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    NHEJ1 non-homologous end joining factor 1 [ Homo sapiens (human) ]

    Gene ID: 79840, updated on 17-Jun-2024

    Summary

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    Official Symbol
    NHEJ1provided by HGNC
    Official Full Name
    non-homologous end joining factor 1provided by HGNC
    Primary source
    HGNC:HGNC:25737
    See related
    Ensembl:ENSG00000187736 MIM:611290; AllianceGenome:HGNC:25737
    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
    XLF
    Summary
    Double-strand breaks in DNA result from genotoxic stresses and are among the most damaging of DNA lesions. This gene encodes a DNA repair factor essential for the nonhomologous end-joining pathway, which preferentially mediates repair of double-stranded breaks. Mutations in this gene cause different kinds of severe combined immunodeficiency disorders. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis (RPKM 11.1), colon (RPKM 7.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NHEJ1 in Genome Data Viewer
    Location:
    2q35
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (219069357..219160815, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (219557705..219649239, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (219934079..220025537, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985987 Neighboring gene uncharacterized LOC124906120 Neighboring gene microRNA 3131 Neighboring gene Indian hedgehog signaling molecule Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:219941606-219942805 Neighboring gene RNA, 7SL, cytoplasmic 764, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12340 Neighboring gene solute carrier family 23 member 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17139 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17140 Neighboring gene Sharpr-MPRA regulatory region 9830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12343 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:220042692-220043192 Neighboring gene cyclin Pas1/PHO80 domain containing 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The canonical non-homologous end joining factor XLF promotes chromosomal deletion rearrangements in human cells. Bhargava R, et al. J Biol Chem, 2020 Jan 3. PMID 31753920, Free PMC Article
    2. Combined Immunodeficiency, Hemolytic Anemia, and Growth Retardation Secondary to a Homozygous Mutation in the NHEJ1 Gene. Al-Marhoobi R, et al. J Pediatr Hematol Oncol, 2020 May. PMID 31259832
    3. Extreme Phenotypes With Identical Mutations: Two Patients With Same Non-sense NHEJ1 Homozygous Mutation. Recio MJ, et al. Front Immunol, 2018. PMID 30666249, Free PMC Article
    4. XLF/Cernunnos: An important but puzzling participant in the nonhomologous end joining DNA repair pathway. Menon V, et al. DNA Repair (Amst), 2017 Oct. PMID 28846869, Free PMC Article
    5. Loss of NHEJ1 Protein Due to a Novel Splice Site Mutation in a Family Presenting with Combined Immunodeficiency, Microcephaly, and Growth Retardation and Literature Review. Sheikh F, et al. J Clin Immunol, 2017 Aug. PMID 28741180

    See all (90) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PAXX binding to the NHEJ machinery explains functional redundancy with XLF.
      Title: PAXX binding to the NHEJ machinery explains functional redundancy with XLF.
    2. X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology.
      Title: X-ray scattering reveals disordered linkers and dynamic interfaces in complexes and mechanisms for DNA double-strand break repair impacting cell and cancer biology.
    3. The conserved Tpk1 regulates non-homologous end joining double-strand break repair by phosphorylation of Nej1, a homolog of the human XLF.
      Title: The conserved Tpk1 regulates non-homologous end joining double-strand break repair by phosphorylation of Nej1, a homolog of the human XLF.
    4. Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.
      Title: Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.
    5. Combined Immunodeficiency, Hemolytic Anemia, and Growth Retardation Secondary to a Homozygous Mutation in the NHEJ1 Gene.
      Title: Combined Immunodeficiency, Hemolytic Anemia, and Growth Retardation Secondary to a Homozygous Mutation in the NHEJ1 Gene.
    6. Absence of XRCC4 and its paralogs in human cells reveal differences in outcomes for DNA repair and V(D)J recombination.
      Title: Absence of XRCC4 and its paralogs in human cells reveal differences in outcomes for DNA repair and V(D)J recombination.
    7. The canonical non-homologous end joining factor XLF promotes chromosomal deletion rearrangements in human cells.
      Title: The canonical non-homologous end joining factor XLF promotes chromosomal deletion rearrangements in human cells.
    8. Description of two unrelated cases with Cernunnos/XLF deficiency and with the same non-sense mutation in the NHEJ1 gene showing significant differences in clinical presentation and immunological profile but a similar DNA repair defect.
      Title: Extreme Phenotypes With Identical Mutations: Two Patients With Same Non-sense NHEJ1 Homozygous Mutation.
    9. The crystal structures of the Ku-binding motifs (KBM) of the non-homologous end joining (NHEJ) proteins APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex are discussed.
      Title: XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining.
    10. PC4 expression correlated with radiosensitivity and was an independent prognostic factor of progression-free survival (PFS) in patients with NSCLC.
      Title: Inhibition of PC4 radiosensitizes non-small cell lung cancer by transcriptionally suppressing XLF.
    Submit: New GeneRIF Correction See all GeneRIFs (61)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Cernunnos-XLF deficiency
    MedGen: C1969799 OMIM: 611291 GeneReviews: Not available
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study in 19 633 Japanese subjects identified LHX3-QSOX2 and IGF1 as adult height loci.
    EBI GWAS Catalog
    Genome-wide association analysis identifies 20 loci that influence adult height.
    EBI GWAS Catalog
    Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ12610

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA end binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA end binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA polymerase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in B cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in DNA ligation involved in DNA repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in T cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in central nervous system development NAS
    Non-traceable Author Statement
    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 immunoglobulin V(D)J recombination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of ligase activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in response to ionizing radiation 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-dependent protein kinase-DNA ligase 4 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    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 
    is_active_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    non-homologous end-joining factor 1
    Names
    XRCC4-like factor
    nonhomologous end-joining factor 1
    protein cernunnos

    NCBI Reference Sequences (RefSeq)

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    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_007880.1 RefSeqGene

      Range
      5001..90542
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_90

    mRNA and Protein(s)

    1. NM_001377498.1 → NP_001364427.1  non-homologous end-joining factor 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC068946, AC097468
      Consensus CDS
      CCDS2432.1
      UniProtKB/Swiss-Prot
      B8ZZA4, Q4ZFW7, Q6IA64, Q96JS9, Q9H9Q4
      Related
      ENSP00000407201.2, ENST00000457600.3
      Conserved Domains (1) summary
      pfam09302
      Location:12 → 174
      XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

    2. NM_001377499.1 → NP_001364428.1  non-homologous end-joining factor 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC068946, AC097468
      Consensus CDS
      CCDS92945.1
      UniProtKB/TrEMBL
      H7C0G7
      Related
      ENSP00000394896.2, ENST00000426304.6
      Conserved Domains (1) summary
      pfam09302
      Location:12 → 174
      XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

    3. NM_024782.3 → NP_079058.1  non-homologous end-joining factor 1 isoform 1

      See identical proteins and their annotated locations for NP_079058.1

      Status: REVIEWED

      Source sequence(s)
      AC097468, AJ972687, DB124934
      Consensus CDS
      CCDS2432.1
      UniProtKB/Swiss-Prot
      B8ZZA4, Q4ZFW7, Q6IA64, Q96JS9, Q9H9Q4
      Related
      ENSP00000349313.5, ENST00000356853.10
      Conserved Domains (1) summary
      pfam09302
      Location:12 → 174
      XLF; XLF-Cernunnos, XRcc4-like factor, NHEJ component

    RNA

    1. NR_165304.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC020575, AC068946, AC097468

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      219069357..219160815 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      219557705..219649239 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H9Q4.1 GenPept UniProtKB/Swiss-Prot:Q9H9Q4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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