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Aliases for XRCC4 Gene

Aliases for XRCC4 Gene

  • X-Ray Repair Cross Complementing 4 2 3 5
  • X-Ray Repair Complementing Defective Repair In Chinese Hamster Cells 4 2 3
  • DNA Repair Protein XRCC4 2 3
  • X-Ray Repair, Complementing Defective, Repair In Chinese Hamster 2
  • X-Ray Repair Cross-Complementing Protein 4 4
  • SSMED 3

External Ids for XRCC4 Gene

Previous GeneCards Identifiers for XRCC4 Gene

  • GC05P081191
  • GC05P082600
  • GC05P082412
  • GC05P082457
  • GC05P082409
  • GC05P077581

Summaries for XRCC4 Gene

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 breaks. This protein plays a role in both non-homologous end joining and the completion of V(D)J recombination. Mutations in this gene can cause short stature, microcephaly, and endocrine dysfunction (SSMED). Alternative splicing generates several transcript variants. [provided by RefSeq, Dec 2015]

GeneCards Summary for XRCC4 Gene

XRCC4 (X-Ray Repair Cross Complementing 4) is a Protein Coding gene. Diseases associated with XRCC4 include Short Stature, Microcephaly, And Endocrine Dysfunction and Microcephalic Primordial Dwarfism-Insulin Resistance Syndrome. Among its related pathways are SUMOylation and HIV Life Cycle. Gene Ontology (GO) annotations related to this gene include ligase activity and protein C-terminus binding.

UniProtKB/Swiss-Prot for XRCC4 Gene

  • 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

Additional gene information for XRCC4 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for XRCC4 Gene

Genomics for XRCC4 Gene

GeneHancer (GH) Regulatory Elements for XRCC4 Gene

Promoters and enhancers for XRCC4 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05I083076 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 559.1 +0.0 25 2.9 HDGF PKNOX1 SMAD1 ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 POLR2B XRCC4 TMEM167A LOC105379052
GH05I083095 Promoter/Enhancer 1.7 EPDnew Ensembl ENCODE 578.6 +19.8 19773 3.8 PKNOX1 ZNF133 FEZF1 GLI4 ZNF2 GLIS2 ZNF213 ZNF302 ATF7 KLF7 XRCC4 ATP6AP1L RPS23 SCARNA18 LOC105379052 TMEM167A RPL13P9
GH05I083156 Enhancer 0.5 FANTOM5 Ensembl 33.7 +79.7 79703 0.6 XRCC4 VCAN TMEM167A RPL13P9
GH05I083145 Enhancer 0.3 ENCODE 33.7 +68.6 68590 1.5 PRDM1 XRCC4 RPL13P9 TMEM167A
GH05I083368 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 2.1 +291.4 291403 1.6 ZNF146 PKNOX1 CEBPB JUNB BATF ATF2 ZNF217 IKZF1 HMBOX1 RUNX3 VCAN TMEM167A XRCC4 LOC105379053 GC05P083318
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around XRCC4 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the XRCC4 gene promoter:

Genomic Locations for XRCC4 Gene

Genomic Locations for XRCC4 Gene
chr5:83,077,409-83,353,787
(GRCh38/hg38)
Size:
276,379 bases
Orientation:
Plus strand
chr5:82,373,317-82,649,606
(GRCh37/hg19)

Genomic View for XRCC4 Gene

Genes around XRCC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
XRCC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for XRCC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for XRCC4 Gene

Proteins for XRCC4 Gene

  • Protein details for XRCC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13426-XRCC4_HUMAN
    Recommended name:
    DNA repair protein XRCC4
    Protein Accession:
    Q13426
    Secondary Accessions:
    • A8K3X4
    • Q9BS72
    • Q9UP94

    Protein attributes for XRCC4 Gene

    Size:
    336 amino acids
    Molecular mass:
    38287 Da
    Quaternary structure:
    • Homodimer and homotetramer in solution. The homodimer associates with LIG4. The LIG4-XRCC4 complex associates in a DNA-dependent manner with the DNA-PK complex composed of PRKDC, XRCC6/Ku70 and XRCC5/Ku86 to form the core non-homologous end joining (NHEJ) complex. Additional components of the NHEJ complex include NHEJ1/XLF and PAXX. Interacts directly with PRKDC but not with the XRCC6/Ku70 and XRCC5/Ku86 dimer. Interacts with APTX and APLF.

    Three dimensional structures from OCA and Proteopedia for XRCC4 Gene

    Alternative splice isoforms for XRCC4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for XRCC4 Gene

Post-translational modifications for XRCC4 Gene

  • Monoubiquitinated.
  • Phosphorylated by PRKDC. The phosphorylation seems not to be necessary for binding to DNA. Phosphorylation by CK2 promotes interaction with APTX.
  • Sumoylation at Lys-210 is required for nuclear localization and recombination efficiency. Has no effect on ubiquitination.
  • Ubiquitination at isoforms=2, 3197

No data available for DME Specific Peptides for XRCC4 Gene

Domains & Families for XRCC4 Gene

Gene Families for XRCC4 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for XRCC4 Gene

Suggested Antigen Peptide Sequences for XRCC4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q13426

UniProtKB/Swiss-Prot:

XRCC4_HUMAN :
  • Belongs to the XRCC4 family.
Family:
  • Belongs to the XRCC4 family.
genes like me logo Genes that share domains with XRCC4: view

Function for XRCC4 Gene

Molecular function for XRCC4 Gene

GENATLAS Biochemistry:
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
UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for XRCC4 Gene

Gene Ontology (GO) - Molecular Function for XRCC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 NOT DNA binding IDA 9259561
GO:0005515 protein binding IPI 9809069
GO:0008022 protein C-terminus binding IPI 9259561
GO:0016874 NOT ligase activity IDA 9242410
GO:0042802 identical protein binding IPI 16169070
genes like me logo Genes that share ontologies with XRCC4: view
genes like me logo Genes that share phenotypes with XRCC4: view

Human Phenotype Ontology for XRCC4 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for XRCC4 Gene

MGI Knock Outs for XRCC4:

Animal Model Products

Clone Products

  • Addgene plasmids for XRCC4

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for XRCC4 Gene

Localization for XRCC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for XRCC4 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for XRCC4 gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 2
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for XRCC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000793 NOT condensed chromosome IDA 12589063
GO:0005634 nucleus NAS 16439205
GO:0005654 nucleoplasm TAS --
GO:0005829 cytosol IDA 9259561
GO:0005958 DNA-dependent protein kinase-DNA ligase 4 complex IDA 15194694
genes like me logo Genes that share ontologies with XRCC4: view

Pathways & Interactions for XRCC4 Gene

genes like me logo Genes that share pathways with XRCC4: view

Pathways by source for XRCC4 Gene

1 KEGG pathway for XRCC4 Gene
1 GeneGo (Thomson Reuters) pathway for XRCC4 Gene
1 Qiagen pathway for XRCC4 Gene

Gene Ontology (GO) - Biological Process for XRCC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA --
GO:0006302 double-strand break repair IDA 9242410
GO:0006303 double-strand break repair via nonhomologous end joining TAS --
GO:0006310 DNA recombination IEA --
GO:0006974 cellular response to DNA damage stimulus IEA --
genes like me logo Genes that share ontologies with XRCC4: view

No data available for SIGNOR curated interactions for XRCC4 Gene

Drugs & Compounds for XRCC4 Gene

(4) Drugs for XRCC4 Gene - From: DrugBank, PharmGKB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Docetaxel Approved May 1996, Investigational Pharma Microtubulin disassembly inhibitor, Tubulin and VEGF inhibitor, Taxanes 2040
S-(Dimethylarsenic)Cysteine Experimental Pharma Target 0

(1) Additional Compounds for XRCC4 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with XRCC4: view

Transcripts for XRCC4 Gene

Unigene Clusters for XRCC4 Gene

X-ray repair complementing defective repair in Chinese hamster cells 4:
Representative Sequences:

Clone Products

  • Addgene plasmids for XRCC4

Alternative Splicing Database (ASD) splice patterns (SP) for XRCC4 Gene

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

Relevant External Links for XRCC4 Gene

GeneLoc Exon Structure for
XRCC4
ECgene alternative splicing isoforms for
XRCC4

Expression for XRCC4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for XRCC4 Gene

Protein differential expression in normal tissues from HIPED for XRCC4 Gene

This gene is overexpressed in Plasma (19.9), Blymphocyte (10.4), Heart (8.7), and Urine (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for XRCC4 Gene



Protein tissue co-expression partners for XRCC4 Gene

NURSA nuclear receptor signaling pathways regulating expression of XRCC4 Gene:

XRCC4

SOURCE GeneReport for Unigene cluster for XRCC4 Gene:

Hs.567359

mRNA Expression by UniProt/SwissProt for XRCC4 Gene:

Q13426-XRCC4_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for XRCC4 Gene

  • Bone marrow(4.3)
  • Liver(4.1)
  • Blood(2.1)
genes like me logo Genes that share expression patterns with XRCC4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for XRCC4 Gene

Orthologs for XRCC4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for XRCC4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia XRCC4 33 34
  • 99.4 (n)
cow
(Bos Taurus)
Mammalia XRCC4 33 34
  • 87.69 (n)
dog
(Canis familiaris)
Mammalia XRCC4 33 34
  • 87.45 (n)
mouse
(Mus musculus)
Mammalia Xrcc4 33 16 34
  • 81.08 (n)
rat
(Rattus norvegicus)
Mammalia Xrcc4 33
  • 78.22 (n)
oppossum
(Monodelphis domestica)
Mammalia XRCC4 34
  • 62 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia XRCC4 34
  • 59 (a)
OneToOne
chicken
(Gallus gallus)
Aves XRCC4 33 34
  • 66.16 (n)
lizard
(Anolis carolinensis)
Reptilia XRCC4 34
  • 50 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia xrcc4 33
  • 59.23 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.32145 33
zebrafish
(Danio rerio)
Actinopterygii xrcc4 33 34
  • 49.54 (n)
Species where no ortholog for XRCC4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for XRCC4 Gene

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

Paralogs for XRCC4 Gene

No data available for Paralogs for XRCC4 Gene

Variants for XRCC4 Gene

Sequence variations from dbSNP and Humsavar for XRCC4 Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs587779351 pathogenic, Ateleiotic dwarfism, Short stature, microcephaly, and endocrine dysfunction, not provided, Short stature, microcephaly, and endocrine dysfunction (SSMED) [MIM:616541] 83,105,046(+) T/C coding_sequence_variant, missense_variant
rs768825050 pathogenic, Short stature, microcephaly, and endocrine dysfunction 83,204,849(+) C/T coding_sequence_variant, stop_gained
rs779773463 pathogenic, Short stature, microcephaly, and endocrine dysfunction 83,195,935(+) C/T coding_sequence_variant, stop_gained
rs797045016 pathogenic, Short stature, microcephaly, and endocrine dysfunction 83,258,607(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, stop_gained
rs797045017 pathogenic, Short stature, microcephaly, and endocrine dysfunction, Short stature, microcephaly, and endocrine dysfunction (SSMED) [MIM:616541] 83,195,936(+) G/A/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for XRCC4 Gene

Variant ID Type Subtype PubMed ID
nsv956460 CNV deletion 24416366
nsv830366 CNV gain 17160897
nsv830365 CNV loss 17160897
nsv598780 CNV loss 21841781
nsv519738 CNV loss 19592680
nsv478540 CNV novel sequence insertion 20440878
nsv473709 CNV novel sequence insertion 20440878
nsv471019 CNV loss 18288195
nsv1140360 OTHER inversion 24896259
nsv1025441 CNV loss 25217958
esv6941 CNV loss 19470904
esv3605632 CNV loss 21293372
esv3605630 CNV loss 21293372
esv3605629 CNV loss 21293372
esv3566196 CNV deletion 23714750
esv3557 CNV loss 18987735
esv3429828 CNV insertion 20981092
esv3429295 CNV insertion 20981092
esv3304480 CNV mobile element insertion 20981092
esv2730400 CNV deletion 23290073
esv2730399 CNV deletion 23290073
esv2730398 CNV deletion 23290073
esv2730397 CNV deletion 23290073
esv2659602 CNV deletion 23128226
esv2312144 CNV deletion 18987734
dgv9906n54 CNV loss 21841781
dgv709n27 CNV loss 19166990
dgv3113n106 CNV deletion 24896259
dgv1028e199 CNV deletion 23128226

Variation tolerance for XRCC4 Gene

Residual Variation Intolerance Score: 68.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.27; 88.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for XRCC4 Gene

Human Gene Mutation Database (HGMD)
XRCC4
SNPedia medical, phenotypic, and genealogical associations of SNPs for
XRCC4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for XRCC4 Gene

Disorders for XRCC4 Gene

MalaCards: The human disease database

(8) MalaCards diseases for XRCC4 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search XRCC4 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

XRCC4_HUMAN
  • Short stature, microcephaly, and endocrine dysfunction (SSMED) [MIM:616541]: A disease characterized by short stature and microcephaly apparent at birth, progressive postnatal growth failure, and endocrine dysfunction. In affected adults endocrine features include hypergonadotropic hypogonadism, multinodular goiter, and diabetes mellitus. Variable features observed in some patients are progressive ataxia, and lymphopenia or borderline leukopenia. {ECO:0000269 PubMed:24389050, ECO:0000269 PubMed:25728776, ECO:0000269 PubMed:25839420, ECO:0000269 PubMed:26255102}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for XRCC4

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with XRCC4: view

No data available for Genatlas for XRCC4 Gene

Publications for XRCC4 Gene

  1. Significant association of XRCC4 single nucleotide polymorphisms with childhood leukemia in Taiwan. (PMID: 20332465) Wu KH … Bau DT (Anticancer research 2010) 3 22 44 58
  2. Lung cancer susceptibility and genetic polymorphism of DNA repair gene XRCC4 in Taiwan. (PMID: 19729825) Hsu NY … Bau DT (Cancer biomarkers : section A of Disease markers 2009) 3 22 44 58
  3. Lung cancer susceptibility and prognosis associated with polymorphisms in the nonhomologous end-joining pathway genes: a multiple genotype-phenotype study. (PMID: 19408343) Tseng RC … Wang YC (Cancer 2009) 3 22 44 58
  4. Combinational polymorphisms of four DNA repair genes XRCC1, XRCC2, XRCC3, and XRCC4 and their association with oral cancer in Taiwan. (PMID: 18410587) Yen CY … Chang HW (Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology 2008) 3 22 44 58
  5. Genotype-phenotype relationship between DNA repair gene genetic polymorphisms and DNA repair capacity. (PMID: 18990028) Shin A … Kang D (Asian Pacific journal of cancer prevention : APJCP 2008) 3 22 44 58

Products for XRCC4 Gene

Sources for XRCC4 Gene

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