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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VARS2 Gene

protein-coding   GIFtS: 61
GCID: GC06P030876

Valyl-TRNA Synthetase 2, Mitochondrial

(Previous names: valyl-tRNA synthetase 2-like, valyl-tRNA synthetase like,...)
(Previous symbols: VARS2L, VARSL)
Microbiology & Infectious Diseases Congress
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Valyl-TRNA Synthetase 2, Mitochondrial1 2     G7a2
VARS2L1 2 3     valRS2
VARSL1 2 3     Valine TRNA Ligase 2, Mitochondrial (Putative)2
Valyl-TRNA Synthetase 2, Mitochondrial (Putative)1 2     Valine--TRNA Ligase, Mitochondrial2
Valyl-TRNA Synthetase Like1 2     Valyl-TRNA Synthetase, Mitochondrial2
EC 6.1.1.93 8     ValRS3
KIAA18853 5     Valyl-TRNA Synthetase3
mitochondrial1     Valyl-TRNA Synthetase-Like3
Valine TRNA Ligase 21     EC 6.1.18
Valyl-TRNA Synthetase 2-Like1     

External Ids:    HGNC: 216421   Entrez Gene: 571762   Ensembl: ENSG000001374117   OMIM: 6128025   UniProtKB: Q5ST303   

Export aliases for VARS2 gene to outside databases

Previous GC identifers: GC06M031816 GC06M031516 GC06M031851 GC06M031852 GC06M031853 GC06Pc31014 GC06P030992 GC06P030682


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for VARS2 Gene: 
VARS2 (valyl-tRNA synthetase 2, mitochondrial) is a protein-coding gene. Diseases associated with VARS2 include pneumonia, and systemic lupus erythematosus, and among its related super-pathways are Cytosolic tRNA aminoacylation and Generic Transcription Pathway. GO annotations related to this gene include valine-tRNA ligase activity and aminoacyl-tRNA editing activity. An important paralog of this gene is VARS.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NT_007592.15  NT_113891.2  NT_167245.1  NT_167246.1  NT_167247.1  NT_167248.1  NC_018917.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VARS2 gene promoter:
         E2F-4   E2F-3a   E2F-5   STAT1   E2F-2   CREB   E2F   E2F-1   STAT3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVARS2 promoter sequence
   Search SABiosciences Chromatin IP Primers for VARS2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VARS2


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6p21.33   Ensembl cytogenetic band:  6p21.33   HGNC cytogenetic band: 6p21.33

VARS2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VARS2 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P030876:  view genomic region     (about GC identifiers)

Start:
30,876,019 bp from pter      End:
30,894,236 bp from pter
Size:
18,218 bases      Orientation:
plus strand

6/10 alternative locations (see all 10):
Chr6+,ALT_REF_LOCI_4 30,920,701-30,938,920      Chr6+,ALT_REF_LOCI_2 30,865,890-30,883,959      Chr6+,NT_167245 2,176,094-2,188,361     
Chr6+,ALT_REF_LOCI_3 30,866,734-30,884,964      Chr6+,NT_113891.2 2,394,057-2,406,163      Chr6+,NT_167246 2,230,061-2,242,317     

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SYVM_HUMAN, Q5ST30 (See protein sequence)
Recommended Name: Valine--tRNA ligase, mitochondrial precursor  
Size: 1063 amino acids; 118490 Da
Subcellular location: Mitochondrion (Potential)
Sequence caution: Sequence=BAB15191.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAB67778.1; Type=Erroneous initiation; Note=Translation N-terminally shortened; Sequence=BAD92716.1;
Type=Miscellaneous discrepancy; Note=The sequence differs from that shown because it seems to be derived from a
pre-mRNA; Sequence=CAM24842.1; Type=Erroneous gene model prediction; Sequence=CAM25404.1; Type=Erroneous gene
model prediction; Sequence=CAQ06763.1; Type=Erroneous gene model prediction; Sequence=CAQ09774.1; Type=Erroneous
gene model prediction; Sequence=CAQ10925.1; Type=Erroneous gene model prediction;
Secondary accessions: A2ABL7 B4DET4 B4E3P5 F5GXJ0 F5H323 Q2M2A0 Q59FI1 Q5SQ96 Q5SS98 Q6DKJ5
Q6ZV24 Q96GN2 Q96H77 Q96Q02 Q9H6R2 Q9UFH7
Alternative splicing: 4 isoforms:  Q5ST30-1   Q5ST30-2   Q5ST30-3   Q5ST30-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for VARS2: NX_Q5ST30

Explore proteomics data for VARS2 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q5ST30

  • 4/28 DME Specific Peptides for VARS2 (Q5ST30) (see all 28)
     DWCVSRQ  PPPNVTG  DALRFTL  GEKKDVS 

    VARS2 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    VARS2 Protein Expression
    REFSEQ proteins (3 alternative transcripts): 
    NP_001161205.1  NP_001161206.1  NP_065175.4  

    ENSEMBL proteins: 
     ENSP00000316092   ENSP00000403749   ENSP00000416390   ENSP00000441000   ENSP00000394802  
     ENSP00000438200  
    Reactome Protein details: Q5ST30
    Human Recombinant Protein Products for VARS2: 
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    OriGene Purified Protein for VARS2
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    Novus Biologicals VARS2 Lysate
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for VARS2 

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005739mitochondrion IEA--

    VARS2 for ontologies           About GeneDecksing



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    LSBio Antibodies in human, mouse, rat for VARS2 

    Assay Products for VARS2: 
    Browse Kits and Assays available from EMD Millipore
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    Cloud-Clone Corp. ELISAs for VARS2 
    Cloud-Clone Corp. CLIAs for VARS2


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    aaRS1: Aminoacyl tRNA synthetases / Class I

    5/7 InterPro protein domains (see all 7):
     IPR001412 aa-tRNA-synth_I_CS
     IPR002303 Valyl-tRNA_ligase
     IPR009080 tRNAsynth_1a_anticodon-bd
     IPR014729 Rossmann-like_a/b/a_fold
     IPR013155 V/L/I-tRNA-synth_anticodon-bd

    Graphical View of Domain Structure for InterPro Entry Q5ST30

    ProtoNet protein and cluster: Q5ST30

    3 Blocks protein domains:
    IPB002300 Aminoacyl-tRNA synthetase
    IPB002303 Valyl-tRNA synthetase signature
    IPB013155 tRNA synthetase


    UniProtKB/Swiss-Prot: SYVM_HUMAN, Q5ST30
    Similarity: Belongs to the class-I aminoacyl-tRNA synthetase family


    VARS2 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SYVM_HUMAN, Q5ST30
    Catalytic activity: ATP + L-valine + tRNA(Val) = AMP + diphosphate + L-valyl-tRNA(Val)

         Genatlas biochemistry entry for VARS2:
    valyl-tRNA synthetase 2,same as G7a,see HTFAG@

         Enzyme Numbers (IUBMB): EC 6.1.1.91 2 EC 6.1.12

         Gene Ontology (GO): 5 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding ----
    GO:0002161aminoacyl-tRNA editing activity IEA--
    GO:0004812aminoacyl-tRNA ligase activity ----
    GO:0004832valine-tRNA ligase activity IEA--
    GO:0005524ATP binding IEA--
         
    VARS2 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for VARS2:
     Decreased melanin production 

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for VARS2 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for VARS2

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for VARS2 
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    Inhib. RNA
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    Gene Editing
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                         Customized lentivirus expression plasmids for stable overexpression of VARS2 

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VARS2


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section

    SuperPaths for VARS2 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1tRNA Aminoacylation
    tRNA Aminoacylation0.57
    Mitochondrial tRNA aminoacylation0.50
    Aminoacyl-tRNA biosynthesis0.54
    2Generic Transcription Pathway
    Gene Expression0.47

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    3        Reactome Pathways for VARS2
        tRNA Aminoacylation
    Gene Expression
    Mitochondrial tRNA aminoacylation


    1         Kegg Pathway  (Kegg details for VARS2):
        Aminoacyl-tRNA biosynthesis


    VARS2 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VARS2

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    5/246 Interacting proteins for VARS2 (Q5ST302, 3 ENSP000003948024) via UniProtKB, MINT, STRING, and/or I2D (see all 246)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ICT1Q141972, 3MINT-8079030 I2D: score=1 
    PIK3CAP423363I2D: score=2 
    AARS2Q5JTZ92MINT-8079030
    AASSQ9UDR52MINT-8079030
    ABCB7O750272MINT-8079030
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006418tRNA aminoacylation for protein translation TAS--
    GO:0006438valyl-tRNA aminoacylation IEA--
    GO:0010467gene expression TAS--

    VARS2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for VARS2 (SYVM)

    5 HMDB Compounds for VARS2    About this table
    CompoundSynonyms CAS #PubMed Ids
    Adenosine monophosphate5'-AMP (see all 28)61-19-8--
    Adenosine triphosphate5'-(tetrahydrogen triphosphate) Adenosine (see all 24)56-65-5--
    L-Valine(2S)-2-Amino-3-methylbutanoate (see all 27)72-18-4--
    Phosphoric acidacide phosphorique (FRENCH) (see all 20)7664-38-2--
    Pyrophosphate(4-)Diphosphoric acid ion (see all 10)14000-31-8--

    Search CenterWatch for drugs/clinical trials and news about VARS2 / SYVM

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for VARS2 gene (3 alternative transcripts): 
    NM_001167733.1  NM_001167734.1  NM_020442.4  

    Unigene Cluster for VARS2:

    Valyl-tRNA synthetase 2, mitochondrial
    Hs.597526  [show with all ESTs]
    Unigene Representative Sequence: NM_001167734
    13 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000477288(uc003nsa.1 uc003nsc.2) ENST00000321897(uc003nsd.3 uc011dmx.2 uc011dmy.2 uc011dmz.2 uc011dna.2 uc011dnb.2 uc011dnc.2)
    ENST00000428017 ENST00000467717 ENST00000421263 ENST00000490699 ENST00000469358(uc011dnd.2 uc010jsg.2)
    ENST00000476162 ENST00000477052 ENST00000473916(uc010jsh.2) ENST00000541562
    ENST00000416670 ENST00000542001
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat VARS2
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    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 3): VARS2 (NM_020442)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for VARS2
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VARS2
    Sirion Biotech Customized lentivirus for stable overexpression of VARS2 
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat VARS2
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat VARS2

    Additional mRNA sequence: 

    AK000511.1 AK025618.1 AK026063.1 AK094483.1 AK125069.1 AK293780.1 AK294451.1 AK303415.1 
    AK304807.1 AK315733.1 AL122037.1 BC008844.2 BC009355.2 BC063427.1 BC073838.1 BC112054.1 
    BC113605.1 BC143534.1 BC143535.1 BC143536.1 

    10 DOTS entries:

    DT.414330  DT.99956622  DT.97848345  DT.101967025  DT.100783857  DT.100783864  DT.100783861  DT.121348680 
    DT.100783856  DT.95370180 

    24/149 AceView cDNA sequences (see all 149):

    BQ056176 BQ061499 BQ061568 BQ065288 BQ642138 BQ059035 BQ057069 BQ064403 
    BQ066769 BQ883157 BG910473 BQ061299 BI829652 BC073838 BQ057980 AI708217 
    BQ642051 AB067472 CD243965 BG910407 BM852646 BQ065373 BQ064294 BX095238 

    GeneLoc Exon Structure

    5/10 Alternative Splicing Database (ASD) splice patterns (SP) for VARS2 (see all 10)    About this scheme

    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:                                -                 -     -                                                                                                   

    ExUns: 14b · 14c
    SP1:            
    SP2:            
    SP3:            
    SP4:            
    SP5:            


    ECgene alternative splicing isoforms for VARS2

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    VARS2 expression in normal human tissues (normalized intensities)      VARS2 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAGCTGCAGG
    VARS2 Expression
    About this image


    VARS2 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/3 selected tissues (see all 3) fully expand
     
     Gut Tube (Gastrointestinal Tract)
             Foregut
     
     Lung (Respiratory System)
     
     Lymph (Hematopoietic System)

     -- (Respiratory System)
             visceral organ   

    See VARS2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VARS2

    SOURCE GeneReport for Unigene cluster: Hs.597526
        SABiosciences Expression via Pathway-Focused PCR Array including VARS2: 
              Amino Acid Metabolism II in human mouse rat

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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VARS2

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

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

    Orthologs for VARS2 gene from 6/13 species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vars21 , 5 valyl-tRNA synthetase 2, mitochondrial (putative)1, 5 84.36(n)1
    84.17(a)1
      17 (18.70 cM)5
    689151  NM_175137.41  NP_780346.31 
     356556345 
    lizard
    (Anolis carolinensis)
    Reptilia VARS26
    valyl-tRNA synthetase 2, mitochondrial
    56(a)
    1 ↔ 1
    2(191552203-191586735)
    zebrafish
    (Danio rerio)
    Actinopterygii vars21 valyl-tRNA synthetase 2, mitochondrial (putative) 57.73(n)
    54.72(a)
      100170827  NM_001130661.1  NP_001124133.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Aats-val3 valyl-tRNA aminoacylation
    glutamate-tRNA ligase
    61(a)
    (best of 2)
      49F7   --
    worm
    (Caenorhabditis elegans)
    Secernentea vrs-23   -- 53(a)
    (best of 2)
      I(13556522-13567394)   --
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes VAS16
    Mitochondrial and cytoplasmic valyl-tRNA synthetas...
    37(a)
    1 → many
    VII(672186-675500)


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for VARS2 gene
    VARS2  
    1 SIMAP similar gene for VARS2 using alignment to 4 protein entries:     SYVM_HUMAN (see all proteins):
    VARS

    VARS2 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/384 SNPs in VARS2 are shown (see all 384)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs32188301,2
    C--30882403(+) TATCCG/ATGGCT 3 -- int1 ese32Minor allele frequency- A:0.01NS NA 180
    rs12643041,2
    C,F,H--30882415(-) ACAGCG/ACCATG 3 -- int115Minor allele frequency- A:0.06NS NA 1908
    rs32188311,2
    C,F,H--30882431(+) GATACC/TATGCA 3 -- int115Minor allele frequency- T:0.04NS EA NA WA 1914
    rs1931507891,2
    --30882506(+) CTAATC/TAGAGA 3 -- int10--------
    rs12643031,2
    C,F,A,H--30882513(-) TTTCCT/CGTCTC 3 -- int1 ese322Minor allele frequency- C:0.20NS EA NA WA 2934
    rs1856052801,2
    --30882565(+) AATGTA/GCTCTC 3 -- int10--------
    rs1892139121,2
    --30882595(+) TCGGCC/GCCTTT 4 A ut51 int1 syn10--------
    rs563726241,2
    C--30882598(+) GCCCCC/TTTCCA 4 P ut51 int1 syn10--------
    rs12643021,2
    C,F,O,H--30882634(-) AAAGAG/AGCGAG 5 /A syn1 int1 ese324Minor allele frequency- A:0.26EA MN NS NA WA EU 10001
    rs1456948631,2
    C,F--30882636(+) CGCCTC/ATTTTC 5 /Y /S mis1 int12Minor allele frequency- A:0.00NA EU 5823

    HapMap Linkage Disequilibrium report for VARS2 (30876019 - 30894236 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for VARS2:    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2088436CNV Deletion18987734
    esv2670269CNV Deletion23128226
    esv2677874CNV Deletion23128226
    esv2731791CNV Deletion23290073
    nsv884126CNV Loss21882294
    nsv523346CNV Loss19592680
    nsv525438CNV Gain19592680

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 612802    OMIM disorders: --

    5 diseases for VARS2:    About MalaCards
    pneumonia    systemic lupus erythematosus    lupus erythematosus    tuberculosis
    breast cancer


    VARS2 for disorders           About GeneDecksing

    Genetic Association Database (GAD): VARS2
    Human Genome Epidemiology (HuGE) Navigator: VARS2 (7 documents)

    Export disorders for VARS2 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for VARS2 gene, integrated from 9 sources (see all 21):
    (articles sorted by number of sources associating them with VARS2)
        Utopia: connect your pdf to the dynamic
    world of online information

    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. (PubMed id 11572484)1, 2, 3 Nagase T....Ohara O. (2001)
    2. Genetic variants in nuclear-encoded mitochondrial gen es influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (2010)
    3. Common genetic variation and the control of HIV-1 in humans. (PubMed id 20041166)1, 4 Fellay J....Goldstein D.B. (2009)
    4. High-density SNP screening of the major histocompatib ility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1, 4 Barcellos L.F....Criswell L.A. (2009)
    5. Overexpression of human mitochondrial valyl tRNA synthetase can partially restore levels of cognate mt-tRNAVal carrying the pathogenic C25U mutation. (PubMed id 18400783)1, 3 Rorbach J....Lightowlers R.N. (2008)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    7. Evidence that gene G7a in the human major histocompatibility complex encodes valyl-tRNA synthetase. (PubMed id 1898367)1, 3 Hsieh H.-L. and Campbell R.D. (1991)
    8. Genome-wide association and longitudinal analyses reve al genetic loci linking pubertal height growth, pubertal timing and childhood ad iposity. (PubMed id 23449627)1 Cousminer D.L....Widen E. (2013)
    9. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    10. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
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      Query String
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    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 57176 HGNC: 21642 AceView: VARS2L Ensembl:ENSG00000137411 euGenes: HUgn57176
    ECgene: VARS2 Kegg: 57176 H-InvDB: VARS2

    (According to HUGE)
    About This Section
    HUGE: KIAA1885

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for VARS2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for VARS2 gene:
    Search GeneIP for patents involving VARS2

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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