mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for HMGCS2
Gene summary
Basic gene Info.Gene symbolHMGCS2
Gene name3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)
Synonyms-
CytomapUCSC genome browser: 1p13-p12
Type of geneprotein-coding
RefGenesNM_001166107.1,
NM_005518.3,
Description3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)HMG-CoA synthasehydroxymethylglutaryl-CoA synthase, mitochondrial
Modification date20141207
dbXrefs MIM : 600234
HGNC : HGNC
Ensembl : ENSG00000134240
HPRD : 02580
Vega : OTTHUMG00000012101
ProteinUniProt: P54868
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HMGCS2
BioGPS: 3158
PathwayNCI Pathway Interaction Database: HMGCS2
KEGG: HMGCS2
REACTOME: HMGCS2
Pathway Commons: HMGCS2
ContextiHOP: HMGCS2
ligand binding site mutation search in PubMed: HMGCS2
UCL Cancer Institute: HMGCS2
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID


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Ligand binding site mutations for HMGCS2

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
G82G82ESKCM2
C166C166FBLCA1
A205R206HCOAD1
N380G379VLUAD1
S258S258FSKCM1
A205R206HSTAD1
Y200P201HUCEC1
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

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.
LBSAAchange of nsSNVRelative stability change
C166C166F-1.6326297
A205R206H-1.4927007
Y200P201H-1.0459632
G82G82E-0.7062771
N380G379V-0.57086138
S258S258F-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 IDPDB titlePDB structure
2WYACRYSTAL 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)
* Left PPI network was created from samples with mutations in the LBS of HMGCS2 and the right PPI network was created from samples without mutations in the LBS of HMGCS2. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for HMGCS2
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C27515323-Hydroxy-3-Methylglutaryl-CoA Synthase 2 Deficiency3Biomarker, GeneticVariation
umls:C0009375Colonic Neoplasms1Biomarker
umls:C0151744Myocardial Ischemia1Biomarker

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype 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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of HMGCS2 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
HMG(3S)-3-HYDROXY-3-METHYLGLUTARYL-COA(5-)2wyaAG82 C166 Y200 A205 S258 N380
HMG(3S)-3-HYDROXY-3-METHYLGLUTARYL-COA(5-)2wyaBG82 C166 Y200 A205 S258 N380
HMG(3S)-3-HYDROXY-3-METHYLGLUTARYL-COA(5-)2wyaCG82 C166 Y200 A205 S258 N380
HMG(3S)-3-HYDROXY-3-METHYLGLUTARYL-COA(5-)2wyaDG82 C166 Y200 A205 S258 N380


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Conservation information for LBS of HMGCS2
Multiple alignments for P54868 in multiple species
LBSAA sequence# speciesSpecies
A165IDTTNACYGGT3Homo sapiens, Bos taurus, Mus musculus
A205YPSGNARPTGG3Homo sapiens, Bos taurus, Mus musculus
A81YNNVEAGKYTV1Homo sapiens
A81FNKVEAGRYTV1Bos taurus
A81FNNVEAGKYTV1Mus musculus
C166DTTNACYGGTA3Homo sapiens, Bos taurus, Mus musculus
E132LEVGTETIIDK3Homo sapiens, Bos taurus, Mus musculus
E80KYNNVEAGKYT1Homo sapiens
E80KFNKVEAGRYT1Bos taurus
E80KFNNVEAGKYT1Mus musculus
F241ENVYDFYKPNL1Homo sapiens
F241ENVYDFYKPDV1Bos taurus
F241ENAYDFYKPNL1Mus musculus
F304IFHTPFCKMVQ2Homo sapiens, Mus musculus
F304IFHTPFCKLVQ1Bos taurus
G255YPLVDGKLSIQ2Bos taurus, Mus musculus
G255YPIVDGKLSIQ1Homo sapiens
G413GAFSYGSGLAA3Homo sapiens, Bos taurus, Mus musculus
G82NNVEAGKYTVG2Homo sapiens, Mus musculus
G82NKVEAGRYTVG1Bos taurus
G87GKYTVGLGQTR2Homo sapiens, Mus musculus
G87GRYTVGLGQTQ1Bos taurus
H301QYMIFHTPFCK3Homo sapiens, Bos taurus, Mus musculus
K306HTPFCKMVQKS2Homo sapiens, Mus musculus
K306HTPFCKLVQKS1Bos taurus
K310CKMVQKSLARL2Homo sapiens, Mus musculus
K310CKLVQKSLARL1Bos taurus
K83NVEAGKYTVGL2Homo sapiens, Mus musculus
K83KVEAGRYTVGL1Bos taurus
N204VYPSGNARPTG3Homo sapiens, Bos taurus, Mus musculus
N380STHNGNMYTSS1Homo sapiens
N380STYNGNMYTSS1Bos taurus
N380STNNGNMYTSS1Mus musculus
P303MIFHTPFCKMV2Homo sapiens, Mus musculus
P303MIFHTPFCKLV1Bos taurus
S258VDGKLSIQCYL3Homo sapiens, Bos taurus, Mus musculus
S414AFSYGSGLAAS3Homo sapiens, Bos taurus, Mus musculus
T208GNARPTGGAGA3Homo sapiens, Bos taurus, Mus musculus
V253SEYPLVDGKLS2Bos taurus, Mus musculus
V253SEYPIVDGKLS1Homo sapiens
V86AGKYTVGLGQT2Homo sapiens, Mus musculus
V86AGRYTVGLGQT1Bos taurus
Y200GDIAVYPSGNA3Homo sapiens, Bos taurus, Mus musculus
Y262LSIQCYLRALD3Homo sapiens, Bos taurus, Mus musculus
Y412IGAFSYGSGLA3Homo sapiens, Bos taurus, Mus musculus


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