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mutLBSgeneDB |
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| Gene summary for RAB3D |
 Gene summary |
| Basic gene Info. | Gene symbol | RAB3D |
| Gene name | RAB3D, member RAS oncogene family | |
| Synonyms | D2-2|GOV|RAB16|RAD3D | |
| Cytomap | UCSC genome browser: 19p13.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_004283.3, | |
| Description | Rab3D upregulated with myeloid differentiationglioblastoma overexpressedras-related protein Rab-3D | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 604350 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000105514 | ||
| HPRD : 05070 | ||
| Vega : OTTHUMG00000180835 | ||
| Protein | UniProt: O95716 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RAB3D | |
| BioGPS: 9545 | ||
| Pathway | NCI Pathway Interaction Database: RAB3D | |
| KEGG: RAB3D | ||
| REACTOME: RAB3D | ||
| Pathway Commons: RAB3D | ||
| Context | iHOP: RAB3D | |
| ligand binding site mutation search in PubMed: RAB3D | ||
| UCL Cancer Institute: RAB3D | ||
| 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 RAB3D |
| 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 | K136 | K136N | COAD | 1 | D138 | D138A | 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 RAB3D |
| 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 | D138 | D138A | -1.27044 | K136 | K136N | -0.3926214 |
| (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 RAB3D from PDB |
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| Differential gene expression and gene-gene network for RAB3D |
| 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 RAB3D |
| 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 RAB3D |
| 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 RAB3D go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | GDP | GUANOSINE-5'-DIPHOSPHATE | 2gf9 | A | K136 D138 |
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| Conservation information for LBS of RAB3D |
| Multiple alignments for O95716 in multiple species |
| LBS | AA sequence | # species | Species | A166 | FFEASAKENIN | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | D138 | VGNKCDLEDER | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | F47 | YADDSFTPAFV | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | G34 | GNSSVGKTSFL | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | K136 | ILVGNKCDLED | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | K167 | FEASAKENINV | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | K35 | NSSVGKTSFLF | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | L139 | GNKCDLEDERV | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | N135 | VILVGNKCDLE | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | S165 | EFFEASAKENI | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | S32 | LIGNSSVGKTS | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | S37 | SVGKTSFLFRY | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | T36 | SSVGKTSFLFR | 3 | Homo sapiens, Rattus norvegicus, Mus musculus | V33 | IGNSSVGKTSF | 3 | Homo sapiens, Rattus norvegicus, Mus musculus |
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