVAVHPDD
  • PPPNVTG
  • DALRFTL
  • LPGCPTPVSFGLL
  • GRKMSKS
  • LPFSKVLLH
  • RYTHLHG
  • SRQLWWGHQIPA
  • VIAEDGTMTSLCGDWLQGLHRFVAREKI
  • YVEAAWYPWW
  • DHAGIATQ
  • LDTWFSS
  • YMELQGLVDPQ
  • MVRDRQGRKMSKSLGNVLDPR
  • QWFVRCQEMG
  • GFFKPEY
  • GPPQVLFSCAD
  • LHIGHALT
  • SVAFPVDGEPD
  • MSKSLGN
  • LHIGHAL
  • GTDALRF
  • DVLDTWFS
  • GEKKDVS
  • SAISDIEV
  • AVTEAFVR

Post-translational modifications for VARS2 Gene

  • Ubiquitination at Lys54, posLast=7474, Lys477, and posLast=684684
  • Modification sites at PhosphoSitePlus

Domains & Families for VARS2 Gene

Gene Families for VARS2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

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

Phenotypes From GWAS Catalog for VARS2 Gene

Gene Ontology (GO) - Molecular Function for VARS2 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 IEA,IBA --
GO:0005524 ATP binding IEA --
GO:0016874 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

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for VARS2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
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 VARS2 gene
Compartment Confidence
mitochondrion 5
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

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 & 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

GO ID Qualified GO term Evidence PubMed IDs
GO:0006412 translation IEA --
GO:0006418 tRNA aminoacylation for protein translation IEA --
GO:0006438 valyl-tRNA aminoacylation IEA,IBA --
GO:0006450 regulation of translational fidelity IEA --
genes like me logo Genes that share ontologies with VARS2: view

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
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
L-Valine Approved Nutra 0
ATP Nutra Agonist 0

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

Transcripts for VARS2 Gene

Unigene Clusters for VARS2 Gene

Valyl-tRNA synthetase 2, mitochondrial:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for VARS2
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for VARS2 Gene



Protein tissue co-expression partners for VARS2 Gene

NURSA nuclear receptor signaling pathways regulating expression of VARS2 Gene:

VARS2

SOURCE GeneReport for Unigene cluster for VARS2 Gene:

Hs.597526

Evidence on tissue expression from TISSUES for VARS2 Gene

  • Nervous system(4.8)
  • Eye(4.1)
  • Skin(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for VARS2 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • head
  • skull
genes like me logo Genes that share expression patterns with VARS2: view

Primer 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 34
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia VARS2 33 34
  • 88.2 (n)
dog
(Canis familiaris)
Mammalia VARS2 33 34
  • 86.48 (n)
mouse
(Mus musculus)
Mammalia Vars2 33 16 34
  • 84.36 (n)
rat
(Rattus norvegicus)
Mammalia Vars2 33
  • 84.22 (n)
oppossum
(Monodelphis domestica)
Mammalia VARS2 34
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia VARS2 34
  • 67 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia VARS2 34
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100493727 33
  • 57.92 (n)
zebrafish
(Danio rerio)
Actinopterygii vars2 33 34
  • 57.4 (n)
fruit fly
(Drosophila melanogaster)
Insecta Aats-val 35
  • 61 (a)
CG5660 35 34
  • 39 (a)
worm
(Caenorhabditis elegans)
Secernentea vrs-2 35
  • 53 (a)
vrs-1 35
  • 38 (a)
vars-1 34
  • 34 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes VAS1 34
  • 38 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 37 (a)
OneToOne
Species where no ortholog for VARS2 was found in the sources mined by GeneCards:
  • 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
rs587777583 Pathogenic, Combined oxidative phosphorylation deficiency 20 (COXPD20) [MIM:615917] 30,918,886(+) CTGTG(A/G)CCGTT reference, missense
rs587777584 Pathogenic, Combined oxidative phosphorylation deficiency 20 (COXPD20) [MIM:615917] 30,921,976(+) TTCTG(A/C)CCTGG reference, missense
rs587777585 Pathogenic, Combined oxidative phosphorylation deficiency 20 (COXPD20) [MIM:615917] 30,918,851(+) AACCA(C/G/T)AAGGC reference, missense
rs1057518559 Uncertain significance 30,923,146(+) CTGCC(A/G)ACATT reference, missense
rs367837827 Uncertain significance 30,922,159(+) GGAAA(C/T)GGGCA reference, missense

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

Variant ID Type Subtype PubMed ID
esv2088436 CNV deletion 18987734
esv2670269 CNV deletion 23128226
esv2677874 CNV deletion 23128226
esv2731791 CNV deletion 23290073
esv3411275 CNV duplication 20981092
esv3567511 CNV deletion 23714750
esv3608518 CNV gain 21293372
nsv1031677 CNV gain 25217958
nsv1074389 CNV deletion 25765185
nsv1122126 CNV deletion 24896259
nsv1144137 CNV deletion 24896259
nsv523346 CNV loss 19592680
nsv525438 CNV gain 19592680
nsv601264 CNV loss 21841781
nsv601481 CNV loss 21841781

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

Human Gene Mutation Database (HGMD)
VARS2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
VARS2

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

Disorders for VARS2 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
combined oxidative phosphorylation deficiency 20
  • coxpd20
- 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 research : an international journal for rapid publication of reports on genes and genomes 2001) 2 3 4 60
  2. VARS2 and TARS2 mutations in patients with mitochondrial encephalomyopathies. (PMID: 24827421) Diodato D … Ghezzi D (Human mutation 2014) 3 4 60
  3. Use of whole-exome sequencing to determine the genetic basis of multiple mitochondrial respiratory chain complex deficiencies. (PMID: 25058219) Taylor RW … Chinnery PF (JAMA 2014) 3 4 60
  4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 45 60
  5. 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 45 60

Products for VARS2 Gene

Sources for VARS2 Gene

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