mutated Ligand Binding Site gene DataBase





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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for XRCC6
Gene summary
Basic gene Info.Gene symbolXRCC6
Gene nameX-ray repair complementing defective repair in Chinese hamster cells 6
CytomapUCSC genome browser: 22q13.2
Type of geneprotein-coding
Description5'-dRP lyase Ku705'-deoxyribose-5-phosphate lyase Ku7070 kDa subunit of Ku antigenATP-dependent DNA helicase 2 subunit 1ATP-dependent DNA helicase II 70 kDa subunitATP-dependent DNA helicase II, 70 kDa subunitCTC box binding factor 75 kDa subunitCT
Modification date20141207
dbXrefs MIM : 152690
Ensembl : ENSG00000196419
HPRD : 01071
Vega : OTTHUMG00000151190
ProteinUniProt: P12956
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_XRCC6
BioGPS: 2547
PathwayNCI Pathway Interaction Database: XRCC6
Pathway Commons: XRCC6
ContextiHOP: XRCC6
ligand binding site mutation search in PubMed: XRCC6
UCL Cancer Institute: XRCC6
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0045893positive regulation of transcription, DNA-templated12145306

Ligand binding site mutations for XRCC6
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
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for XRCC6
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.
LBSAAchange of nsSNVRelative stability change
(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 XRCC6 from PDB

Differential gene expression and gene-gene network for XRCC6
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)
* Left PPI network was created from samples with mutations in the LBS of XRCC6 and the right PPI network was created from samples without mutations in the LBS of XRCC6. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for XRCC6
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for XRCC6
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of XRCC6 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NUCNucleic Acids1jeyAK282 P285 R403
NUCNucleic Acids1jeyAQ278

Conservation information for LBS of XRCC6
Multiple alignments for P12956 in multiple species
LBSAA sequence# speciesSpecies
A255ETRKRALSRLK1Homo sapiens
A255KEVKRIMFQCP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A255KEIKRIKFRCP1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
A255DFLRRCLGHFS1Drosophila melanogaster
A255QKPKRAHFHLK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A255ETKKRVLSRLK1Mus musculus
A255VLAKRIAKRIT1Arabidopsis thaliana
A255MMKKRKVKTLA1Oryza sativa subsp. japonica
K282VQKALKPPPIK1Homo sapiens
K282YTHEKAGVRYK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K282VSHEIPGSKYK1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
K282FQRRAYPRKVQ1Drosophila melanogaster
K282LKRLESAKTNW1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K282VQKANKPFPVR1Mus musculus
K282LRPAIPGSITW1Arabidopsis thaliana
K282IRSTTPGAITW1Oryza sativa subsp. japonica
K338ETEELKRFDDP1Homo sapiens
K338QDQIVMEAYTQ1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K338ENLKIQSGYSE1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
K338QLNRVRNLHKP1Drosophila melanogaster
K338ELNKVRSFEPP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K338ETEELKRFDEP1Mus musculus
K338ELSQVKRISTG1Arabidopsis thaliana
K338ELSDVKRVSSH1Oryza sativa subsp. japonica
L256TRKRALSRLKL1Homo sapiens
L256EVKRIMFQCPL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L256EIKRIKFRCPL1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
L256FLRRCLGHFSF1Drosophila melanogaster
L256KPKRAHFHLKM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L256TKKRVLSRLKF1Mus musculus
L256LAKRIAKRITF1Arabidopsis thaliana
L256MKKRKVKTLAF1Oryza sativa subsp. japonica
P285ALKPPPIKLYR1Homo sapiens
P285EKAGVRYKLVY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P285EIPGSKYKLVY1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
P285RAYPRKVQILR1Drosophila melanogaster
P285LESAKTNWVYA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P285ANKPFPVRLYR1Mus musculus
P285AIPGSITWLDS1Arabidopsis thaliana
P285TTPGAITWLDS1Oryza sativa subsp. japonica
Q278IYNLVQKALKP1Homo sapiens
Q278GYTMYTHEKAG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Q278GYTIVSHEIPG1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Q278YYNYFQRRAYP1Drosophila melanogaster
Q278AFILLKRLESA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Q278IYNLVQKANKP1Mus musculus
Q278GYALLRPAIPG1Arabidopsis thaliana
Q278TYALIRSTTPG1Oryza sativa subsp. japonica
R254KETRKRALSRL1Homo sapiens
R254KKEVKRIMFQC1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R254TKEIKRIKFRC1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
R254QDFLRRCLGHF1Drosophila melanogaster
R254LQKPKRAHFHL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R254KETKKRVLSRL1Mus musculus
R254RVLAKRIAKRI1Arabidopsis thaliana
R254RMMKKRKVKTL1Oryza sativa subsp. japonica
R403CRYTPRRNIPP1Homo sapiens
R403LWGKLKSNSHP1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R403VWGKLRPNSPP1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
R403CLFMCKRKSIP1Drosophila melanogaster
R403AWFVSRPNANP1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R403CRYTPRKNVSP1Mus musculus
R403AFYGGTTP--P1Arabidopsis thaliana
R403AFYGNPTR--P1Oryza sativa subsp. japonica
R404RYTPRRNIPPY1Homo sapiens
R404WGKLKSNSHPS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R404WGKLRPNSPPS1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
R404LFMCKRKSIPR1Drosophila melanogaster
R404WFVSRPNANPC1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R404RYTPRKNVSPY1Mus musculus
R404FYGGTTP--PR1Arabidopsis thaliana
R404FYGNPTR--PQ1Oryza sativa subsp. japonica
R80IISSDRDLLAV2Homo sapiens, Mus musculus
R80VITRPGTAIGC1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
R80VVVMPSTAVGC1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
R80LLVNDKDLIGL1Drosophila melanogaster
R80VITNPSDIMGV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
R80IINRSNDEIAI1Arabidopsis thaliana
R80IIGRSYDEVAI1Oryza sativa subsp. japonica
S257RKRALSRLKLK1Homo sapiens
S257VKRIMFQCPLI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S257IKRIKFRCPLM1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
S257LRRCLGHFSFY1Drosophila melanogaster
S257PKRAHFHLKMD1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S257KKRVLSRLKFK1Mus musculus
S257AKRIAKRITFV1Arabidopsis thaliana
S257KKRKVKTLAFA1Oryza sativa subsp. japonica
S78SKIISSDRDLL2Homo sapiens, Mus musculus
S78QLVITRPGTAI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S78QLVVVMPSTAV1Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
S78SGLLVNDKDLI1Drosophila melanogaster
S78QRVITNPSDIM1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S78AHIINRSNDEI1Arabidopsis thaliana
S78TQIIGRSYDEV1Oryza sativa subsp. japonica

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