mutLBSgeneDB |
Gene summary for RAB5A |
Gene summary |
Basic gene Info. | Gene symbol | RAB5A |
Gene name | RAB5A, member RAS oncogene family | |
Synonyms | RAB5 | |
Cytomap | UCSC genome browser: 3p24-p22 | |
Type of gene | protein-coding | |
RefGenes | NM_001292048.1, NM_004162.4, | |
Description | RAS-associated protein RAB5Aras-related protein Rab-5A | |
Modification date | 20141207 | |
dbXrefs | MIM : 179512 | |
HGNC : HGNC | ||
Ensembl : ENSG00000144566 | ||
HPRD : 01542 | ||
Vega : OTTHUMG00000129889 | ||
Protein | UniProt: P20339 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RAB5A | |
BioGPS: 5868 | ||
Pathway | NCI Pathway Interaction Database: RAB5A | |
KEGG: RAB5A | ||
REACTOME: RAB5A | ||
Pathway Commons: RAB5A | ||
Context | iHOP: RAB5A | |
ligand binding site mutation search in PubMed: RAB5A | ||
UCL Cancer Institute: RAB5A | ||
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 | GO:0006897 | endocytosis | 15378032 | GO:0036465 | synaptic vesicle recycling | 16141272 | GO:0051489 | regulation of filopodium assembly | 14978216 |
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Ligand binding site mutations for RAB5A |
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 | D136,K134 | A135V | COAD | 1 | Y82,E80 | R81Q | KIRC | 1 | G78 | G78R | LUAD | 1 | S34 | S34L | UCEC | 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 RAB5A |
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 | S34 | S34L | 0.42990124 | Y82 | R81Q | -1.4216287 | E80 | R81Q | -1.4216287 | G78 | G78R | -0.42799599 | K134 | A135V | -0.20863643 | D136 | A135V | -0.20863643 |
(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 RAB5A from PDB |
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Differential gene expression and gene-gene network for RAB5A |
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 RAB5A |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0151744 | Myocardial Ischemia | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for RAB5A |
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 | DB02467 | L-methionine (S)-S-oxide | Small molecule | |
Experimental | DB04137 | Guanosine-5'-Triphosphate | Small molecule | |
Experimental | DB04315 | Guanosine-5'-Diphosphate | Small molecule |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of RAB5A go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CO | COBALT(2+) | 1tu4 | B | E80 | CO | COBALT(2+) | 1tu4 | D | E80 | AF3 | ALUMINIUM TRIFLUORIDE | 1n6k | A | G78 | MG | MAGNESIUM(2+) | 1n6h | A | S34 | MG | MAGNESIUM(2+) | 1n6i | A | S34 | MG | MAGNESIUM(2+) | 1n6k | A | S34 | MG | MAGNESIUM(2+) | 1n6l | A | S34 | MG | MAGNESIUM(2+) | 1n6n | A | S34 | MG | MAGNESIUM(2+) | 1n6o | A | S34 | MG | MAGNESIUM(2+) | 1n6p | A | S34 | MG | MAGNESIUM(2+) | 1n6r | A | S34 | MG | MAGNESIUM(2+) | 1r2q | A | S34 | MG | MAGNESIUM(2+) | 1tu3 | A | S34 | MG | MAGNESIUM(2+) | 1tu3 | B | S34 | MG | MAGNESIUM(2+) | 1tu3 | C | S34 | MG | MAGNESIUM(2+) | 1tu3 | D | S34 | MG | MAGNESIUM(2+) | 1tu3 | E | S34 | CO | COBALT(2+) | 1tu4 | B | S34 | CO | COBALT(2+) | 1tu4 | D | S34 | MG | MAGNESIUM(2+) | 3mjh | A | S34 | MG | MAGNESIUM(2+) | 3mjh | C | S34 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1n6h | A | S34 G78 K134 D136 | GTP | GTP | 1n6l | A | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1n6n | A | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1n6o | A | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1n6p | A | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1n6r | A | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1r2q | A | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1tu3 | A | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1tu3 | B | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1tu3 | C | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1tu3 | D | S34 G78 K134 D136 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1tu3 | E | S34 G78 K134 D136 | GTP | GTP | 3mjh | A | S34 G78 K134 D136 | GTP | GTP | 3mjh | C | S34 G78 K134 D136 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1n6i | A | S34 K134 D136 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1n6k | A | S34 K134 D136 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1tu4 | A | S34 K134 D136 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1tu4 | B | S34 K134 D136 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1tu4 | C | S34 K134 D136 | GDP | GUANOSINE-5'-DIPHOSPHATE | 1tu4 | D | S34 K134 D136 | CO | COBALT(2+) | 1tu4 | A | Y82 | CO | COBALT(2+) | 1tu4 | C | Y82 |
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Conservation information for LBS of RAB5A |
Multiple alignments for P20339 in multiple species |
LBS | AA sequence | # species | Species | A164 | FMETSAKTSMN | 4 | Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus | A164 | FMETSAKTATN | 2 | Arabidopsis thaliana, Arabidopsis thaliana | A164 | FMETSAKTPMN | 1 | Rattus norvegicus | A30 | LLGESAVGKSS | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | A30 | LLGDVGAGKSS | 2 | Arabidopsis thaliana, Arabidopsis thaliana | D136 | SGNKADLANKR | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | D136 | AGNKSDLLDAR | 1 | Arabidopsis thaliana | D136 | AGNKADLLDAR | 1 | Arabidopsis thaliana | D75 | KFEIWDTAGQE | 7 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana | E47 | KGQFHEFQEST | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | E47 | KDQFVEFQEST | 2 | Arabidopsis thaliana, Arabidopsis thaliana | E50 | FHEFQESTIGA | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | E50 | FVEFQESTIGA | 2 | Arabidopsis thaliana, Arabidopsis thaliana | E80 | DTAGQERYHSL | 7 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana | F45 | FVKGQFHEFQE | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | F45 | FVKDQFVEFQE | 2 | Arabidopsis thaliana, Arabidopsis thaliana | F48 | GQFHEFQESTI | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | F48 | DQFVEFQESTI | 2 | Arabidopsis thaliana, Arabidopsis thaliana | G32 | GESAVGKSSLV | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | G32 | GDVGAGKSSLV | 2 | Arabidopsis thaliana, Arabidopsis thaliana | G78 | IWDTAGQERYH | 7 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana | H46 | VKGQFHEFQES | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | H46 | VKDQFVEFQES | 2 | Arabidopsis thaliana, Arabidopsis thaliana | H83 | GQERYHSLAPM | 7 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana | K134 | ALSGNKADLAN | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | K134 | ALAGNKSDLLD | 1 | Arabidopsis thaliana | K134 | ALAGNKADLLD | 1 | Arabidopsis thaliana | K165 | METSAKTSMNV | 4 | Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus | K165 | METSAKTATNV | 2 | Arabidopsis thaliana, Arabidopsis thaliana | K165 | METSAKTPMNV | 1 | Rattus norvegicus | K33 | ESAVGKSSLVL | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | K33 | DVGAGKSSLVL | 2 | Arabidopsis thaliana, Arabidopsis thaliana | L137 | GNKADLANKRA | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | L137 | GNKSDLLDARK | 1 | Arabidopsis thaliana | L137 | GNKADLLDARK | 1 | Arabidopsis thaliana | N133 | IALSGNKADLA | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | N133 | MALAGNKSDLL | 1 | Arabidopsis thaliana | N133 | MALAGNKADLL | 1 | Arabidopsis thaliana | Q49 | QFHEFQESTIG | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | Q49 | QFVEFQESTIG | 2 | Arabidopsis thaliana, Arabidopsis thaliana | S163 | LFMETSAKTSM | 4 | Homo sapiens, Mus musculus, Canis lupus familiaris, Bos taurus | S163 | FFMETSAKTAT | 2 | Arabidopsis thaliana, Arabidopsis thaliana | S163 | LFMETSAKTPM | 1 | Rattus norvegicus | S29 | VLLGESAVGKS | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | S29 | VLLGDVGAGKS | 2 | Arabidopsis thaliana, Arabidopsis thaliana | S34 | SAVGKSSLVLR | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | S34 | VGAGKSSLVLR | 2 | Arabidopsis thaliana, Arabidopsis thaliana | S35 | AVGKSSLVLRF | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | S35 | GAGKSSLVLRF | 2 | Arabidopsis thaliana, Arabidopsis thaliana | S51 | HEFQESTIGAA | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | S51 | VEFQESTIGAA | 2 | Arabidopsis thaliana, Arabidopsis thaliana | T52 | EFQESTIGAAF | 7 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana | V31 | LGESAVGKSSL | 5 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus | V31 | LGDVGAGKSSL | 2 | Arabidopsis thaliana, Arabidopsis thaliana | Y82 | AGQERYHSLAP | 7 | Homo sapiens, Rattus norvegicus, Mus musculus, Canis lupus familiaris, Bos taurus, Arabidopsis thaliana, Arabidopsis thaliana |
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