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mutLBSgeneDB |
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| Gene summary for RAB5C |
 Gene summary |
| Basic gene Info. | Gene symbol | RAB5C |
| Gene name | RAB5C, member RAS oncogene family | |
| Synonyms | L1880|RAB5CL|RAB5L|RABL | |
| Cytomap | UCSC genome browser: 17q21.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001252039.1, NM_004583.3,NM_201434.2, | |
| Description | RAB5C, member of RAS oncogene familyras-related protein Rab-5C | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 604037 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000108774 | ||
| HPRD : 04947 | ||
| Vega : OTTHUMG00000169703 | ||
| Protein | UniProt: P51148 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RAB5C | |
| BioGPS: 5878 | ||
| Pathway | NCI Pathway Interaction Database: RAB5C | |
| KEGG: RAB5C | ||
| REACTOME: RAB5C | ||
| Pathway Commons: RAB5C | ||
| Context | iHOP: RAB5C | |
| ligand binding site mutation search in PubMed: RAB5C | ||
| UCL Cancer Institute: RAB5C | ||
| 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:0006184 | GTP catabolic process | 17562788 |
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| Ligand binding site mutations for RAB5C |
| 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 | E48 | E48K | PRAD | 1 | S35 | S35F | SKCM | 1 | S30 | S30F | SKCM | 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 RAB5C |
| 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 | S35 | S35F | 0.14171368 | E48 | E48K | -1.2622446 | S30 | S30F | -0.40846382 |
| (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 RAB5C from PDB |
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| Differential gene expression and gene-gene network for RAB5C |
| 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 RAB5C |
| 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 RAB5C |
| 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 RAB5C go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 4kyi | B | S30 S35 E48 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 4kyi | D | S30 S35 E48 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 4kyi | F | S30 S35 E48 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 4kyi | H | S30 S35 E48 | MG | MAGNESIUM(2+) | 4kyi | B | S35 | MG | MAGNESIUM(2+) | 4kyi | D | S35 | MG | MAGNESIUM(2+) | 4kyi | F | S35 | MG | MAGNESIUM(2+) | 4kyi | H | S35 |
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| Conservation information for LBS of RAB5C |
| Multiple alignments for P51148 in multiple species |
| LBS | AA sequence | # species | Species | A165 | FMETSAKTAMN | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | A31 | LLGESAVGKSS | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | D137 | AGNKADLASKR | 4 | Homo sapiens, Bos taurus, Canis lupus familiaris, Mus musculus | D137 | AGNKADLATKR | 1 | Gallus gallus | E48 | KGQFHEYQEST | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | F46 | FVKGQFHEYQE | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | G33 | GESAVGKSSLV | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | H47 | VKGQFHEYQES | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | K135 | ALAGNKADLAS | 4 | Homo sapiens, Bos taurus, Canis lupus familiaris, Mus musculus | K135 | ALAGNKADLAT | 1 | Gallus gallus | K166 | METSAKTAMNV | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | K34 | ESAVGKSSLVL | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | L138 | GNKADLASKRA | 4 | Homo sapiens, Bos taurus, Canis lupus familiaris, Mus musculus | L138 | GNKADLATKRA | 1 | Gallus gallus | N134 | IALAGNKADLA | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | S164 | LFMETSAKTAM | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | S30 | VLLGESAVGKS | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | S35 | SAVGKSSLVLR | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | S36 | AVGKSSLVLRF | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | S52 | HEYQESTIGAA | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | T53 | EYQESTIGAAF | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus | V32 | LGESAVGKSSL | 5 | Homo sapiens, Gallus gallus, Bos taurus, Canis lupus familiaris, Mus musculus |
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