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mutLBSgeneDB |
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| Gene summary for VLDLR |
 Gene summary |
| Basic gene Info. | Gene symbol | VLDLR |
| Gene name | very low density lipoprotein receptor | |
| Synonyms | CARMQ1|CHRMQ1|VLDLRCH | |
| Cytomap | UCSC genome browser: 9p24 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001018056.1, NM_003383.3, | |
| Description | VLDL receptorVLDL-Rvery low-density lipoprotein receptor | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 192977 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000147852 | ||
| HPRD : 01895 | ||
| Vega : OTTHUMG00000019447 | ||
| Protein | UniProt: P98155 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_VLDLR | |
| BioGPS: 7436 | ||
| Pathway | NCI Pathway Interaction Database: VLDLR | |
| KEGG: VLDLR | ||
| REACTOME: VLDLR | ||
| Pathway Commons: VLDLR | ||
| Context | iHOP: VLDLR | |
| ligand binding site mutation search in PubMed: VLDLR | ||
| UCL Cancer Institute: VLDLR | ||
| 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:0006898 | receptor-mediated endocytosis | 10571240 | GO:0034436 | glycoprotein transport | 10571240 | GO:0034447 | very-low-density lipoprotein particle clearance | 8083232 |
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| Ligand binding site mutations for VLDLR |
| 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 | D145 | D145G | COAD | 1 | D145 | D145A | OV | 1 | D139 | D141G | 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 VLDLR |
| 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 | D139 | D141G | -1.1780853 | D145 | D145G | -0.69736407 | D145 | D145A | -0.48664035 |
| (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 VLDLR from PDB |
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| Differential gene expression and gene-gene network for VLDLR |
| 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 VLDLR |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0394006 | Dysequilibrium syndrome | 6 | Biomarker, GeneticVariation |
| umls:C0004352 | Autistic Disorder | 2 | Biomarker |
| umls:C0028754 | Obesity | 2 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for VLDLR |
| 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 VLDLR go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CA | CALCIUM(2+) | 1v9u | 5 | D139 D145 |
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| Conservation information for LBS of VLDLR |
| Multiple alignments for P98155 in multiple species |
| LBS | AA sequence | # species | Species | D135 | VSWRCDGENDC | 2 | Homo sapiens, Mus musculus | D135 | VSWKCDGEKDC | 1 | Gallus gallus | D139 | CDGENDCDSGE | 1 | Homo sapiens | D139 | CDGEKDCDSGE | 1 | Gallus gallus | D139 | CDGENDCDNGE | 1 | Mus musculus | D145 | CDSGEDEENCG | 2 | Homo sapiens, Gallus gallus | D145 | CDNGEDEENCG | 1 | Mus musculus | E137 | WRCDGENDCDS | 1 | Homo sapiens | E137 | WKCDGEKDCDS | 1 | Gallus gallus | E137 | WRCDGENDCDN | 1 | Mus musculus | E146 | DSGEDEENCGN | 2 | Homo sapiens, Gallus gallus | E146 | DNGEDEENCGN | 1 | Mus musculus | N138 | RCDGENDCDSG | 1 | Homo sapiens | N138 | KCDGEKDCDSG | 1 | Gallus gallus | N138 | RCDGENDCDNG | 1 | Mus musculus | W132 | CIPVSWRCDGE | 2 | Homo sapiens, Mus musculus | W132 | CIPVSWKCDGE | 1 | Gallus gallus |
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