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mutLBSgeneDB |
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| Gene summary for COL3A1 |
 Gene summary |
| Basic gene Info. | Gene symbol | COL3A1 |
| Gene name | collagen, type III, alpha 1 | |
| Synonyms | EDS4A | |
| Cytomap | UCSC genome browser: 2q31 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000090.3, | |
| Description | Ehlers-Danlos syndrome type IV, autosomal dominantalpha1 (III) collagencollagen alpha-1(III) chaincollagen, fetal | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 120180 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000168542 | ||
| HPRD : 00365 | ||
| Vega : OTTHUMG00000132648 | ||
| Protein | UniProt: P02461 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_COL3A1 | |
| BioGPS: 1281 | ||
| Pathway | NCI Pathway Interaction Database: COL3A1 | |
| KEGG: COL3A1 | ||
| REACTOME: COL3A1 | ||
| Pathway Commons: COL3A1 | ||
| Context | iHOP: COL3A1 | |
| ligand binding site mutation search in PubMed: COL3A1 | ||
| UCL Cancer Institute: COL3A1 | ||
| 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 | GO:0007160 | cell-matrix adhesion | 16912226 | GO:0007179 | transforming growth factor beta receptor signaling pathway | 16360482 | GO:0009314 | response to radiation | 14736764 | GO:0018149 | peptide cross-linking | 16754721 | GO:0034097 | response to cytokine | 16360482 | GO:0042060 | wound healing | 1466622 |
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| Ligand binding site mutations for COL3A1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | N1282 | N1282I | LUAD | 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 COL3A1 |
| 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 | N1282 | N1282I | -0.63220873 |
| (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 COL3A1 from PDB |
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| Differential gene expression and gene-gene network for COL3A1 |
| 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 COL3A1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0268338 | EHLERS-DANLOS SYNDROME, TYPE IV, AUTOSOMAL DOMINANT | 39 | Biomarker, GeneticVariation |
| umls:C0013720 | Ehlers-Danlos Syndrome | 30 | Biomarker, GeneticVariation |
| umls:C0023890 | Liver Cirrhosis | 6 | Biomarker, GeneticVariation |
| umls:C0023895 | Liver Diseases | 2 | Biomarker |
| umls:C0020456 | Hyperglycemia | 1 | Biomarker |
| umls:C0003504 | Aortic Valve Insufficiency | 1 | Biomarker |
| umls:C0860207 | Drug-Induced Liver Injury | 1 | Biomarker |
| umls:C0553980 | Endomyocardial Fibrosis | 1 | Biomarker |
| umls:C0015695 | Fatty Liver | 1 | Biomarker |
| umls:C0016059 | Fibrosis | 1 | Biomarker |
| umls:C0020443 | Hypercholesterolemia | 1 | Biomarker |
| umls:C0020459 | Hyperinsulinism | 1 | Biomarker |
| umls:C0020538 | Hypertension | 1 | Biomarker |
| umls:C0149721 | Hypertrophy, Left Ventricular | 1 | Biomarker |
| umls:C0022548 | Keloid | 1 | Biomarker |
| umls:C0023891 | Liver Cirrhosis, Alcoholic | 1 | Biomarker |
| umls:C0023893 | Liver Cirrhosis, Experimental | 1 | Biomarker |
| umls:C0238288 | Muscular Dystrophy, Facioscapulohumeral | 1 | Biomarker |
| umls:C0036341 | Schizophrenia | 1 | Biomarker |
| umls:C0041956 | Ureteral Obstruction | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for COL3A1 |
| 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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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Approved|investigational | DB00048 | Collagenase clostridium histolyticum | Biotech |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of COL3A1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS |
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| Conservation information for LBS of COL3A1 |
| Multiple alignments for P02461 in multiple species |
| LBS | AA sequence | # species | Species | C1285 | DPNQGCKMDAI | 2 | Mus musculus, Rattus norvegicus | C1285 | DPNQGCKLDAI | 1 | Homo sapiens | D1280 | GEYWVDPNQGC | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | D1288 | QGCKMDAIKVF | 2 | Mus musculus, Rattus norvegicus | D1288 | QGCKLDAIKVF | 1 | Homo sapiens | N1282 | YWVDPNQGCKM | 2 | Mus musculus, Rattus norvegicus | N1282 | YWVDPNQGCKL | 1 | Homo sapiens | Q1283 | WVDPNQGCKMD | 2 | Mus musculus, Rattus norvegicus | Q1283 | WVDPNQGCKLD | 1 | Homo sapiens |
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