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mutLBSgeneDB |
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| Gene summary for MDC1 |
 Gene summary |
| Basic gene Info. | Gene symbol | MDC1 |
| Gene name | mediator of DNA-damage checkpoint 1 | |
| Synonyms | NFBD1 | |
| Cytomap | UCSC genome browser: 6p21.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_014641.2, | |
| Description | homologue to Drosophila photoreceptor protein calphotinmediator of DNA damage checkpoint 1mediator of DNA damage checkpoint protein 1nuclear factor with BRCT domains 1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 607593 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000137337 | ||
| HPRD : 16252 | ||
| Vega : OTTHUMG00000031075 | ||
| Protein | UniProt: Q14676 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_MDC1 | |
| BioGPS: 9656 | ||
| Pathway | NCI Pathway Interaction Database: MDC1 | |
| KEGG: MDC1 | ||
| REACTOME: MDC1 | ||
| Pathway Commons: MDC1 | ||
| Context | iHOP: MDC1 | |
| ligand binding site mutation search in PubMed: MDC1 | ||
| UCL Cancer Institute: MDC1 | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID |
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| Ligand binding site mutations for MDC1 |
| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | G1899 | V1900A | COAD | 1 | A124 | L122F | HNSC | 1 | R1933 | R1933Q | STAD | 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. |
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| Protein structure related information for MDC1 |
| 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 |
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| 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 | A124 | L122F | -1.5630054 | G1899 | V1900A | -1.2155671 | R1933 | R1933Q | -0.89961754 |
| (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 MDC1 from PDB |
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| Differential gene expression and gene-gene network for MDC1 |
| 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) |
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| Phenotype information for MDC1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for MDC1 |
| 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. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of MDC1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (GLU,ASP,THR,GLN,MET,ILE,ASP,TRP) | 3uot | A | A124 | III | Peptide ligand (GLU,ASP,THR,GLN,MET,ILE,ASP,TRP) | 3uot | B | A124 | III | Peptide ligand (ALA,SER,GLN,GLU,TYR) | 2azm | A | G1899 R1933 | III | Peptide ligand (ALA,SER,GLN,GLU,TYR) | 2azm | B | G1899 R1933 | III | Peptide ligand (SER,GLN,GLU,TYR,NH2) | 3k05 | A | G1899 R1933 | III | Peptide ligand (SER,GLN,GLU,TYR,NH2) | 3k05 | B | G1899 R1933 |
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| Conservation information for LBS of MDC1 |
| Multiple alignments for Q14676 in multiple species |
| LBS | AA sequence | # species | Species | A124 | ELILFADLLCQ | 3 | Homo sapiens, Macaca mulatta, Pan troglodytes | A124 | ELILFADFPCQ | 2 | Mus musculus, Rattus norvegicus | D125 | LILFADLLCQY | 3 | Homo sapiens, Macaca mulatta, Pan troglodytes | D125 | LILFADFPCQY | 2 | Mus musculus, Rattus norvegicus | G1899 | KVLFTGVVDAR | 2 | Homo sapiens, Pan troglodytes | G1899 | KVLFTGVVDAQ | 1 | Macaca mulatta | G1899 | KVLFTGVMDSR | 1 | Mus musculus | G1899 | KVLFTGVVDSR | 1 | Rattus norvegicus | I71 | LPFPSISKQHA | 5 | Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus | K1936 | IRRTVKFLCAL | 4 | Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus | K1936 | IRRTVKFLCAV | 1 | Rattus norvegicus | K73 | FPSISKQHAEI | 3 | Homo sapiens, Macaca mulatta, Pan troglodytes | K73 | FPSISKQHAVI | 2 | Mus musculus, Rattus norvegicus | L95 | RDCGSLNGTQI | 3 | Homo sapiens, Macaca mulatta, Pan troglodytes | L95 | QDCGSLNGTQI | 2 | Mus musculus, Rattus norvegicus | M59 | NVVGRMPDCSV | 3 | Homo sapiens, Macaca mulatta, Pan troglodytes | M59 | NVVGRSPDCSV | 2 | Mus musculus, Rattus norvegicus | N96 | DCGSLNGTQIL | 3 | Homo sapiens, Macaca mulatta, Pan troglodytes | N96 | DCGSLNGTQIV | 2 | Mus musculus, Rattus norvegicus | P2009 | TPGVQPPPPQM | 5 | Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus | P69 | VALPFPSISKQ | 5 | Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus | Q2008 | VTPGVQPPPPQ | 5 | Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus | R1932 | VTDRIRRTVKF | 5 | Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus | R1933 | TDRIRRTVKFL | 5 | Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus | R58 | KNVVGRMPDCS | 3 | Homo sapiens, Macaca mulatta, Pan troglodytes | R58 | KNVVGRSPDCS | 2 | Mus musculus, Rattus norvegicus | S70 | ALPFPSISKQH | 5 | Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus | S72 | PFPSISKQHAE | 3 | Homo sapiens, Macaca mulatta, Pan troglodytes | S72 | PFPSISKQHAV | 2 | Mus musculus, Rattus norvegicus | T1898 | PKVLFTGVVDA | 3 | Homo sapiens, Macaca mulatta, Pan troglodytes | T1898 | PKVLFTGVMDS | 1 | Mus musculus | T1898 | PKVLFTGVVDS | 1 | Rattus norvegicus | T1934 | DRIRRTVKFLC | 5 | Homo sapiens, Macaca mulatta, Pan troglodytes, Mus musculus, Rattus norvegicus |
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