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mutLBSgeneDB |
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| Gene summary for HMGCS2 |
 Gene summary |
| Basic gene Info. | Gene symbol | HMGCS2 |
| Gene name | 3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial) | |
| Synonyms | - | |
| Cytomap | UCSC genome browser: 1p13-p12 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001166107.1, NM_005518.3, | |
| Description | 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)HMG-CoA synthasehydroxymethylglutaryl-CoA synthase, mitochondrial | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 600234 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000134240 | ||
| HPRD : 02580 | ||
| Vega : OTTHUMG00000012101 | ||
| Protein | UniProt: P54868 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_HMGCS2 | |
| BioGPS: 3158 | ||
| Pathway | NCI Pathway Interaction Database: HMGCS2 | |
| KEGG: HMGCS2 | ||
| REACTOME: HMGCS2 | ||
| Pathway Commons: HMGCS2 | ||
| Context | iHOP: HMGCS2 | |
| ligand binding site mutation search in PubMed: HMGCS2 | ||
| UCL Cancer Institute: HMGCS2 | ||
| 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 HMGCS2 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | G82 | G82E | SKCM | 2 | C166 | C166F | BLCA | 1 | A205 | R206H | COAD | 1 | N380 | G379V | LUAD | 1 | S258 | S258F | SKCM | 1 | A205 | R206H | STAD | 1 | Y200 | P201H | 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 HMGCS2 |
| 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 | C166 | C166F | -1.6326297 | A205 | R206H | -1.4927007 | Y200 | P201H | -1.0459632 | G82 | G82E | -0.7062771 | N380 | G379V | -0.57086138 | S258 | S258F | -0.4678994 |
| (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 HMGCS2 from PDB |
| PDB ID | PDB title | PDB structure | 2WYA | CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A SYNTHASE 2 (HMGCS2) |  |
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| Differential gene expression and gene-gene network for HMGCS2 |
| 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 HMGCS2 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C2751532 | 3-Hydroxy-3-Methylglutaryl-CoA Synthase 2 Deficiency | 3 | Biomarker, GeneticVariation |
| umls:C0009375 | Colonic Neoplasms | 1 | Biomarker |
| 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 HMGCS2 |
| 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 HMGCS2 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | HMG | (3S)-3-HYDROXY-3-METHYLGLUTARYL-COA(5-) | 2wya | A | G82 C166 Y200 A205 S258 N380 | HMG | (3S)-3-HYDROXY-3-METHYLGLUTARYL-COA(5-) | 2wya | B | G82 C166 Y200 A205 S258 N380 | HMG | (3S)-3-HYDROXY-3-METHYLGLUTARYL-COA(5-) | 2wya | C | G82 C166 Y200 A205 S258 N380 | HMG | (3S)-3-HYDROXY-3-METHYLGLUTARYL-COA(5-) | 2wya | D | G82 C166 Y200 A205 S258 N380 |
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| Conservation information for LBS of HMGCS2 |
| Multiple alignments for P54868 in multiple species |
| LBS | AA sequence | # species | Species | A165 | IDTTNACYGGT | 3 | Homo sapiens, Bos taurus, Mus musculus | A205 | YPSGNARPTGG | 3 | Homo sapiens, Bos taurus, Mus musculus | A81 | YNNVEAGKYTV | 1 | Homo sapiens | A81 | FNKVEAGRYTV | 1 | Bos taurus | A81 | FNNVEAGKYTV | 1 | Mus musculus | C166 | DTTNACYGGTA | 3 | Homo sapiens, Bos taurus, Mus musculus | E132 | LEVGTETIIDK | 3 | Homo sapiens, Bos taurus, Mus musculus | E80 | KYNNVEAGKYT | 1 | Homo sapiens | E80 | KFNKVEAGRYT | 1 | Bos taurus | E80 | KFNNVEAGKYT | 1 | Mus musculus | F241 | ENVYDFYKPNL | 1 | Homo sapiens | F241 | ENVYDFYKPDV | 1 | Bos taurus | F241 | ENAYDFYKPNL | 1 | Mus musculus | F304 | IFHTPFCKMVQ | 2 | Homo sapiens, Mus musculus | F304 | IFHTPFCKLVQ | 1 | Bos taurus | G255 | YPLVDGKLSIQ | 2 | Bos taurus, Mus musculus | G255 | YPIVDGKLSIQ | 1 | Homo sapiens | G413 | GAFSYGSGLAA | 3 | Homo sapiens, Bos taurus, Mus musculus | G82 | NNVEAGKYTVG | 2 | Homo sapiens, Mus musculus | G82 | NKVEAGRYTVG | 1 | Bos taurus | G87 | GKYTVGLGQTR | 2 | Homo sapiens, Mus musculus | G87 | GRYTVGLGQTQ | 1 | Bos taurus | H301 | QYMIFHTPFCK | 3 | Homo sapiens, Bos taurus, Mus musculus | K306 | HTPFCKMVQKS | 2 | Homo sapiens, Mus musculus | K306 | HTPFCKLVQKS | 1 | Bos taurus | K310 | CKMVQKSLARL | 2 | Homo sapiens, Mus musculus | K310 | CKLVQKSLARL | 1 | Bos taurus | K83 | NVEAGKYTVGL | 2 | Homo sapiens, Mus musculus | K83 | KVEAGRYTVGL | 1 | Bos taurus | N204 | VYPSGNARPTG | 3 | Homo sapiens, Bos taurus, Mus musculus | N380 | STHNGNMYTSS | 1 | Homo sapiens | N380 | STYNGNMYTSS | 1 | Bos taurus | N380 | STNNGNMYTSS | 1 | Mus musculus | P303 | MIFHTPFCKMV | 2 | Homo sapiens, Mus musculus | P303 | MIFHTPFCKLV | 1 | Bos taurus | S258 | VDGKLSIQCYL | 3 | Homo sapiens, Bos taurus, Mus musculus | S414 | AFSYGSGLAAS | 3 | Homo sapiens, Bos taurus, Mus musculus | T208 | GNARPTGGAGA | 3 | Homo sapiens, Bos taurus, Mus musculus | V253 | SEYPLVDGKLS | 2 | Bos taurus, Mus musculus | V253 | SEYPIVDGKLS | 1 | Homo sapiens | V86 | AGKYTVGLGQT | 2 | Homo sapiens, Mus musculus | V86 | AGRYTVGLGQT | 1 | Bos taurus | Y200 | GDIAVYPSGNA | 3 | Homo sapiens, Bos taurus, Mus musculus | Y262 | LSIQCYLRALD | 3 | Homo sapiens, Bos taurus, Mus musculus | Y412 | IGAFSYGSGLA | 3 | Homo sapiens, Bos taurus, Mus musculus |
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