mutLBSgeneDB |
Gene summary for XRCC4 |
Gene summary |
Basic gene Info. | Gene symbol | XRCC4 |
Gene name | X-ray repair complementing defective repair in Chinese hamster cells 4 | |
Synonyms | - | |
Cytomap | UCSC genome browser: 5q14.2 | |
Type of gene | protein-coding | |
RefGenes | NM_003401.3, NM_022406.2,NM_022550.2, | |
Description | DNA repair protein XRCC4X-ray repair cross-complementing protein 4X-ray repair, complementing defective, repair in Chinese hamster | |
Modification date | 20141222 | |
dbXrefs | MIM : 194363 | |
HGNC : HGNC | ||
Ensembl : ENSG00000152422 | ||
HPRD : 15951 | ||
Vega : OTTHUMG00000131319 | ||
Protein | UniProt: Q13426 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_XRCC4 | |
BioGPS: 7518 | ||
Pathway | NCI Pathway Interaction Database: XRCC4 | |
KEGG: XRCC4 | ||
REACTOME: XRCC4 | ||
Pathway Commons: XRCC4 | ||
Context | iHOP: XRCC4 | |
ligand binding site mutation search in PubMed: XRCC4 | ||
UCL Cancer Institute: XRCC4 | ||
Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO Term | PubMed ID | GO:0006302 | double-strand break repair | 9242410 | GO:0006303 | double-strand break repair via nonhomologous end joining | 12517771 | GO:0010165 | response to X-ray | 9242410 | GO:0051103 | DNA ligation involved in DNA repair | 12517771 | GO:0051351 | positive regulation of ligase activity | 9242410 |
Top |
Ligand binding site mutations for XRCC4 |
Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.) : non-synonymous mutation on LBS, Circle size denotes number of samples. |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | R179 | R179W | KIRC | 1 |
cf) Cancer type abbreviation. BLCA: Bladder urothelial carcinoma, BRCA: Breast invasive carcinoma, CESC: Cervical squamous cell carcinoma and endocervical adenocarcinoma, COAD: Colon adenocarcinoma, GBM: Glioblastoma multiforme, LGG: Brain lower grade glioma, HNSC: Head and neck squamous cell carcinoma, KICH: Kidney chromophobe, KIRC: Kidney renal clear cell carcinoma, KIRP: Kidney renal papillary cell carcinoma, LAML: Acute myeloid leukemia, LUAD: Lung adenocarcinoma, LUSC: Lung squamous cell carcinoma, OV: Ovarian serous cystadenocarcinoma, PAAD: Pancreatic adenocarcinoma, PRAD: Prostate adenocarcinoma, SKCM: Skin cutaneous melanoma, STAD: Stomach adenocarcinoma, THCA: Thyroid carcinoma, UCEC: Uterine corpus endometrial carcinoma. |
Top |
Protein structure related information for XRCC4 |
Relative protein structure stability change (ΔΔE) using Mupro 1.1 Mupro score denotes assessment of the effect of mutations on thermodynamic stability. (ΔΔE<0: mutation decreases stability, ΔΔE>0: mutation increases stability) |
: nsSNV at non-LBS: nsSNV at LBS |
nsSNVs sorted by the relative stability change of protein structure by each mutation Blue: mutations of positive stability change. and red : the most recurrent mutation for this gene. |
LBS | AAchange of nsSNV | Relative stability change | R179 | R179W | -0.76790834 |
(MuPro1.1: Jianlin Cheng et al., Prediction of Protein Stability Changes for Single-Site Mutations Using Support Vector Machines, PROTEINS: Structure, Function, and Bioinformatics. 2006, 62:1125-1132) |
Structure image for XRCC4 from PDB |
Top |
Differential gene expression and gene-gene network for XRCC4 |
Differential gene expression between mutated and non-mutated LBS samples in all 16 major cancer types |
Differential co-expressed gene network based on protein-protein interaction data (CePIN) |
Top |
Top |
Phenotype information for XRCC4 |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0008625 | Chromosome Aberrations | 1 | Biomarker |
umls:C0342573 | Pituitary dwarfism 1 | 1 | Biomarker, GeneticVariation |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
Top |
Pharmacological information for XRCC4 |
Gene expression profile of anticancer drug treated cell-lines (CCLE) Heatmap showing the correlation between gene expression and drug response across all the cell-lines. We chose the top 20 among 138 drugs.We used Pearson's correlation coefficient. |
Gene-centered drug-gene interaction network |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Experimental | DB03963 | S-(Dimethylarsenic)Cysteine | Small molecule |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of XRCC4 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (ALA,ARG,GLU,TYR,ASP,CYS,TYR,GLY,ASP,SER,TYR,PHE,ILE,ASP,THR,ASP,LEU,ASN,GLN,LEU,LYS,GLU,VAL,PHE,SER,GLY,ILE,LYS) | 1ik9 | B | R179 |
Top |
Conservation information for LBS of XRCC4 |
Multiple alignments for Q13426 in multiple species |
LBS | AA sequence | # species | Species |
Copyright © 2016-Present - The University of Texas Health Science Center at Houston |