mutLBSgeneDB |
Gene summary for VTA1 |
Gene summary |
Basic gene Info. | Gene symbol | VTA1 |
Gene name | vesicle (multivesicular body) trafficking 1 | |
Synonyms | C6orf55|DRG-1|DRG1|LIP5|My012|SBP1 | |
Cytomap | UCSC genome browser: 6q24.1 | |
Type of gene | protein-coding | |
RefGenes | NM_001286371.1, NM_001286372.1,NM_016485.4, | |
Description | LYST-interacting protein 5SKD1-binding protein 1Vps20-associated 1 homologdopamine-responsive gene 1 proteinhomolog of mouse SKD1-binding protein 1vacuolar protein sorting-associated protein VTA1 homolog | |
Modification date | 20141207 | |
dbXrefs | MIM : 610902 | |
HGNC : HGNC | ||
Ensembl : ENSG00000009844 | ||
HPRD : 09855 | ||
Protein | UniProt: Q9NP79 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_VTA1 | |
BioGPS: 51534 | ||
Pathway | NCI Pathway Interaction Database: VTA1 | |
KEGG: VTA1 | ||
REACTOME: VTA1 | ||
Pathway Commons: VTA1 | ||
Context | iHOP: VTA1 | |
ligand binding site mutation search in PubMed: VTA1 | ||
UCL Cancer Institute: VTA1 | ||
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 |
Top |
Ligand binding site mutations for VTA1 |
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 | M47 | G46A | BLCA | 1 | R57 | E55K | HNSC | 1 | S61 | K62R | LUSC | 1 | L40,Y36 | C38G | 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. |
Top |
Protein structure related information for VTA1 |
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 | M47 | G46A | -1.0548435 | R57 | E55K | -0.8043653 | Y36 | C38G | -0.61421582 | L40 | C38G | -0.61421582 | S61 | K62R | -0.54087914 |
(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 VTA1 from PDB |
Top |
Differential gene expression and gene-gene network for VTA1 |
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) |
Top |
Top |
Phenotype information for VTA1 |
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 |
Top |
Pharmacological information for VTA1 |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of VTA1 go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (ASP,PHE,ASP,ASP,LEU,SER,ARG,ARG,PHE,GLU,GLU,LEU,LYS,LYS) | 4u7e | B | L40 M47 S61 | III | Peptide ligand (GLN,ASP,GLU,LEU,SER,GLN,ARG,LEU,ALA,ARG,LEU,ARG,ASP,GLN,VAL) | 4txr | A | Y36 L40 M47 R57 S61 | III | Peptide ligand (ASP,GLU,LEU,SER,GLN,ARG,LEU,ALA,ARG,LEU,ARG,ASP,GLN) | 4txq | A | Y36 L40 M47 S61 | III | Peptide ligand (ALA,GLU,GLN,ASP,GLU,LEU,SER,GLN,ARG,LEU,ALA,ARG,LEU,ARG,ASP,GLN,VAL) | 4txq | B | Y36 L40 M47 S61 |
Top |
Conservation information for LBS of VTA1 |
Multiple alignments for Q9NP79 in multiple species |
LBS | AA sequence | # species | Species |
Copyright © 2016-Present - The University of Texas Health Science Center at Houston |