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Aliases for NHEJ1 Gene

Aliases for NHEJ1 Gene

  • Non-Homologous End Joining Factor 1 2 3 5
  • XRCC4-Like Factor 2 3 4
  • Nonhomologous End-Joining Factor 1 2 3
  • Protein Cernunnos 3 4
  • XLF 3 4
  • Non-Homologous End-Joining Factor 1 3

External Ids for NHEJ1 Gene

Previous GeneCards Identifiers for NHEJ1 Gene

  • GC02M219648
  • GC02M219941
  • GC02M211793

Summaries for NHEJ1 Gene

Entrez Gene Summary for NHEJ1 Gene

  • 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]

GeneCards Summary for NHEJ1 Gene

NHEJ1 (Non-Homologous End Joining Factor 1) is a Protein Coding gene. Diseases associated with NHEJ1 include Severe Combined Immunodeficiency With Microcephaly, Growth Retardation, And Sensitivity To Ionizing Radiation and Severe Combined Immunodeficiency. Among its related pathways are DNA Damage and DNA Double-Strand Break Repair.

UniProtKB/Swiss-Prot for NHEJ1 Gene

  • DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration of the end bound NHEJ factors to allow XRCC4 access to the DNA termini. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary (PubMed:16439204, PubMed:16439205, PubMed:17470781). Binds DNA in a length-dependent manner (PubMed:17317666).

Gene Wiki entry for NHEJ1 Gene

Additional gene information for NHEJ1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NHEJ1 Gene

Genomics for NHEJ1 Gene

Regulatory Elements for NHEJ1 Gene

Enhancers for NHEJ1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02H219594 1.7 FANTOM5 ENCODE dbSUPER 32.8 -436.0 -436038 4.3 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 NHEJ1 DNPEP STK11IP RN7SKP213
GH02H218566 1.8 FANTOM5 ENCODE dbSUPER 20.2 +591.5 591548 4.7 HDGF PKNOX1 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B AAMP CNOT9 USP37 PLCD4 BCS1L NHEJ1 CNPPD1 SLC23A3 ZNF142 RNF25
GH02H219641 1.6 Ensembl ENCODE dbSUPER 22.2 -481.6 -481586 1.7 HDGF ZFP64 ARID4B SIN3A DMAP1 ZNF2 ZNF207 ZNF143 CEBPZ ZHX2 DNPEP NHEJ1 OBSL1 TMEM198 CHPF ENSG00000267919 GC02M219631
GH02H218269 1.4 ENCODE dbSUPER 23.9 +888.2 888226 7.1 HDGF PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ENSG00000261338 USP37 NHEJ1 AAMP ARPC2 CNOT9 PNKD TMBIM1 MIR6513
GH02H219121 1.5 Ensembl ENCODE dbSUPER 22.2 +35.8 35797 7.2 FOXA2 ATF1 ARID4B YBX1 TCF12 FOS ATF7 RUNX3 SP5 REST SLC23A3 NHEJ1 IHH LOC100129175 MIR375 FEV CRYBA2 LINC00608 CNPPD1 RETREG2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NHEJ1 on UCSC Golden Path with GeneCards custom track

Promoters for NHEJ1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000130510 265 1201 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 SLC30A9 GLIS2 ZNF143

Genomic Locations for NHEJ1 Gene

Genomic Locations for NHEJ1 Gene
chr2:219,075,317-219,160,865
(GRCh38/hg38)
Size:
85,549 bases
Orientation:
Minus strand
chr2:219,940,039-220,025,587
(GRCh37/hg19)

Genomic View for NHEJ1 Gene

Genes around NHEJ1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NHEJ1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NHEJ1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NHEJ1 Gene

Proteins for NHEJ1 Gene

  • Protein details for NHEJ1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9H9Q4-NHEJ1_HUMAN
    Recommended name:
    Non-homologous end-joining factor 1
    Protein Accession:
    Q9H9Q4
    Secondary Accessions:
    • B8ZZA4
    • Q4ZFW7
    • Q6IA64
    • Q96JS9

    Protein attributes for NHEJ1 Gene

    Size:
    299 amino acids
    Molecular mass:
    33337 Da
    Quaternary structure:
    • Exists mainly as a homodimer. Associates with the non-homologous end joining (NHEJ) complex which is at least composed of the core proteins XRCC5/Ku80, XRCC6/Ku70, PRKDC/DNA-PKcs, LIG4 and XRCC4.
    Miscellaneous:
    • Was named Cernunnos after the enigmatic Celtic god of hunting, the underworld and fertility.

    Three dimensional structures from OCA and Proteopedia for NHEJ1 Gene

    Alternative splice isoforms for NHEJ1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NHEJ1 Gene

Post-translational modifications for NHEJ1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NHEJ1 Gene

No data available for DME Specific Peptides for NHEJ1 Gene

Domains & Families for NHEJ1 Gene

Gene Families for NHEJ1 Gene

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

Protein Domains for NHEJ1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NHEJ1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9H9Q4

UniProtKB/Swiss-Prot:

NHEJ1_HUMAN :
  • The coiled-coil region mediates homodimerization.
  • Belongs to the XLF family.
Domain:
  • The coiled-coil region mediates homodimerization.
Family:
  • Belongs to the XLF family.
genes like me logo Genes that share domains with NHEJ1: view

Function for NHEJ1 Gene

Molecular function for NHEJ1 Gene

UniProtKB/Swiss-Prot Function:
DNA repair protein involved in DNA nonhomologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. May serve as a bridge between XRCC4 and the other NHEJ factors located at DNA ends, or may participate in reconfiguration of the end bound NHEJ factors to allow XRCC4 access to the DNA termini. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are noncomplementary or partially complementary (PubMed:16439204, PubMed:16439205, PubMed:17470781). Binds DNA in a length-dependent manner (PubMed:17317666).

Phenotypes From GWAS Catalog for NHEJ1 Gene

Gene Ontology (GO) - Molecular Function for NHEJ1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 16439205
GO:0045027 DNA end binding IBA --
genes like me logo Genes that share ontologies with NHEJ1: view
genes like me logo Genes that share phenotypes with NHEJ1: view

Human Phenotype Ontology for NHEJ1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for NHEJ1 Gene

MGI Knock Outs for NHEJ1:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for NHEJ1 Gene

Localization for NHEJ1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NHEJ1 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 NHEJ1 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (3)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NHEJ1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IDA,IEA 16439204
GO:0005654 nucleoplasm TAS --
GO:0032807 DNA ligase IV complex IBA --
GO:0070419 nonhomologous end joining complex IDA 20383123
genes like me logo Genes that share ontologies with NHEJ1: view

Pathways & Interactions for NHEJ1 Gene

genes like me logo Genes that share pathways with NHEJ1: view

Pathways by source for NHEJ1 Gene

1 Cell Signaling Technology pathway for NHEJ1 Gene
1 BioSystems pathway for NHEJ1 Gene
1 KEGG pathway for NHEJ1 Gene

SIGNOR curated interactions for NHEJ1 Gene

Other effect:

Gene Ontology (GO) - Biological Process for NHEJ1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006281 DNA repair IEA --
GO:0006302 double-strand break repair IEA --
GO:0006303 double-strand break repair via nonhomologous end joining TAS --
GO:0006974 cellular response to DNA damage stimulus IEA --
GO:0007417 central nervous system development NAS 16439204
genes like me logo Genes that share ontologies with NHEJ1: view

Drugs & Compounds for NHEJ1 Gene

No Compound Related Data Available

Transcripts for NHEJ1 Gene

Unigene Clusters for NHEJ1 Gene

Nonhomologous end-joining factor 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for NHEJ1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b · 3c · 3d ^ 4a · 4b · 4c ^ 5a · 5b ^ 6a · 6b · 6c · 6d · 6e ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10a · 10b ^
SP1: - - - - - - -
SP2: - - - -
SP3: - - - - - - -
SP4:
SP5:
SP6:
SP7: - - - -
SP8: - - -
SP9: - - - -
SP10:
SP11:
SP12:
SP13: - - - - -
SP14:
SP15:
SP16:

ExUns: 11 ^ 12a · 12b ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20a · 20b ^ 21 ^ 22a · 22b ^ 23 ^ 24a · 24b · 24c · 24d · 24e · 24f
SP1: - - - - - - - - -
SP2: - - - - - - - - - -
SP3:
SP4: - - - - - -
SP5: - - - -
SP6: -
SP7:
SP8:
SP9:
SP10: -
SP11: - - - - -
SP12:
SP13:
SP14: -
SP15: -
SP16:

Relevant External Links for NHEJ1 Gene

GeneLoc Exon Structure for
NHEJ1
ECgene alternative splicing isoforms for
NHEJ1

Expression for NHEJ1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NHEJ1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for NHEJ1 Gene

This gene is overexpressed in Testis (14.3), Blymphocyte (8.3), and Peripheral blood mononuclear cells (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for NHEJ1 Gene



Protein tissue co-expression partners for NHEJ1 Gene

NURSA nuclear receptor signaling pathways regulating expression of NHEJ1 Gene:

NHEJ1

SOURCE GeneReport for Unigene cluster for NHEJ1 Gene:

Hs.225988

mRNA Expression by UniProt/SwissProt for NHEJ1 Gene:

Q9H9Q4-NHEJ1_HUMAN
Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for NHEJ1 Gene

  • Bone marrow(4.2)
  • Skin(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for NHEJ1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • skeleton
Organs:
Head and neck:
  • brain
  • chin
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • nose
  • skull
General:
  • blood
  • coagulation system
  • red blood cell
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with NHEJ1: view

No data available for mRNA differential expression in normal tissues for NHEJ1 Gene

Orthologs for NHEJ1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for NHEJ1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NHEJ1 33 34
  • 99.44 (n)
cow
(Bos Taurus)
Mammalia NHEJ1 33 34
  • 86.85 (n)
dog
(Canis familiaris)
Mammalia NHEJ1 33 34
  • 85.62 (n)
rat
(Rattus norvegicus)
Mammalia Nhej1 33
  • 82.61 (n)
mouse
(Mus musculus)
Mammalia Nhej1 33 16 34
  • 81.13 (n)
oppossum
(Monodelphis domestica)
Mammalia NHEJ1 34
  • 60 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NHEJ1 34
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves NHEJ1 33 34
  • 57.68 (n)
lizard
(Anolis carolinensis)
Reptilia NHEJ1 34
  • 45 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia nhej1 33
  • 52.8 (n)
Str.3483 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.2343 33
zebrafish
(Danio rerio)
Actinopterygii nhej1 33 34
  • 48.61 (n)
Species where no ortholog for NHEJ1 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 NHEJ1 Gene

ENSEMBL:
Gene Tree for NHEJ1 (if available)
TreeFam:
Gene Tree for NHEJ1 (if available)

Paralogs for NHEJ1 Gene

No data available for Paralogs for NHEJ1 Gene

Variants for NHEJ1 Gene

Sequence variations from dbSNP and Humsavar for NHEJ1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs118204451 Pathogenic, Severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID) [MIM:611291] 219,158,194(-) GCCAG(C/G)GAGCC reference, missense
rs118204452 Pathogenic, Severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID) [MIM:611291] 219,157,495(-) TCCAC(C/T)GCATG reference, missense
rs118204453 Pathogenic 219,146,736(-) CAGAT(C/T)GATTG reference, stop-gained
rs886037606 Pathogenic 219,158,183(-) CCAAG(GTA/TT)AGTAT splice-donor-variant
rs886037607 Pathogenic 219,158,351(-) GAACT(-/T)GGAGC reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for NHEJ1 Gene

Variant ID Type Subtype PubMed ID
esv2546592 CNV deletion 19546169
esv2721481 CNV deletion 23290073
nsv1142976 CNV tandem duplication 24896259
nsv472306 CNV novel sequence insertion 20440878
nsv477603 CNV novel sequence insertion 20440878
nsv508200 CNV deletion 20534489

Variation tolerance for NHEJ1 Gene

Residual Variation Intolerance Score: 44.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.13; 61.32% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NHEJ1 Gene

Human Gene Mutation Database (HGMD)
NHEJ1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NHEJ1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NHEJ1 Gene

Disorders for NHEJ1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for NHEJ1 Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation
  • scid, autosomal recessive, t cell-negative, b cell-negative, nk cell-positive, with microcephaly, growth retardation, and sensitivity to ionizing radiation, nhej1 syndrome
severe combined immunodeficiency
  • combined t and b cell inborn immunodeficiency
lig4 syndrome
  • dna ligase iv deficiency
kidney hypertrophy
  • hypertrophy of kidney
microcephaly
  • microcephalus
- elite association - COSMIC cancer census association via MalaCards
Search NHEJ1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

NHEJ1_HUMAN
  • Note=A chromosomal aberration involving NHEJ1 is found in a patient with polymicrogyria. Translocation t(2;7)(q35;p22). {ECO:0000269 PubMed:12604777}.
  • Severe combined immunodeficiency due to NHEJ1 deficiency (NHEJ1-SCID) [MIM:611291]: SCID refers to a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia and low or absent antibody levels. Patients with SCID present in infancy with recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. NHEJ1-SCID is characterized by a profound T- and B-lymphocytopenia associated with increased cellular sensitivity to ionizing radiation, microcephaly and growth retardation. Some patients may manifest SCID with sensitivity to ionizing radiation without microcephaly and mild growth retardation, probably due to hypomorphic NHEJ1 mutations. {ECO:0000269 PubMed:16439204, ECO:0000269 PubMed:16439205, ECO:0000269 PubMed:17317666}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for NHEJ1

Genetic Association Database (GAD)
NHEJ1
Human Genome Epidemiology (HuGE) Navigator
NHEJ1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NHEJ1
genes like me logo Genes that share disorders with NHEJ1: view

No data available for Genatlas for NHEJ1 Gene

Publications for NHEJ1 Gene

  1. XLF interacts with the XRCC4-DNA ligase IV complex to promote DNA nonhomologous end-joining. (PMID: 16439205) Ahnesorg P … Jackson SP (Cell 2006) 2 3 4 22 60
  2. Crystal structure of human XLF/Cernunnos reveals unexpected differences from XRCC4 with implications for NHEJ. (PMID: 18046455) Li Y … Blundell TL (The EMBO journal 2008) 3 4 22 60
  3. Cernunnos/XLF promotes the ligation of mismatched and noncohesive DNA ends. (PMID: 17470781) Tsai CJ … Chu G (Proceedings of the National Academy of Sciences of the United States of America 2007) 3 4 22 60
  4. Length-dependent binding of human XLF to DNA and stimulation of XRCC4.DNA ligase IV activity. (PMID: 17317666) Lu H … Lieber MR (The Journal of biological chemistry 2007) 3 4 22 60
  5. Cernunnos, a novel nonhomologous end-joining factor, is mutated in human immunodeficiency with microcephaly. (PMID: 16439204) Buck D … Revy P (Cell 2006) 2 3 4 60

Products for NHEJ1 Gene

Sources for NHEJ1 Gene

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