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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	7518
Gene name	X-ray repair cross complementing 4
Gene symbol	XRCC4
Synonyms (NCBI Gene)	SSMEDhXRCC4
Chromosome	5
Chromosome location	5q14.2
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.

Show/Hide all (10)

SNP ID	Visualize variation	Clinical significance	Consequence
rs587779351	T>C	Pathogenic	Coding sequence variant, missense variant
rs768825050	C>T	Pathogenic	Coding sequence variant, stop gained
rs779773463	C>T	Pathogenic	Coding sequence variant, stop gained
rs797045016	C>T	Pathogenic	Coding sequence variant, genic downstream transcript variant, stop gained
rs797045017	G>A,T	Pathogenic	Coding sequence variant, missense variant
rs869320677	C>-	Pathogenic	Coding sequence variant, frameshift variant
rs869320678	G>T	Pathogenic	Splice acceptor variant
rs879255258	T>A,G	Pathogenic	Coding sequence variant, missense variant
rs879255259	G>-	Pathogenic	Coding sequence variant, genic downstream transcript variant, frameshift variant
rs991596636	A>T	Likely-pathogenic	Stop gained, coding sequence variant

Show/Hide all (9)

miRTarBase ID	miRNA	Experiments
MIRT1497385	hsa-miR-3121-5p	CLIP-seq
MIRT1497386	hsa-miR-3657	CLIP-seq
MIRT1497387	hsa-miR-4517	CLIP-seq
MIRT1497388	hsa-miR-4669	CLIP-seq
MIRT2441710	hsa-miR-203	CLIP-seq
MIRT2441711	hsa-miR-4279	CLIP-seq
MIRT1497386	hsa-miR-3657	CLIP-seq
MIRT1497387	hsa-miR-4517	CLIP-seq
MIRT1497388	hsa-miR-4669	CLIP-seq

Show/Hide all (45)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000793	Component	Condensed chromosome	IDA	12589063
GO:0003677	Function	DNA binding	EXP	38898102
GO:0003677	Function	DNA binding	IDA	9259561
GO:0005515	Function	Protein binding	IPI	9259561, 9809069, 11702069, 15380105, 15385968, 16189514, 16275660, 16439205, 16713569, 17124166, 17290226, 17353262, 17389648, 17396150, 18064046, 18158905, 21070942, 21349273, 21637298, 21768349, 22529269, 22658747, 23178593, 23219551, 24095731, 25416956, 25910212, 25934149, 26496
GO:0005634	Component	Nucleus	IDA	25597996
GO:0005634	Component	Nucleus	IDA	9259561, 12589063, 25934149
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	16439205
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005694	Component	Chromosome	IEA
GO:0005737	Component	Cytoplasm	IDA	33725486
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA	9259561
GO:0005958	Component	DNA-dependent protein kinase-DNA ligase 4 complex	IBA
GO:0005958	Component	DNA-dependent protein kinase-DNA ligase 4 complex	IDA	15194694, 34352203
GO:0005958	Component	DNA-dependent protein kinase-DNA ligase 4 complex	IEA
GO:0006281	Process	DNA repair	IEA
GO:0006284	Process	Base-excision repair	IDA	19589734
GO:0006302	Process	Double-strand break repair	IDA	9242410, 19589734
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	12517771, 15385968, 17290226, 25597996, 25934149, 26774286, 27437582, 28453785, 28500754
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IEA
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	IMP	9809069, 25742519
GO:0006303	Process	Double-strand break repair via nonhomologous end joining	NAS	16439205
GO:0006310	Process	DNA recombination	IEA
GO:0006974	Process	DNA damage response	IEA
GO:0010165	Process	Response to X-ray	IBA
GO:0010165	Process	Response to X-ray	IDA	9242410
GO:0010165	Process	Response to X-ray	IEA
GO:0016874	Function	Ligase activity	IDA	9242410
GO:0019899	Function	Enzyme binding	IPI	19589734
GO:0032807	Component	DNA ligase IV complex	IBA
GO:0032807	Component	DNA ligase IV complex	IDA	9242410
GO:0033152	Process	Immunoglobulin V(D)J recombination	IBA
GO:0035861	Component	Site of double-strand break	IDA	26774286, 27437582, 28500754
GO:0035861	Component	Site of double-strand break	IDA	31548606
GO:0042802	Function	Identical protein binding	IPI	16169070, 21070942, 21768349, 25416956, 31515488, 32296183
GO:0051351	Process	Positive regulation of ligase activity	IDA	9242410
GO:0070419	Component	Nonhomologous end joining complex	IDA	20383123, 25941166
GO:0070975	Function	FHA domain binding	IPI	15385968
GO:0071285	Process	Cellular response to lithium ion	IEA
GO:1905782	Process	Positive regulation of phosphatidylserine exposure on apoptotic cell surface	IDA	33725486
GO:1990166	Process	Protein localization to site of double-strand break	IDA	31548606

MIM	HGNC	e!Ensembl
194363	12831	ENSG00000152422

Q13426

Protein name

DNA repair protein XRCC4 (hXRCC4) (X-ray repair cross-complementing protein 4) [Cleaved into: Protein XRCC4, C-terminus (XRCC4/C)]

Protein function

[DNA repair protein XRCC4]: DNA non-homologous end joining (NHEJ) core factor, required for double-strand break repair and V(D)J recombination (PubMed:10757784, PubMed:10854421, PubMed:12517771, PubMed:16412978, PubMed:17124166, PubMed:17290226,

PDB

1FU1 , 1IK9 , 3II6 , 3MUD , 3Q4F , 3RWR , 3SR2 , 3W03 , 4XA4 , 5CHX , 5CJ0 , 5CJ4 , 5E50 , 5WJ7 , 5WLZ , 6ABO , 7LSY , 7LT3 , 7M3P , 7NFC , 7NFE , 8BH3 , 8BHV , 8BHY , 8BOT , 8EZA , 8EZB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF06632	XRCC4	1 → 334	DNA double-strand break repair and V(D)J recombination protein XRCC4	Family

Tissue specificity

TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:8548796}.

Sequence

MERKISRIHLVSEPSITHFLQVSWEKTLESGFVITLTDGHSAWTGTVSESEISQEADDMA
MEKGKYVGELRKALLSGAGPADVYTFNFSKESCYFFFEKNLKDVSFRLGSFNLEKVENPA
EVIRELICYCLDTIAENQAKNEHLQKENERLLRDWNDVQGRFEKCVSAKEALETDLYKRF
ILVLNEKKTKIRSLHNKLLNAAQEREKDIKQEGETAICSEMTADRDPVYDESTDEESENQ
TDLSGLASAAVSKDDSIISSLDVTDIAPSRKRRQRMQRNLGTEPKMAPQENQLQEKENSR
PDSSLPETSKKEHISAENMSLETLRNSSPEDLFDEI

Sequence length

336

Interactions

View interactions

	KEGG		Reactome
	Non-homologous end-joining		2-LTR circle formation SUMOylation of DNA damage response and repair proteins Nonhomologous End-Joining (NHEJ)

Show/Hide Causal Diseases (3)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Ateleiotic dwarfism	Likely pathogenic; Pathogenic	rs587779351	RCV000115044
Short stature, microcephaly, and endocrine dysfunction	Likely pathogenic; Pathogenic	rs772562216, rs587779351, rs986271387, rs869320677, rs797045016, rs869320678, rs768825050, rs779773463, rs879255258, rs797045017, rs879255259, rs1746416323, rs991596636	RCV001536009 RCV001797975 RCV000190521 RCV005036653 RCV000190522 RCV000190523 RCV000190524 RCV000190525 RCV000190526 RCV000190527 RCV000190528 RCV000190529 RCV003333350 RCV000826091
XRCC4-related disorder	Likely pathogenic; Pathogenic	rs587779351, rs779773463	RCV004748579 RCV003401038

Show/Hide Unknown Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign	rs1805377	RCV005919606
Colorectal cancer	Benign	rs1805377	RCV005919604
Familial cancer of breast	Benign	rs1805377	RCV005919600
Nonpapillary renal cell carcinoma	Benign	rs1805377	RCV005919601
Ovarian cancer	Benign	rs1805377	RCV005919602
Uterine carcinosarcoma	Benign	rs1805377	RCV005919605
Uveal melanoma	Benign	rs1805377	RCV005919603

Show/Hide Text Mining Associations (66)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	34486486
Autosomal Recessive Primary Microcephaly	Associate	25839420
Brain Neoplasms	Associate	27613841
Breast Neoplasms	Associate	16091150, 18383855, 20496165, 24062231, 25360583, 25501155, 27571987, 31030479, 33017027
Breast Neoplasms	Stimulate	33184404
Carcinogenesis	Associate	18383855, 18630527, 19443403, 19729825, 24378850, 30429230
Carcinoma Adenoid Cystic	Associate	26035306
Carcinoma Hepatocellular	Stimulate	25337275
Carcinoma Hepatocellular	Associate	25337275, 32258128, 36524359
Carcinoma Non Small Cell Lung	Associate	19408343, 23924833
Carcinoma Pancreatic Ductal	Associate	38012734
Carcinoma Renal Cell	Associate	18768505
Colorectal Neoplasms	Associate	20920336, 25058500, 25662981, 30429230
Colorectal Neoplasms	Inhibit	20920336
Deafness oligodontia syndrome	Associate	40114033
Developmental Disabilities	Associate	40114033
Diastrophic dysplasia	Associate	18177646
DNA Virus Infections	Associate	28426349
Endometrial Hyperplasia	Associate	30275440
Essential Tremor	Associate	40114033
Facial Dysmorphism with Multiple Malformations	Associate	25839420
Fanconi Anemia	Associate	11124945
Fatty Liver	Associate	40114033
Genetic Diseases Inborn	Associate	24636752
Glaucoma 3 Primary Congenital A	Associate	40114033
Glioma	Associate	23663450, 25973104
Glioma	Stimulate	23663450
Growth Disorders	Associate	25728776, 25742519, 25839420, 33842963, 40114033
HIV Infections	Associate	36312587
Hypertension	Associate	21626137
Immune System Diseases	Associate	34173222
Immunologic Deficiency Syndromes	Associate	33842963
Leiomyoma	Stimulate	18177646
Leukemic Infiltration	Associate	24378850
Lung Neoplasms	Associate	19729825
Lymphatic Metastasis	Associate	21319141
Lymphoma Follicular	Associate	25178586
Lymphoma Non Hodgkin	Associate	20813000, 25178586
Metabolic Syndrome	Associate	25742519
Microcephaly	Associate	25742519, 33842963, 34173222, 40114033
Mouth Neoplasms	Associate	18630527, 22726897
Multiple Myeloma	Associate	20148879, 22183071
Multiple Myeloma	Stimulate	25790254
Myoma	Associate	18177646
Neoplasm Metastasis	Associate	37240218
Neoplasms	Associate	24378850, 24666523, 25058500, 25527410, 31030479, 37240218
Pancreatic Neoplasms	Associate	26045837, 26345895
Piebaldism	Associate	27613841
Pituitary dwarfism 1	Associate	24389050, 25728776
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	21987080, 38423600
Pulmonary Disease Chronic Obstructive	Associate	24053728
Renal Insufficiency	Associate	25742519
Retinoblastoma	Associate	29415984
Salivary Gland Neoplasms	Associate	26035306
Schizophrenia	Associate	20920336
Seckel syndrome 1	Associate	25728776, 40114033
Seizures	Associate	40114033
Severe Combined Immunodeficiency	Associate	25728776
Squamous Cell Carcinoma of Head and Neck	Associate	34528560
Stomach Neoplasms	Associate	25527410
Thumb deformity alopecia pigmentation anomaly	Associate	40114033
Triple Negative Breast Neoplasms	Associate	25360583, 30842344
Urinary Bladder Neoplasms	Associate	19443403, 24666523
Uterine Cervical Dysplasia	Associate	37217238
Uterine Cervical Neoplasms	Associate	21319141, 37217238
Venous Thrombosis	Associate	32915819

XRCC4 (X-ray repair cross complementing 4)