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XRCC4 Gene

protein-coding   GIFtS: 65
GCID: GC05P082409

X-Ray Repair Complementing Defective Repair In Chinese Hamster...

Microbiology & Infectious Diseases Congress
  See related diseases
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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
X-Ray Repair Complementing Defective Repair In Chinese Hamster Cells
41 2
     Repair In Chinese Hamster1
DNA Repair Protein XRCC41 2     X-Ray Repair1
X-Ray Repair Cross-Complementing Protein 42 3     X-Ray Repair, Complementing Defective, Repair In Chinese Hamster2
Complementing Defective1     

External Ids:    HGNC: 128311   Entrez Gene: 75182   Ensembl: ENSG000001524227   OMIM: 1943635   UniProtKB: Q134263   

Export aliases for XRCC4 gene to outside databases

Previous GC identifers: GC05P081191 GC05P082600 GC05P082412 GC05P082457 GC05P077581


(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 XRCC4 Gene:
The protein encoded by this gene functions together with DNA ligase IV and the DNA-dependent protein kinase in the
repair of DNA double-strand break by non-homologous end joining and the completion of V(D)J recombination events.
The non-homologous end-joining pathway is required both for normal development and for suppression of tumors.
This gene functionally complements XR-1 Chinese hamster ovary cell mutant, which is impaired in DNA double-strand
breaks produced by ionizing radiation and restriction enzymes. Alternative transcription initiation and
alternative splicing generates several transcript variants. (provided by RefSeq, Sep 2008)

GeneCards Summary for XRCC4 Gene:
XRCC4 (X-ray repair complementing defective repair in Chinese hamster cells 4) is a protein-coding gene. Diseases associated with XRCC4 include xeroderma pigmentosum, group d, and artemis deficiency. GO annotations related to this gene include protein C-terminus binding and ligase activity.

UniProtKB/Swiss-Prot: XRCC4_HUMAN, Q13426
Function: Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J
recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ
ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is
dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends

Gene Wiki entry for XRCC4 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_000005.10  NT_034772.7  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the XRCC4 gene promoter:
         STAT5B   AML1a   NRSF form 1   NRSF form 2   POU2F1   POU2F1b   POU2F1a   FOXO1a   POU2F1c   FOXO1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): XRCC4 promoter sequence
   Search Chromatin IP Primers for XRCC4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat XRCC4


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

Entrez Gene cytogenetic band: 5q14.2   Ensembl cytogenetic band:  5q14.2   HGNC cytogenetic band: 5q14.2

XRCC4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
XRCC4 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P082409:  view genomic region     (about GC identifiers)

Start:
82,373,317 bp from pter      End:
82,649,606 bp from pter
Size:
276,290 bases      Orientation:
plus 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: XRCC4_HUMAN, Q13426 (See protein sequence)
Recommended Name: DNA repair protein XRCC4  
Size: 336 amino acids; 38287 Da
Subunit: Homodimer and homotetramer in solution. The homodimer associates with LIG4, and the LIG4-XRCC4 complex
associates in a DNA-dependent manner with the DNA-PK complex formed by the Ku p70/p86 dimer (XRCC6/XRCC5) and
PRKDC. Seems to interact directly with PRKDC but not with the Ku p70/86 dimer. Interacts with XLF/Cernunnos.
Interacts with APTX and APLF
Selected PDB 3D structures from and Proteopedia for XRCC4 (see all 8):
1FU1 (3D)        1IK9 (3D)        3II6 (3D)        3MUD (3D)        3Q4F (3D)        3RWR (3D)    
Secondary accessions: A8K3X4 Q9BS72 Q9UP94
Alternative splicing: 3 isoforms:  Q13426-1   Q13426-2   Q13426-3   

Explore the universe of human proteins at neXtProt for XRCC4: NX_Q13426

Explore proteomics data for XRCC4 at MOPED

Post-translational modifications: 

  • Phosphorylated by PRKDC. The phosphorylation seems not to be necessary for binding to DNA. Phosphorylation by CK2
    promotes interaction with APTX1
  • Monoubiquitinated1
  • Sumoylation at Lys-210 is required for nuclear localization and recombination efficiency. Has no effect on
    ubiquitination1
  • Ubiquitination2 at Lys197
  • Modification sites at PhosphoSitePlus

  • See XRCC4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_003392.1  NP_071801.1  NP_072044.1  

    ENSEMBL proteins: 
     ENSP00000342011   ENSP00000379344   ENSP00000421491   ENSP00000282268  
    Reactome Protein details: Q13426

    XRCC4 Human Recombinant Protein Products:

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    Cloud-Clone Corp. ELISAs for XRCC4
    Cloud-Clone Corp. CLIAs for XRCC4


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    3 InterPro protein domains:
     IPR009089 XRCC4_N
     IPR014751 XRCC4_C
     IPR010585 DNA_repair_prot_XRCC4

    Graphical View of Domain Structure for InterPro Entry Q13426

    ProtoNet protein and cluster: Q13426

    UniProtKB/Swiss-Prot: XRCC4_HUMAN, Q13426
    Similarity: Belongs to the XRCC4 family


    XRCC4 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: XRCC4_HUMAN, Q13426
    Function: Involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J
    recombination. Binds to DNA and to DNA ligase IV (LIG4). The LIG4-XRCC4 complex is responsible for the NHEJ
    ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is
    dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends

         Genatlas biochemistry entry for XRCC4:
    repair X-ray defect,complementing defect in CHO cells,4 with CAG repeat,involved in DNA double-strand break repair
    by end joining (non homologous recombination) and V(D)J recombination. Also involved in neurogenesis

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677NOT DNA binding IDA9259561
    GO:0005515protein binding IPI15380105
    GO:0008022protein C-terminus binding IPI9259651
    GO:0016874NOT ligase activity IDA9242410
         
    XRCC4 for ontologies           About GeneDecksing


    Phenotypes:
         2 GenomeRNAi human phenotypes for XRCC4:
     Decreased number of cells in m  Increased gamma-H2AX phosphory 

         13 MGI mutant phenotypes (inferred from 3 alleles(MGI details for Xrcc4):
     cellular  craniofacial  endocrine/exocrine gland  growth/size/body  hematopoietic system 
     homeostasis/metabolism  immune system  integument  mortality/aging  nervous system 
     reproductive system  skeleton  tumorigenesis 

    XRCC4 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for XRCC4: Xrcc4tm1Fwa Xrcc4tm2.1Fwa

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for XRCC4
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       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for XRCC4

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    hsa-miR-141* hsa-miR-944 hsa-miR-380 hsa-miR-507
    SwitchGear 3'UTR luciferase reporter plasmidXRCC4 3' UTR sequence
    Inhib. RNA
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    GenScript: all cDNA clones in your preferred vector (see all 3): XRCC4 (NM_022406)
    Browse Sino Biological Human cDNA Clones
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    (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
    XRCC4_HUMAN, Q13426: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol5
    nucleus5
    mitochondrion1

    Gene Ontology (GO): Selected cellular component terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000793NOT condensed chromosome IDA12589063
    GO:0005634nucleus NAS16439205
    GO:0005654nucleoplasm TAS--
    GO:0005730NOT nucleolus IDA--
    GO:0005813centrosome IDA--

    XRCC4 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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    SuperPaths for XRCC4 About   (see all 6)  
    See pathways by source

    SuperPathContained pathways About
    1Non-homologous end-joining
    Non-homologous end-joining0.37
    Non-homologous end joining0.00
    DNA damage NHEJ mechanisms of DSBs repair0.37
    2HIV Life Cycle
    HIV Life Cycle0.91
    Integration of provirus0.00
    HIV Infection0.62
    2-LTR circle formation0.00
    Early Phase of HIV Life Cycle0.00
    3Homologous Recombination Repair
    Double-Strand Break Repair0.70
    Nonhomologous End-joining (NHEJ)0.00
    4DNA Repair
    DNA Repair0.45
    5Chks in Checkpoint Regulation
    DNA Repair Mechanisms0.32

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for XRCC4
        DNA Repair Mechanisms

    1 GeneGo (Thomson Reuters) Pathway for XRCC4
        DNA damage NHEJ mechanisms of DSBs repair

    1 BioSystems Pathway for XRCC4
        Non-homologous end joining

    2 Reactome Pathways for XRCC4
        Nonhomologous End-joining (NHEJ)
    2-LTR circle formation


    1 Kegg Pathway  (Kegg details for XRCC4):
        Non-homologous end-joining


    XRCC4 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Arrays including XRCC4: 
              Cancer PathwayFinder in human mouse rat
              p53 Signaling Pathway in human mouse rat
              DNA Repair in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for XRCC4

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

    Selected Interacting proteins for XRCC4 (Q134261, 2, 3 ENSP000003420114) via UniProtKB, MINT, STRING, and/or I2D (see all 40)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PNKPQ96T601, 2, 3, ENSP000003235114EBI-717592,EBI-1045072 MINT-51171 MINT-8200112 MINT-8200097 MINT-51174 MINT-51172 MINT-8200126 MINT-51173 MINT-51175 I2D: score=4 STRING: ENSP00000323511
    APTXQ7Z2E31, 2, 3, ENSP000004008064EBI-717592,EBI-847814 MINT-51155 MINT-2864227 MINT-51156 I2D: score=3 STRING: ENSP00000400806
    NHEJ1Q9H9Q41, 2, 3, ENSP000003493134EBI-717592,EBI-847807 MINT-6175948 MINT-8094510 MINT-6175964 I2D: score=3 STRING: ENSP00000349313
    XRCC5P130102, 3MINT-6175948 MINT-8094510 MINT-6175964 I2D: score=1 
    BIN1O004991, 3, ENSP000003167794EBI-717592,EBI-719094 I2D: score=2 STRING: ENSP00000316779
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 23):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001701in utero embryonic development IEA--
    GO:0002328pro-B cell differentiation IEA--
    GO:0006266DNA ligation ----
    GO:0006281DNA repair TAS--
    GO:0006302double-strand break repair TAS--

    XRCC4 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 XRCC4

    1 DrugBank Compound for XRCC4    About this table
    CompoundSynonyms CAS #TypeActionsPubMed Ids
    S-(Dimethylarsenic)Cysteine-- --target--17139284 17016423

    3 Novoseek inferred chemical compound relationships for XRCC4 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    polynucleotide 56.3 3 18644470 (1), 17353262 (1), 15380105 (1)
    wortmannin 35.7 4 12140331 (4)
    alanine 13.7 1 14599745 (1)

    1 PharmGKB related drug/compound annotation for XRCC4 gene    About this table
    Drug/compound PharmGKB Annotation
    docetaxelCA  



    XRCC4 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,
    Conferences by KenesGroup, 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 XRCC4 gene (3 alternative transcripts): 
    NM_003401.3  NM_022406.2  NM_022550.2  

    Unigene Cluster for XRCC4:

    X-ray repair complementing defective repair in Chinese hamster cells 4
    Hs.567359  [show with all ESTs]
    Unigene Representative Sequence: NM_022550
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000338635 ENST00000542685(uc003kia.1) ENST00000396027 ENST00000511817(uc003kig.3)
    ENST00000509268 ENST00000282268(uc003kib.3 uc003kic.3 uc003kid.3 uc003kie.3)

    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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    4 qRT-PCR Assays for microRNAs that regulate XRCC4:
    hsa-miR-141* hsa-miR-944 hsa-miR-380 hsa-miR-507
    SwitchGear 3'UTR luciferase reporter plasmidXRCC4 3' UTR sequence
    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat XRCC4

    Additional mRNA sequence: 

    AB017445.1 AK290739.1 BC005259.1 BC010655.1 BC016314.1 BT007216.1 U40622.1 

    16 DOTS entries:

    DT.95269018  DT.40220026  DT.312131  DT.92436833  DT.120875805  DT.100819225  DT.120875672  DT.100819221 
    DT.101986016  DT.100819224  DT.100819223  DT.120875671  DT.40109549  DT.92436831  DT.92436832  DT.95269017 

    Selected AceView cDNA sequences (see all 128):

    AI795996 AI270686 BX279574 AA314379 BM564730 BM471375 AI289105 AL558342 
    CB144620 CA394395 BX281210 CR617390 AL551668 CR602998 BI760531 BU171074 
    AL543920 BX362079 BG204714 BE781259 R39148 BQ226357 CR599717 BC005259 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for XRCC4    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b
    SP1:                                -                       -                     
    SP2:                                -                       -                     
    SP3:                                                                              
    SP4:              -                                                               


    ECgene alternative splicing isoforms for XRCC4

    (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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    XRCC4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CCTATAATTA
    XRCC4 Expression
    About this image


    XRCC4 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    XRCC4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    XRCC4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.567359

    UniProtKB/Swiss-Prot: XRCC4_HUMAN, Q13426
    Tissue specificity: Widely expressed

        Pathway & Disease-focused RT2 Profiler PCR Arrays including XRCC4: 
              Cancer PathwayFinder in human mouse rat
              p53 Signaling Pathway in human mouse rat
              DNA Repair in human mouse rat

    Primer
    Products:
    OriGene qPCR primer pairs and template standards for XRCC4
    OriGene qSTAR qPCR primer pairs in human, mouse for XRCC4
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat XRCC4
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    QuantiFast Probe-based Assays in human, mouse, rat XRCC4
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for XRCC4

    (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 chordates.

    Orthologs for XRCC4 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Xrcc41 , 5 X-ray repair complementing defective repair in Chinese more1, 5 81.08(n)1
    76.07(a)1
      13 (45.50 cM)5
    1081381  NM_028012.41  NP_082288.11 
     897740275 
    chicken
    (Gallus gallus)
    Aves XRCC41 X-ray repair complementing defective repair in Chinese more 66.16(n)
    55.62(a)
      427325  XM_424905.4  XP_424905.4 
    lizard
    (Anolis carolinensis)
    Reptilia XRCC46
    X-ray repair complementing defective repair in Chi...
    50(a)
    1 ↔ 1
    2(18376204-18503394)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.321452 Xenopus laevis transcribed sequence with weak similarity more 74.05(n)    CD302243.1 
    zebrafish
    (Danio rerio)
    Actinopterygii xrcc41 X-ray repair complementing defective repair in Chinese more 49.54(n)
    40.92(a)
      393759  NM_200786.1  NP_957080.1 


    ENSEMBL Gene Tree for XRCC4 (if available)
    TreeFam Gene Tree for XRCC4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section

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    (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 XRCC4 (see all 5696)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1447946681,2
    --82375394(+) CCAGGA/GTGGAG 3 -- int10--------
    rs1157584321,2
    C,F--82375484(+) GTAACC/TGGGAC 3 -- int11Minor allele frequency- T:0.02WA 118
    rs131637431,2
    C,F,A,H--82375485(+) TAACCG/AGGACC 3 -- int19Minor allele frequency- A:0.14NS EA NA 546
    rs1395912701,2
    --82375595(+) TGATCC/GTCCCG 3 -- int10--------
    rs1442725011,2
    C--82375643(+) CCACCA/GCACCA 3 -- int10--------
    rs1135435391,2
    C,F--82375649(+) CACCAC/TGTCTG 3 -- int11Minor allele frequency- T:0.50CSA 2
    rs1832270291,2
    --82375708(+) ACTTTA/GGTTTC 3 -- int10--------
    rs774650921,2
    C,F--82375844(+) GTTTGG/ACATAC 3 -- int11Minor allele frequency- A:0.10EA 120
    rs1461026641,2
    --82375873(+) GTTGGC/GTATTA 3 -- int10--------
    rs1875130201,2
    --82375899(+) TCTTTA/GCTAAA 3 -- int10--------

    HapMap Linkage Disequilibrium report for XRCC4 (82373317 - 82623317 bp, first 250kb of XRCC4)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for XRCC4 (see all 19):    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2730400CNV Deletion23290073
    esv2659602CNV Deletion23128226
    esv2730399CNV Deletion23290073
    esv2730397CNV Deletion23290073
    dgv1028e199CNV Deletion23128226
    esv2312144CNV Deletion18987734
    esv3557CNV Deletion18987735
    esv2730398CNV Deletion23290073
    esv270814CNV Insertion20981092
    esv268758CNV Insertion20981092

    Human Gene Mutation Database (HGMD): XRCC4
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing XRCC4
    DNA2.0 Custom Variant and Variant Library Synthesis for XRCC4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 194363    OMIM disorders: --

    Selected diseases for XRCC4 (see all 62):    
    About MalaCards
    xeroderma pigmentosum, group d    artemis deficiency    dna ligase iv deficiency    primary immunodeficiency disease
    microtia    acoustic neuroma    myoma    neuroma
    apraxia    childhood leukemia    xeroderma pigmentosum    synovial sarcoma
    lung cancer susceptibility    follicular lymphoma    severe combined immunodeficiency    albinism
    stomach cancer    microcephaly    oral cancer    diffuse large b-cell lymphoma


    XRCC4 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    5 Novoseek inferred disease relationships for XRCC4 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    autoimmune response 23.4 1 12218164 (1)
    leukemia 12 3 20332465 (3)
    breast cancer 0 4 12750264 (2), 9259561 (1), 16485136 (1)
    tumors 0 1 16227403 (1)
    cancer 0 1 12698192 (1)

    Genetic Association Database (GAD): XRCC4
    Human Genome Epidemiology (HuGE) Navigator: XRCC4 (60 documents)

    Export disorders for XRCC4 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 XRCC4 gene, integrated from 10 sources (see all 234):
    (articles sorted by number of sources associating them with XRCC4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Monoubiquitination of the nonhomologous end joining protein XRCC4. (PubMed id 16412978)1, 2, 9 Foster R.E.... Frank K.M. (Biochem. Biophys. Res. Commun. 2006)
    2. Mammalian DNA double-strand break repair protein XRCC4 interacts with DNA ligase IV. (PubMed id 9259561)1, 2, 9 Critchlow S.E.... Jackson S.P. (Curr. Biol. 1997)
    3. Tetramerization and DNA ligase IV interaction of the DNA double- strand break repair protein XRCC4 are mutually exclusive. (PubMed id 14607114)1, 2, 9 Modesti M.... Kanaar R. (J. Mol. Biol. 2003)
    4. Polymorphisms of LIG4 and XRCC4 involved in the NHEJ pathway interact to modify risk of glioma. (PubMed id 18165945)1, 4, 9 Liu Y....Zhou L. (Hum. Mutat. 2008)
    5. Significant association of XRCC4 single nucleotide polymorphisms with childhood leukemia in Taiwan. (PubMed id 20332465)1, 4, 9 Wu K.H....Bau D.T. (Anticancer Res. 2010)
    6. Lung cancer susceptibility and prognosis associated with polymorphisms in the nonhomologous end-joining pathway genes: a multiple genotype-phenotype study. (PubMed id 19408343)1, 4, 9 Tseng R.C....Wang Y.C. (Cancer 2009)
    7. Identification of DNA-PKcs phosphorylation sites in XRCC4 and effects of mutations at these sites on DNA end joining in a cell-free system. (PubMed id 15177042)1, 2, 9 Lee K.J.... Dynan W.S. (DNA Repair 2004)
    8. The ataxia-oculomotor apraxia 1 gene product has a role distinct from ATM and interacts with the DNA strand break repair proteins XRCC1 and XRCC4. (PubMed id 15380105)1, 2, 9 Clements P.M....Caldecott K.W. (DNA Repair 2004)
    9. Defining interactions between DNA-PK and ligase IV/XRCC4. (PubMed id 12509254)1, 2, 9 Hsu H.-L.... Chen D.J. (DNA Repair 2002)
    10. Crystal structure of an Xrcc4-DNA ligase IV complex. (PubMed id 11702069)1, 2, 9 Sibanda B.L.... Pellegrini L. (Nat. Struct. Biol. 2001)

    (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)
    About This Section

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    Entrez Gene: 7518 HGNC: 12831 AceView: XRCC4 Ensembl:ENSG00000152422 euGenes: HUgn7518
    ECgene: XRCC4 Kegg: 7518 H-InvDB: XRCC4

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

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    NameDescription
    PharmGKB entry for XRCC4 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for XRCC4 Genetics and Cytogenetics in Oncology and Haematology
    NIEHS-SNPshttp://egp.gs.washington.edu/data/xrcc4/

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for XRCC4 gene:
    Search GeneIP for patents involving XRCC4

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



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