Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	79840
Gene name Gene Name - the full gene name approved by the HGNC.	Non-homologous end joining factor 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	NHEJ1
Synonyms (NCBI Gene) Gene synonyms aliases	IMD124, MCOPCB13, XLF
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2q35
Summary Summary of gene provided in NCBI Entrez 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 b

Show/Hide all(13)

SNP ID	Visualize variation	Clinical significance	Consequence
rs118204451	G>A,C	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant, missense variant
rs118204452	A>G	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs118204453	G>A,T	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant, synonymous variant
rs786205547	C>G	Likely-pathogenic	Splice donor variant
rs886037606	TAC>AA	Pathogenic	Splice donor variant, intron variant
rs886037607	->A	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs886041973	->C	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1064793763	T>A	Pathogenic	Splice acceptor variant
rs1064796857	AATC>-	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1064797028	A>C	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs1064797042	A>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1553542017	G>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1553548393	->TTCC	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant

Show/Hide all(83)

miRTarBase ID	miRNA	Experiments
MIRT1184236	hsa-miR-193a-5p	CLIP-seq
MIRT1184237	hsa-miR-3064-5p	CLIP-seq
MIRT1184238	hsa-miR-3126-3p	CLIP-seq
MIRT1184239	hsa-miR-3150b-3p	CLIP-seq
MIRT1184240	hsa-miR-3652	CLIP-seq
MIRT1184241	hsa-miR-3921	CLIP-seq
MIRT1184242	hsa-miR-4283	CLIP-seq
MIRT1184243	hsa-miR-4311	CLIP-seq
MIRT1184244	hsa-miR-4430	CLIP-seq
MIRT1184245	hsa-miR-4433	CLIP-seq
MIRT1184246	hsa-miR-4489	CLIP-seq
MIRT1184247	hsa-miR-4492	CLIP-seq
MIRT1184248	hsa-miR-4498	CLIP-seq
MIRT1184249	hsa-miR-4505	CLIP-seq
MIRT1184250	hsa-miR-4649-3p	CLIP-seq
MIRT1184251	hsa-miR-4653-5p	CLIP-seq
MIRT1184252	hsa-miR-4667-5p	CLIP-seq
MIRT1184253	hsa-miR-4689	CLIP-seq
MIRT1184254	hsa-miR-4700-5p	CLIP-seq
MIRT1184255	hsa-miR-4784	CLIP-seq
MIRT1184256	hsa-miR-4794	CLIP-seq
MIRT1184257	hsa-miR-4795-5p	CLIP-seq
MIRT1184258	hsa-miR-593	CLIP-seq
MIRT1184259	hsa-miR-637	CLIP-seq
MIRT1184260	hsa-miR-661	CLIP-seq
MIRT1184261	hsa-miR-665	CLIP-seq
MIRT1184262	hsa-miR-762	CLIP-seq
MIRT2053440	hsa-miR-3122	CLIP-seq
MIRT2053441	hsa-miR-34c-3p	CLIP-seq
MIRT2053442	hsa-miR-3689a-3p	CLIP-seq
MIRT2053443	hsa-miR-3689c	CLIP-seq
MIRT2053444	hsa-miR-3913-5p	CLIP-seq
MIRT1184245	hsa-miR-4433	CLIP-seq
MIRT2053445	hsa-miR-4728-5p	CLIP-seq
MIRT2053446	hsa-miR-541	CLIP-seq
MIRT2053447	hsa-miR-654-5p	CLIP-seq
MIRT1184261	hsa-miR-665	CLIP-seq
MIRT2282648	hsa-miR-1285	CLIP-seq
MIRT2282649	hsa-miR-214	CLIP-seq
MIRT2053440	hsa-miR-3122	CLIP-seq
MIRT2282650	hsa-miR-3187-5p	CLIP-seq
MIRT2053441	hsa-miR-34c-3p	CLIP-seq
MIRT2282651	hsa-miR-3619-5p	CLIP-seq
MIRT2053442	hsa-miR-3689a-3p	CLIP-seq
MIRT2053443	hsa-miR-3689c	CLIP-seq
MIRT2282652	hsa-miR-3691-3p	CLIP-seq
MIRT2282653	hsa-miR-3913-3p	CLIP-seq
MIRT2053444	hsa-miR-3913-5p	CLIP-seq
MIRT2282654	hsa-miR-4291	CLIP-seq
MIRT1184243	hsa-miR-4311	CLIP-seq
MIRT1184245	hsa-miR-4433	CLIP-seq
MIRT2282655	hsa-miR-4436a	CLIP-seq
MIRT2053445	hsa-miR-4728-5p	CLIP-seq
MIRT2282656	hsa-miR-489	CLIP-seq
MIRT2282657	hsa-miR-516a-5p	CLIP-seq
MIRT2053446	hsa-miR-541	CLIP-seq
MIRT2282658	hsa-miR-612	CLIP-seq
MIRT2282659	hsa-miR-646	CLIP-seq
MIRT2053447	hsa-miR-654-5p	CLIP-seq
MIRT1184260	hsa-miR-661	CLIP-seq
MIRT1184261	hsa-miR-665	CLIP-seq
MIRT2282660	hsa-miR-761	CLIP-seq
MIRT2282661	hsa-miR-922	CLIP-seq
MIRT2455135	hsa-miR-3145-3p	CLIP-seq
MIRT2455136	hsa-miR-3173-3p	CLIP-seq
MIRT2455137	hsa-miR-3612	CLIP-seq
MIRT2455138	hsa-miR-4428	CLIP-seq
MIRT2455139	hsa-miR-4695-5p	CLIP-seq
MIRT2455140	hsa-miR-650	CLIP-seq
MIRT2053440	hsa-miR-3122	CLIP-seq
MIRT2053442	hsa-miR-3689a-3p	CLIP-seq
MIRT2053443	hsa-miR-3689c	CLIP-seq
MIRT2053444	hsa-miR-3913-5p	CLIP-seq
MIRT2053445	hsa-miR-4728-5p	CLIP-seq
MIRT2053446	hsa-miR-541	CLIP-seq
MIRT2053447	hsa-miR-654-5p	CLIP-seq
MIRT2053440	hsa-miR-3122	CLIP-seq
MIRT2053442	hsa-miR-3689a-3p	CLIP-seq
MIRT2053443	hsa-miR-3689c	CLIP-seq
MIRT2053444	hsa-miR-3913-5p	CLIP-seq
MIRT2053445	hsa-miR-4728-5p	CLIP-seq
MIRT2053446	hsa-miR-541	CLIP-seq
MIRT2053447	hsa-miR-654-5p	CLIP-seq

Show/Hide all(30)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000723	Process	Telomere maintenance	IMP	28369633
GO:0001650	Component	Fibrillar center	IDA
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	16439205, 18064046, 18158905, 21070942, 21349273, 21768349, 24095731, 27437582, 28500754, 29997244, 31548606
GO:0005634	Component	Nucleus	IDA	20558749
GO:0005634	Component	Nucleus	IDA	16439204, 16439205
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005958	Component	DNA-dependent protein kinase-DNA ligase 4 complex	IDA	34352203
GO:0006281	Process	DNA repair	IEA
GO:0006302	Process	Double-strand break repair	IEA
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IBA
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IDA	17717001, 18158905, 18644470, 19056826, 20558749, 27437582, 28500754, 30250067
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IEA
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IMP	16439204, 16439205
GO:0006974	Process	DNA damage response	IEA
GO:0007417	Process	Central nervous system development	NAS	16439204
GO:0010212	Process	Response to ionizing radiation	IDA	16439205
GO:0030183	Process	B cell differentiation	IMP	16439204
GO:0030217	Process	T cell differentiation	IMP	16439204
GO:0032807	Component	DNA ligase IV complex	IBA
GO:0033152	Process	Immunoglobulin V(D)J recombination	IDA	20558749
GO:0035861	Component	Site of double-strand break	IDA	18064046, 18644470, 27437582, 28500754
GO:0045027	Function	DNA end binding	IBA
GO:0045027	Function	DNA end binding	IDA	18158905
GO:0051351	Process	Positive regulation of ligase activity	NAS	16439205
GO:0070182	Function	DNA polymerase binding	IPI	30250067
GO:0070419	Component	Nonhomologous end joining complex	IDA	20383123, 25941166

MIM	HGNC	e!Ensembl
611290	25737	ENSG00000187736

Protein

UniProt ID

Q9H9Q4

Protein name

Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)

Protein function

DNA repair protein involved in DNA non-homologous end joining (NHEJ); it is required for double-strand break (DSB) repair and V(D)J recombination and is also involved in telomere maintenance (PubMed:16439204, PubMed:16439205, PubMed:17317666, Pu

PDB

2QM4 , 2R9A , 3Q4F , 3RWR , 3SR2 , 3W03 , 6ERG , 6ERH , 7LSY , 7LT3 , 7NFC , 7NFE , 7ZYG , 8BHV , 8BHY , 8BOT , 8EZA , 8EZB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF09302	XLF	12 → 182	XLF-Cernunnos, XRcc4-like factor, NHEJ component	Family

Tissue specificity

TISSUE SPECIFICITY: Ubiquitously expressed. {ECO:0000269|PubMed:16439204}.

Sequence

MEELEQGLLMQPWAWLQLAENSLLAKVFITKQGYALLVSDLQQVWHEQVDTSVVSQRAKE
LNKRLTAPPAAFLCHLDNLLRPLLKDAAHPSEATFSCDCVADALILRVRSELSGLPFYWN
FHCMLASPSLVSQHLIRPLMGMSLALQCQVRELATLLHMKDLEIQDYQESGATLIRDRLK
TEPFEENSFLEQFMIEKLPEACSIGDGKPFVMNLQDLYMAVTTQEVQVGQKHQGAGDPHT
SNSASLQGIDSQCVNQPEQLVSSAPTLSAPEKESTGTSGPLQRPQLSKVKRKKPRGLFS

Sequence length

299

Interactions

View interactions

	KEGG		Reactome
	Non-homologous end-joining		Nonhomologous End-Joining (NHEJ)

Show/Hide Causal Diseases (2)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Severe combined immunodeficiency with microcephaly, growth retardation, and sensitivity to ionizing radiation	cernunnos-xlf deficiency	rs118204453, rs886037606, rs886037607, rs1064793763, rs1553542017, rs1949865586, rs753495484, rs118204452	N/A
severe combined immunodeficiency disease	Severe combined immunodeficiency disease	rs886037607	N/A

Show/Hide Unknown Diseases (2)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Duodenal Ulcer	Duodenal ulcer	N/A	N/A	GWAS
Metabolic Syndrome	Serum polyunsaturated fatty acid concentration x sex interaction in metabolic syndrome	N/A	N/A	GWAS

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Anemia Hemolytic Autoimmune	Associate	30898087
Carcinogenesis	Associate	26225792
Chromosome 7 monosomy	Associate	35812385
Colorectal Neoplasms	Associate	31806933
DNA Virus Infections	Associate	26225792, 28426349
Esophageal Squamous Cell Carcinoma	Associate	25321468
Genetic Diseases Inborn	Associate	24636752
Graft vs Host Disease	Associate	17317666, 19223975
Hematologic Diseases	Associate	35812385
Hyperpigmentation	Associate	35812385
Immunologic Deficiency Syndromes	Associate	16439204, 19223975, 30666249
Microcephaly	Associate	19223975, 30898087
Microphthalmia Syndromic 6	Associate	19223975
Neoplasms Basal Cell	Associate	26540568
Primary Immunodeficiency Diseases	Associate	32265901
Retinal Dysplasia	Associate	35812385
Seckel syndrome 1	Associate	35812385
Severe Combined Immunodeficiency	Associate	17317666, 30898087, 32265901, 32691468, 35303369, 40457861
Werner Syndrome	Inhibit	24626809

NHEJ1 (non-homologous end joining factor 1)