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SETX Gene

protein-coding   GIFtS: 59
GCID: GC09M135136

Senataxin

(Previous names: amyotrophic lateral sclerosis 4, spinocerebellar ataxia,...)
(Previous symbols: ALS4, SCAR1)
  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)
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Aliases
senataxin1 2     Spinocerebellar Ataxia, Recessive, Non-Friedreich Type 11
ALS41 2 3 5     bA479K20.22
SCAR11 2 3 5     Probable Helicase Senataxin2
Amyotrophic Lateral Sclerosis 4 Protein2 3     EC 3.6.4.-3
SEN1 Homolog2 3     KIAA06253
AOA22 5     EC 3.6.18
Amyotrophic Lateral Sclerosis 41     

External Ids:    HGNC: 4451   Entrez Gene: 230642   Ensembl: ENSG000001072907   OMIM: 6084655   UniProtKB: Q7Z3333   

Export aliases for SETX gene to outside databases

Previous GC identifers: GC09M132170 GC09M134129 GC09M104630


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SETX Gene:
This gene encodes a protein named for its homology to the Sen1p protein of fungi which has RNA helicase activity
encoded by a domain at the C-terminal end of the protein. The protein encoded by this gene contains a DNA/RNA
helicase domain at its C-terminal end which suggests that it may be involved in both DNA and RNA processing.
Mutations in this gene have been associated with ataxia-ocular apraxia-2 (AOA2) and an autosomal dominant form of
juvenile amyotrophic lateral sclerosis (ALS4). (provided by RefSeq, Jul 2008)

GeneCards Summary for SETX Gene:
SETX (senataxin) is a protein-coding gene. Diseases associated with SETX include setx-related amyotrophic lateral sclerosis, and amyotrophic lateral sclerosis, type 4. GO annotations related to this gene include DNA helicase activity. An important paralog of this gene is ZNFX1.

UniProtKB/Swiss-Prot: SETX_HUMAN, Q7Z333
Function: Probable helicase, which may be involved in RNA maturation (By similarity). Involved in DNA
double-strand breaks damage response generated by oxidative stress

Gene Wiki entry for SETX Gene


(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:
NC_000009.12  NT_008470.20  NC_018920.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SETX gene promoter:
         ISGF-3   FOXO3   FOXD3   Cdc5   FOXO3b   MEF-2A   POU2F1   POU2F1a   FOXO3a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SETX

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SETX


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

Entrez Gene cytogenetic band: 9q34.13   Ensembl cytogenetic band:  9q34.13   HGNC cytogenetic band: 9q34

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

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09M135136:  view genomic region     (about GC identifiers)

Start:
135,136,743 bp from pter      End:
135,230,372 bp from pter
Size:
93,630 bases      Orientation:
minus strand

(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, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SETX_HUMAN, Q7Z333 (See protein sequence)
Recommended Name: Probable helicase senataxin  
Size: 2677 amino acids; 302880 Da
Sequence caution: Sequence=BAA91701.1; Type=Erroneous initiation; Note=Translation N-terminally extended;
Sequence=BAB14299.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAD97857.1;
Type=Frameshift; Positions=1626;
Secondary accessions: A2A396 B2RPB2 B5ME16 C9JQ10 O75120 Q3KQX4 Q5JUJ1 Q68DW5 Q6AZD7 Q7Z3J6
Q8WX33 Q9H9D1 Q9NVP9
Alternative splicing: 3 isoforms:  Q7Z333-1   Q7Z333-3   Q7Z333-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SETX: NX_Q7Z333

Explore proteomics data for SETX at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys19, Lys49, Lys339
  • Modification sites at PhosphoSitePlus
  • 4 DME Specific Peptides for SETX (Q7Z333)
     SPATDDA  LVCAPSN  DRGIIVS  LTVQYRM 


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

    REFSEQ proteins: NP_055861.3  
    ENSEMBL proteins: 
     ENSP00000409143   ENSP00000224140   ENSP00000361242   ENSP00000376913  

    SETX Human Recombinant Protein Products:

    Browse Purified and Recombinant Proteins at EMD Millipore
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    Browse recombinant and purified proteins available from Enzo Life Sciences
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    Browse OriGene Protein Over-expression Lysates
    OriGene Custom MassSpec
    OriGene Custom Protein Services for SETX
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    Novus Biologicals SETX Protein
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for SETX

    SETX Antibody Products:

    Browse EMD Millipore's Extensive Line of Mono- and Polyclonal Antibodies
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    OriGene Antibodies for SETX
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    Novus Biologicals SETX Antibodies
    Search for Antibodies for SETX at Abcam
    Cloud-Clone Corp. Antibodies for SETX
    Search ThermoFisher Antibodies for SETX
    LSBio Antibodies in human, mouse, rat for SETX

    SETX Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    GenScript Custom Assay Services for SETX
    Browse Enzo Life Sciences for kits & assays
    Cloud-Clone Corp. ELISAs for SETX
    Cloud-Clone Corp. CLIAs for SETX


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR026121 Senataxin
     IPR027417 P-loop_NTPase

    Graphical View of Domain Structure for InterPro Entry Q7Z333

    ProtoNet protein and cluster: Q7Z333

    UniProtKB/Swiss-Prot: SETX_HUMAN, Q7Z333
    Similarity: Belongs to the DNA2/NAM7 helicase family


    SETX 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,
    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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SETX_HUMAN, Q7Z333
    Function: Probable helicase, which may be involved in RNA maturation (By similarity). Involved in DNA
    double-strand breaks damage response generated by oxidative stress

         Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.-1

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IC17562789
    GO:0003678DNA helicase activity TAS17562789
    GO:0005515protein binding ----
    GO:0005524ATP binding IEA--
         
    SETX for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for SETX:
     Increased homologous recombina 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for SETX
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for SETX

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for SETX
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for SETX

    miRNA
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    miRTarBase miRNAs that target SETX:
    hsa-mir-335-5p (MIRT016893), hsa-mir-18a-3p (MIRT040922)

    Block miRNA regulation of human, mouse, rat SETX using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SETX (see all 21):
    hsa-miR-300 hsa-miR-181c hsa-miR-488 hsa-miR-340 hsa-miR-23a hsa-miR-3143 hsa-miR-181b hsa-miR-3163
    SwitchGear 3'UTR luciferase reporter plasmidSETX 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SETX

    Gene Editing
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    OriGene ORF clones in mouse, rat for SETX
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SETX (NM_015046)
    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SETX
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SETX

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for SETX 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SETX


    (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
    SETX_HUMAN, Q7Z333: Nucleus, nucleoplasm. Nucleus, nucleolus. Cytoplasm. Note=May be detected in the nucleolus
    only in cycling cells (By similarity). Most abundant in the nucleus. Detected in granules. Colocalized in cycling
    cells with FBL in the nucleolus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2
    mitochondrion1
    plasma membrane1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA17562789
    GO:0005654nucleoplasm IDA17562789
    GO:0005730nucleolus IEA--
    GO:0005737cytoplasm IDA17562789

    SETX for ontologies           About GeneDecksing


    (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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SETX
    Interactions:

        GeneGlobe Interaction Network for SETX

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SETX (Q7Z3332, 3 ENSP000002241404) via UniProtKB, MINT, STRING, and/or I2D (see all 850)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    EXOSC10Q017802, ENSP000003661354MINT-7945693 MINT-7947479 STRING: ENSP00000366135
    MRE11AP499592, ENSP000003258634MINT-7945693 MINT-7947479 STRING: ENSP00000325863
    RAD50Q928782, ENSP000002653354MINT-7945693 MINT-7947479 STRING: ENSP00000265335
    CDC5LQ994592, ENSP000003605324MINT-7945693 MINT-7947479 STRING: ENSP00000360532
    CDK9P507502, ENSP000003623614MINT-7945693 MINT-7947479 STRING: ENSP00000362361
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006302double-strand break repair IDA17562789
    GO:0006369termination of RNA polymerase II transcription IEA--
    GO:0006396RNA processing TAS17562789
    GO:0007623circadian rhythm IEA--
    GO:0008219cell death IEA--

    SETX for ontologies           About GeneDecksing



    (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 SETX

    2 Novoseek inferred chemical compound relationships for SETX gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    vitamin-e 31.4 3 17112370 (1), 16193447 (1), 19141356 (1)
    alpha tocopherol 26 3 17112370 (1), 16193447 (1)



    SETX for compounds           About GeneDecksing



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for SETX gene: 
    NM_015046.5  

    Unigene Cluster for SETX:

    Senataxin
    Hs.460317  [show with all ESTs]
    Unigene Representative Sequence: NM_015046
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000477049 ENST00000436441 ENST00000224140(uc004cbk.3) ENST00000464133
    ENST00000474172 ENST00000372169(uc004cbj.3) ENST00000393220(uc010mzt.3)

    miRNA
    Products:
         
    Block miRNA regulation of human, mouse, rat SETX using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate SETX (see all 21):
    hsa-miR-300 hsa-miR-181c hsa-miR-488 hsa-miR-340 hsa-miR-23a hsa-miR-3143 hsa-miR-181b hsa-miR-3163
    SwitchGear 3'UTR luciferase reporter plasmidSETX 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SETX
    Clone
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    OriGene ORF clones in mouse, rat for SETX
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector: SETX (NM_015046)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for SETX
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat SETX
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for SETX
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat SETX
      QuantiTect SYBR Green Assays in human, mouse, rat SETX
      QuantiFast Probe-based Assays in human, mouse, rat SETX

    Additional mRNA sequence: 

    AB014525.2 AK001456.1 AK022902.1 AK024331.1 AK025601.1 AK125448.1 AK226007.1 AK302394.1 
    AK307608.1 AY362728.1 BC032600.2 BC032622.1 BC078166.1 BC106017.1 BC137350.1 BX537849.1 
    BX538166.1 CR749249.1 

    18 DOTS entries:

    DT.95149009  DT.92439864  DT.454599  DT.121150438  DT.121150483  DT.100784916  DT.95152255  DT.86841179 
    DT.92439876  DT.92439878  DT.40129268  DT.95148864  DT.95345721  DT.97822805  DT.97823827  DT.121150474 
    DT.91646793  DT.97783983 

    Selected AceView cDNA sequences (see all 395):

    BF477616 BQ026818 AI248414 Z40775 AA505301 BE259907 AI333472 AA704244 
    AA253472 BP871766 AA904455 CA445491 BQ271780 BM054862 AA962467 AL046658 
    BF939450 AA864908 CA419586 Z45213 BM718142 AA284334 AI290332 AI951150 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for SETX (see all 8)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                                                                                                            
    SP4:        -                                                                                                                                                   
    SP5:                                                                                -     -     -                                                               

    ExUns: 22a · 22b ^ 23 ^ 24a · 24b ^ 25a · 25b ^ 26a · 26b ^ 27 ^ 28 ^ 29 ^ 30a · 30b
    SP1:        -                                         -                 -               
    SP2:                                                                                    
    SP3:                                                  -                                 
    SP4:                                                                                    
    SP5:                                                                                    


    ECgene alternative splicing isoforms for SETX

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

    SETX Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SETX Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.460317

    UniProtKB/Swiss-Prot: SETX_HUMAN, Q7Z333
    Tissue specificity: Highly expressed in skeletal muscle. Expressed in heart, fibroblast, placenta and liver.
    Weakly expressed in brain and lung. Expressed in the cortex of the kidney (highly expressed in tubular epithelial
    cells but low expression in the glomerulus)

        Custom PCR Arrays for SETX
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SETX

    (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 SETX gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Setx1 , 5 senataxin1, 5 80.01(n)1
    73.57(a)1
      2 (19.45 cM)5
    2692541  NM_198033.21  NP_932150.21 
     291241815 
    chicken
    (Gallus gallus)
    Aves SETX1 senataxin 63.42(n)
    56.13(a)
      417170  XM_004945911.1  XP_004945968.1 
    lizard
    (Anolis carolinensis)
    Reptilia SETX6
    senataxin
    39(a)
    1 ↔ 1
    GL344844.1(47-19376)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia setx1 senataxin 56.86(n)
    50.64(a)
      100145435  XM_002936175.2  XP_002936221.1 
    zebrafish
    (Danio rerio)
    Actinopterygii CF594441.12   -- 76.65(n)    CF594441.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG75046
    --
    20(a)
    many ↔ many
    3L(8124529-8130598)
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes SEN1(YLR430W)4 Presumed helicase required for RNA polymerase II transcription more   --   12(993434-1000129) 851150  NP_013534.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SETX gene
    ZNFX12  AQR2  

    SETX 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), 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 SETX (see all 2656)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1163330611,2,,4
    C,FSpinocerebellar ataxia, autosomal recessive, 1 (SCAR1)4 pathogenic1135219907(+) GTCTTG/TCACTT 2 K Q mis13Minor allele frequency- T:0.01WA NA EU 5977
    rs1162050321,2,,4
    C,FSpinocerebellar ataxia, autosomal recessive, 1 (SCAR1)4 pathogenic1135220057(+) AGTGTT/CACATG 2 /N /D mis13Minor allele frequency- C:0.01WA NA EU 5927
    rs290015841,2,,4
    CAmyotrophic lateral sclerosis 4 (ALS4)4 pathogenic1135220698(-) AACATT/CAGCCA 2 /S /L mis11Minor allele frequency- C:0.00EU 1323
    rs290016651,2,,4
    CSpinocerebellar ataxia, autosomal recessive, 1 (SCAR1)4 pathogenic1135221559(-) ATATAC/TGGAAC 2 R W mis10--------
    VAR_0366494
    Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1)4--see VAR_0366492 R C mis40--------
    VAR_0366504
    Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1)4--see VAR_0366502 P R mis40--------
    VAR_0187774
    Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1)4--see VAR_0187772 W C mis40--------
    VAR_0187904
    Amyotrophic lateral sclerosis 4 (ALS4)4--see VAR_0187902 R H mis40--------
    VAR_0187884
    Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1)4--see VAR_0187882 F S mis40--------
    VAR_0366464
    Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1)4--see VAR_0366462 M I mis40--------

    HapMap Linkage Disequilibrium report for SETX (135136743 - 135230372 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for SETX:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv989756CNV Deletion20482838
    esv2739126CNV Deletion23290073
    esv1132189CNV Deletion17803354
    nsv509328CNV Insertion20534489
    nsv433506CNV Loss18776910
    dgv8318n71CNV Loss21882294
    nsv894020CNV Gain21882294
    nsv894021CNV Gain21882294

    Human Gene Mutation Database (HGMD): SETX
    Locus Specific Mutation Databases (LSDB): SETX

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

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 608465   
    OMIM disorders: 606002  602433  
    UniProtKB/Swiss-Prot: SETX_HUMAN, Q7Z333
  • Spinocerebellar ataxia, autosomal recessive, 1 (SCAR1) [MIM:606002]: Spinocerebellar ataxia is a
    clinically and genetically heterogeneous group of cerebellar disorders. Patients show progressive incoordination
    of gait and often poor coordination of hands, speech and eye movements, due to degeneration of the cerebellum
    with variable involvement of the brainstem and spinal cord. SCAR1 is an autosomal recessive form associated with
    peripheral neuropathy and elevated serum alpha-fetoprotein, immunoglobulins and, less commonly, creatine kinase
    levels. Some SCAR1 patients manifest oculomotor apraxia. Note=The disease is caused by mutations affecting the
    gene represented in this entry
  • Amyotrophic lateral sclerosis 4 (ALS4) [MIM:602433]: A form of amyotrophic lateral sclerosis with
    childhood- or adolescent-onset, and characterized by slow disease progression and the sparing of bulbar and
    respiratory muscles. Amyotrophic lateral sclerosis is a neurodegenerative disorder affecting upper motor neurons
    in the brain and lower motor neurons in the brain stem and spinal cord, resulting in fatal paralysis. Sensory
    abnormalities are absent. The pathologic hallmarks of the disease include pallor of the corticospinal tract due
    to loss of motor neurons, presence of ubiquitin-positive inclusions within surviving motor neurons, and
    deposition of pathologic aggregates. The etiology of amyotrophic lateral sclerosis is likely to be
    multifactorial, involving both genetic and environmental factors. The disease is inherited in 5-10% of the cases.
    Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for SETX (see all 29):    
    About MalaCards
    setx-related amyotrophic lateral sclerosis    amyotrophic lateral sclerosis, type 4    amyotrophic lateral sclerosis 4, juvenile    spinocerebellar ataxia autosomal recessive 1
    ataxia with oculomotor apraxia type 2    apraxia    amyotrophic lateral sclerosis type 2    proximal spinal muscular atrophy
    lateral sclerosis    doid:4019    ataxia    cerebellar ataxia
    friedreich ataxia    spinal muscular atrophy    amyotrophic lateral sclerosis    splenic marginal zone lymphoma
    spinocerebellar ataxia    distal hereditary motor neuropathy    muscular atrophy    axonal neuropathy

    7 diseases from the University of Copenhagen DISEASES database for SETX:
    Apraxia     DOID:4019     Cerebellar ataxia     Amyotrophic lateral sclerosis
    Ataxia telangiectasia     Friedreich ataxia     Neuropathy

    SETX for disorders           About GeneDecksing

    8 Novoseek inferred disease relationships for SETX gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    third-nerve palsy 93 1 18405395 (1)
    cerebellar ataxia early onset 92.1 1 16193447 (1)
    apraxias 91.5 23 17562789 (2), 19884310 (1), 15279807 (1), 17112370 (1) (see all 14)
    vitamin e deficiency 70.6 3 17112370 (1), 16193447 (1), 19141356 (1)
    friedreich ataxia 69.5 5 15279807 (1), 17112370 (1), 16193447 (1), 19141356 (1)
    amyotrophic lateral sclerosis 66.5 4 19884310 (1), 19058054 (1)
    atrophy 61.7 2 18405395 (2)
    neurological disorders 27 2 19884310 (1)

    GeneTests: SETX
    GeneReviews: SETX
    Genetic Association Database (GAD): SETX
    Human Genome Epidemiology (HuGE) Navigator: SETX (4 documents)

    Export disorders for SETX 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 SETX gene, integrated from 10 sources (see all 86):
    (articles sorted by number of sources associating them with SETX)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. In cis autosomal dominant mutation of Senataxin associated with tremor/ataxia syndrome. (PubMed id 17096168)1, 2, 9 Bassuk A.G....Bennett C.L. (Neurogenetics 2007)
    2. Autosomal recessive ataxia with peripheral neuropathy and elevated AFP: novel mutations in SETX. (PubMed id 16717225)1, 2, 9 Asaka T.... Matsushima A. (Neurology 2006)
    3. DNA/RNA helicase gene mutations in a form of juvenile amyotrophic lateral sclerosis (ALS4). (PubMed id 15106121)1, 2, 9 Chen Y.-Z.... Chance P.F. (Am. J. Hum. Genet. 2004)
    4. Senataxin, defective in ataxia oculomotor apraxia type 2, is involved in the defense against oxidative DNA damage. (PubMed id 17562789)1, 2, 9 Suraweera A.... Lavin M.F. (J. Cell Biol. 2007)
    5. Senataxin, the ortholog of a yeast RNA helicase, is mutant in ataxia- ocular apraxia 2. (PubMed id 14770181)1, 2, 9 Moreira M.-C.... Koenig M. (Nat. Genet. 2004)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    7. Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study. (PubMed id 20800603)1, 4 Flachsbart F....Nebel A. (Mutat. Res. 2010)
    8. A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (Nat. Biotechnol. 2006)
    9. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    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: 23064 HGNC: 445 AceView: KIAA0625 Ensembl:ENSG00000107290 euGenes: HUgn23064
    ECgene: SETX H-InvDB: SETX

    (According to HUGE)
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    HUGE: KIAA0625

    (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 SETX Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=SETX[genesymbol]

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

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



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