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    XRCC4 X-ray repair cross complementing 4 [ Homo sapiens (human) ]

    Gene ID: 7518, updated on 3-May-2024

    Summary

    Official Symbol
    XRCC4provided by HGNC
    Official Full Name
    X-ray repair cross complementing 4provided by HGNC
    Primary source
    HGNC:HGNC:12831
    See related
    Ensembl:ENSG00000152422 MIM:194363; AllianceGenome:HGNC:12831
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SSMED; hXRCC4
    Summary
    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). Alternate transcript variants such as NM_022406 are unlikely to be expressed in some individuals due to a polymorphism (rs1805377) in the last splice acceptor site. [provided by RefSeq, Oct 2019]
    Expression
    Ubiquitous expression in testis (RPKM 2.7), lymph node (RPKM 2.1) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See XRCC4 in Genome Data Viewer
    Location:
    5q14.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (83077547..83374473)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (83566676..83868132)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (82373366..82649579)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105379052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22739 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:82322441-82323288 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:82323395-82323896 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:82323897-82324396 Neighboring gene transmembrane protein 167A Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:82372329-82373294 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:82373295-82374260 Neighboring gene small Cajal body-specific RNA 18 Neighboring gene ribosomal protein L13 pseudogene 9 Neighboring gene MPRA-validated peak5318 silencer Neighboring gene coenzyme Q10B pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22741 Neighboring gene MPRA-validated peak5319 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22742 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr5:82650217-82651159 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16152 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:82674443-82675136 Neighboring gene uncharacterized LOC105379053 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22743 Neighboring gene ferritin heavy chain 1 pseudogene 9

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Short stature, microcephaly, and endocrine dysfunction
    MedGen: C4225288 OMIM: 616541 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

    Description
    Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
    EBI GWAS Catalog
    Meta-analysis identifies loci affecting levels of the potential osteoarthritis biomarkers sCOMP and uCTX-II with genome wide significance.
    EBI GWAS Catalog
    Two-marker association tests yield new disease associations for coronary artery disease and hypertension.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables FHA domain binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    NOT enables ligase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA ligation involved in DNA repair IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in DNA ligation involved in DNA repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to lithium ion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in double-strand break repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in double-strand break repair via nonhomologous end joining IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in double-strand break repair via nonhomologous end joining IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in double-strand break repair via nonhomologous end joining IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in double-strand break repair via nonhomologous end joining NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in immunoglobulin V(D)J recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of ligase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein localization to site of double-strand break IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to X-ray IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in response to X-ray IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of DNA ligase IV complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of DNA ligase IV complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of DNA-dependent protein kinase-DNA ligase 4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of DNA-dependent protein kinase-DNA ligase 4 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    NOT located_in condensed chromosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of nonhomologous end joining complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    DNA repair protein XRCC4
    Names
    X-ray repair complementing defective repair in Chinese hamster cells 4

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_047086.2 RefSeqGene

      Range
      5002..281215
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001318012.3NP_001304941.1  DNA repair protein XRCC4 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses alternate splice sites in the 5' UTR and in the 3' coding region compared to variant 1. The encoded isoform (2) is longer than isoform 1. Variants 2 and 4 encode the same isoform (2).
      Source sequence(s)
      BC010655, BC016314, DA067761
      Consensus CDS
      CCDS4059.1
      UniProtKB/Swiss-Prot
      A8K3X4, Q13426, Q9BS72, Q9UP94
      Related
      ENSP00000421491.1, ENST00000511817.1
      Conserved Domains (1) summary
      pfam06632
      Location:2334
      XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
    2. NM_001318013.2NP_001304942.1  DNA repair protein XRCC4 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 3' coding region and 3' UTR compared to variant 1. The encoded isoform (3) has a distinct, shorter C-terminus than isoform 1.
      Source sequence(s)
      BC005259, DA067761
      Related
      ENST00000542685.5
      Conserved Domains (1) summary
      pfam06632
      Location:2308
      XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
    3. NM_003401.5NP_003392.1  DNA repair protein XRCC4 isoform 1

      See identical proteins and their annotated locations for NP_003392.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1. Variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      BC010655, BC016314, BT007216, DA067761, U40622
      Consensus CDS
      CCDS4058.1
      Related
      ENSP00000379344.4, ENST00000396027.9
      Conserved Domains (1) summary
      pfam06632
      Location:2332
      XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
    4. NM_022406.5NP_071801.1  DNA repair protein XRCC4 isoform 2

      See identical proteins and their annotated locations for NP_071801.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is longer than isoform 1. Variants 2 and 4 encode the same isoform (2).
      Source sequence(s)
      BC010655, BC016314, BT007216, DA067761
      Consensus CDS
      CCDS4059.1
      UniProtKB/Swiss-Prot
      A8K3X4, Q13426, Q9BS72, Q9UP94
      Related
      ENSP00000342011.6, ENST00000338635.10
      Conserved Domains (1) summary
      pfam06632
      Location:2334
      XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
    5. NM_022550.4NP_072044.1  DNA repair protein XRCC4 isoform 1

      See identical proteins and their annotated locations for NP_072044.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1 and 3 encode the same isoform (1).
      Source sequence(s)
      BC010655, BC016314, DA067761, U40622
      Consensus CDS
      CCDS4058.1
      Related
      ENSP00000282268.3, ENST00000282268.7
      Conserved Domains (1) summary
      pfam06632
      Location:2332
      XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      83077547..83374473
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047417695.1XP_047273651.1  DNA repair protein XRCC4 isoform X3

    2. XM_017009827.3XP_016865316.1  DNA repair protein XRCC4 isoform X3

    3. XM_047417696.1XP_047273652.1  DNA repair protein XRCC4 isoform X4

    4. XM_047417697.1XP_047273653.1  DNA repair protein XRCC4 isoform X5

    5. XM_017009828.3XP_016865317.1  DNA repair protein XRCC4 isoform X5

    6. XM_047417698.1XP_047273654.1  DNA repair protein XRCC4 isoform X6

    7. XM_011543626.2XP_011541928.1  DNA repair protein XRCC4 isoform X1

      See identical proteins and their annotated locations for XP_011541928.1

      UniProtKB/Swiss-Prot
      A8K3X4, Q13426, Q9BS72, Q9UP94
      Conserved Domains (1) summary
      pfam06632
      Location:2334
      XRCC4; DNA double-strand break repair and V(D)J recombination protein XRCC4
    8. XM_047417694.1XP_047273650.1  DNA repair protein XRCC4 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      83566676..83868132
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054353431.1XP_054209406.1  DNA repair protein XRCC4 isoform X3

    2. XM_054353432.1XP_054209407.1  DNA repair protein XRCC4 isoform X3

    3. XM_054353433.1XP_054209408.1  DNA repair protein XRCC4 isoform X4

    4. XM_054353435.1XP_054209410.1  DNA repair protein XRCC4 isoform X5

    5. XM_054353434.1XP_054209409.1  DNA repair protein XRCC4 isoform X5

    6. XM_054353436.1XP_054209411.1  DNA repair protein XRCC4 isoform X6

    7. XM_054353429.1XP_054209404.1  DNA repair protein XRCC4 isoform X1

      UniProtKB/Swiss-Prot
      A8K3X4, Q13426, Q9BS72, Q9UP94
    8. XM_054353430.1XP_054209405.1  DNA repair protein XRCC4 isoform X2