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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
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Genomic context

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