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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)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for VARS2 Gene:
VARS2 (valyl-tRNA synthetase 2, mitochondrial) is a protein-coding gene. 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000006.11  NC_018917.2  NT_007592.16  NT_113891.3  NT_167245.2  NT_167246.2  NT_167247.2  NT_167248.2  
Regulatory elements:
   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 Chromatin IP Primers for VARS2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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

Selected alternative locations (see all 10):
Chr6+,NT_167248 2,174,967-2,187,232      Chr6+,NT_113891.2 2,394,057-2,406,163      Chr6+,NT_167245 2,176,094-2,188,361     
Chr6+,ALT_REF_LOCI_6 30,865,607-30,883,835      Chr6+,ALT_REF_LOCI_3 30,866,734-30,884,964      Chr6+,ALT_REF_LOCI_4 30,920,701-30,938,920     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: SYVM_HUMAN, Q5ST30 (See protein sequence)
Recommended Name: Valine--tRNA ligase, mitochondrial precursor  
Size: 1063 amino acids; 118490 Da
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: 

  • Ubiquitination2 at Lys54, Lys74, Lys477, Lys684
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for VARS2 (Q5ST30) (see all 28)
     DWCVSRQ  PPPNVTG  DALRFTL  GEKKDVS 


    See VARS2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    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

    VARS2 Human Recombinant Protein Products:

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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

     
    Search eBioscience for Proteins for VARS2 

     
    Search antibodies-online for proteins for VARS2 

     
    antibodies-online peptides for VARS2

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    antibodies-online antibodies for VARS2 (4 products) 

    VARS2 Assay Products:

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    Cloud-Clone Corp. ELISAs for VARS2
    Cloud-Clone Corp. CLIAs for VARS2
    Search eBioscience for ELISAs for VARS2 
    antibodies-online kits for VARS2 (5 products) 


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

    Selected InterPro protein domains (see all 7):
     IPR013155 V/L/I-tRNA-synth_anticodon-bd
     IPR002300 aa-tRNA-synth_Ia
     IPR001412 aa-tRNA-synth_I_CS
     IPR002303 Valyl-tRNA_ligase
     IPR009080 tRNAsynth_1a_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


    Find genes that share domains with VARS2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    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:    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--
         
    Find genes that share ontologies with VARS2           About GenesLikeMe


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

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for VARS2

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    Gene Editing
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    GenScript: all cDNA clones in your preferred vector (see all 3): VARS2 (NM_020442)
    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat VARS2

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for VARS2


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SYVM_HUMAN, Q5ST30: Mitochondrion (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    mitochondrion3
    cytosol1
    nucleus1

    Gene Ontology (GO): 1 cellular component term:    About this table

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

    Find genes that share ontologies with VARS2           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    SuperPaths for VARS2 About    
    See pathways by source

    SuperPathContained pathways About
    1tRNA Aminoacylation
    tRNA Aminoacylation0.57
    Mitochondrial tRNA aminoacylation0.50
    Aminoacyl-tRNA biosynthesis0.52
    2Gene Expression
    Gene Expression0.40


    Find genes that share SuperPaths with VARS2           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 Reactome Pathway for VARS2
        Mitochondrial tRNA aminoacylation


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

        Pathway & Disease-focused RT2 Profiler PCR Array including VARS2: 
              Amino Acid Metabolism II in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for VARS2

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

    Selected Interacting proteins for VARS2 (Q5ST302, 3 ENSP000003948024) via UniProtKB, MINT, STRING, and/or I2D (see all 245)
    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:    About this table

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

    Find genes that share ontologies with VARS2           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    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--



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    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
    miRNA
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    Inhib. RNA
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat VARS2
      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 

    Selected AceView cDNA sequences (see all 149):

    BQ642051 BM558402 BQ064276 BC073838 BQ883157 BQ057069 BQ064403 BQ063810 
    BQ065288 BQ065988 CB161826 AA496582 BQ057929 BQ642138 BQ066441 BQ066769 
    AW439283 BQ056176 BQ898198 BQ061499 BG910407 BQ896611 BQ061610 BQ643980 

    GeneLoc Exon Structure

    Selected 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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    VARS2 expression in normal human tissues (normalized intensities)
    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
     selected tissues (see all 3) fully expand
     
     Gut Tube (Gastrointestinal Tract)
             Foregut
     
     Lung (Respiratory System)
     
     Lymph (Hematopoietic System)
    VARS2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VARS2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.597526
        Pathway & Disease-focused RT2 Profiler PCR Array including VARS2: 
              Amino Acid Metabolism II in human mouse rat

    Primer
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    In Situ
    Assay Products:
     

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

    Orthologs for VARS2 gene from Selected species (see all 14)    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)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia LOC1004937271 valine--tRNA ligase, mitochondrial-like 57.92(n)
    56.08(a)
      100493727  XM_004917033.1  XP_004917090.1 
    zebrafish
    (Danio rerio)
    Actinopterygii vars21 valyl-tRNA synthetase 2, mitochondrial (putative) 57.4(n)
    54.1(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...
    38(a)
    1 → many
    VII(672186-675500) YGR094W


    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)
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    Paralogs for VARS2 gene
    VARS2  
    1 SIMAP similar gene for VARS2 using alignment to 4 protein entries:     SYVM_HUMAN (see all proteins):
    VARS

    Find genes that share paralogs with VARS2           About GenesLikeMe



    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for VARS2 (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

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing VARS2
    DNA2.0 Custom Variant and Variant Library Synthesis for VARS2

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


    Find genes that share disorders with VARS2           About GenesLikeMe

    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)
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    PubMed articles for VARS2 gene, integrated from 10 sources (see all 22):
    (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. (DNA Res. 2001)
    2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PubMed id 20877624)1, 4 Hendrickson S.L....O'Brien S.J. (PLoS ONE 2010)
    3. Common genetic variation and the control of HIV-1 in humans. (PubMed id 20041166)1, 4 Fellay J....Goldstein D.B. (PLoS Genet. 2009)
    4. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PubMed id 19851445)1, 4 Barcellos L.F....Criswell L.A. (PLoS Genet. 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. (Nucleic Acids Res. 2008)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 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. (Biochem. J. 1991)
    8. Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity. (PubMed id 23449627)1 Cousminer D.L....WidAcn E. (Hum. Mol. Genet. 2013)
    9. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    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)
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    Entrez Gene: 57176 HGNC: 21642 AceView: VARS2L Ensembl:ENSG00000137411 euGenes: HUgn57176
    ECgene: VARS2 Kegg: 57176 H-InvDB: VARS2

    (According to HUGE)
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    HUGE: KIAA1885

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    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.)
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    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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