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

Summary

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; IMD124; MCOPCB13
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

Location:: 2q35

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (219069357..219160815, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (219557705..219649239, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (219934079..220025537, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PAXX binding to the NHEJ machinery explains functional redundancy with XLF.
Title: PAXX binding to the NHEJ machinery explains functional redundancy with XLF.
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.
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.
Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.
Title: Cryo-EM of NHEJ supercomplexes provides insights into DNA repair.
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.
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.
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.
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.
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.
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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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	not available

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 EBI GWAS CatalogPubMed
Genome-wide association analysis identifies 20 loci that influence adult height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies of adult height in East Asians identifies 17 novel loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH48754 (e-PCR)
- UniSTS:37804

SLC23A3_1795 (e-PCR)
- UniSTS:281012

D2S2788 (e-PCR)
- UniSTS:3808

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

NG_007880.1 RefSeqGene

Range

5001..90542

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_90

mRNA and Protein(s)

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
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
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