mutated Ligand Binding Site gene DataBase





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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 HMGCS1
Gene summary
Basic gene Info.Gene symbolHMGCS1
Gene name3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble)
CytomapUCSC genome browser: 5p14-p13
Type of geneprotein-coding
Description3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) synthase3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 (soluble)hydroxymethylglutaryl-CoA synthase, cytoplasmic
Modification date20141207
dbXrefs MIM : 142940
Ensembl : ENSG00000112972
HPRD : 07515
Vega : OTTHUMG00000162231
ProteinUniProt: Q01581
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HMGCS1
BioGPS: 3157
PathwayNCI Pathway Interaction Database: HMGCS1
Pathway Commons: HMGCS1
ContextiHOP: HMGCS1
ligand binding site mutation search in PubMed: HMGCS1
UCL Cancer Institute: HMGCS1
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for HMGCS1

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for HMGCS1
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
(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 HMGCS1 from PDB

Differential gene expression and gene-gene network for HMGCS1
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 HMGCS1 and the right PPI network was created from samples without mutations in the LBS of HMGCS1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for HMGCS1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for HMGCS1
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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
ExperimentalDB07740(3R,5S,7R,12S,13R)-13-FORMYL-12,14-DIHYDROXY-3,5,7-TRIMETHYLTETRADECANOIC ACIDSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of HMGCS1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
COACOENZYME A2p8uAY267 K269 K273
COACOENZYME A2p8uBY267 K269 K273

Conservation information for LBS of HMGCS1
Multiple alignments for Q01581 in multiple species
LBSAA sequence# speciesSpecies
A168YATGNARPTGG3Homo sapiens, Gallus gallus, Mus musculus
A168YAEGPARPTGG1Arabidopsis thaliana
A168YASGNARPTGG1Rattus norvegicus
A168YDKGAARPTGG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A168YAKGNARPTGG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
A44YDGVDAGKYTI4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
A44HDGASKGKYTI1Arabidopsis thaliana
A44FDGVSQGKYTI1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
A44HDGVSTGKYTI1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
D43KYDGVDAGKYT4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
D43AHDGASKGKYT1Arabidopsis thaliana
D43KFDGVSQGKYT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
D43AHDGVSTGKYT1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G218YPVVDGKLSIQ3Gallus gallus, Mus musculus, Rattus norvegicus
G218YPIVDGKLSIQ1Homo sapiens
G218YPVVDGKLSQT1Arabidopsis thaliana
G218YPYVDGHFSLT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G218YPYVDGHFSLE1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G45DGVDAGKYTIG4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
G45DGASKGKYTIG1Arabidopsis thaliana
G45DGVSQGKYTIG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G45DGVSTGKYTIG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
G50GKYTIGLGQAR2Mus musculus, Rattus norvegicus
G50GKYTIGLGQAK1Homo sapiens
G50GKYTIGLGQDC1Arabidopsis thaliana
G50GKYTIGLGQSK1Gallus gallus
G50GKYTIGLGQTN1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
G50GKYTIGLGLTK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
I222DGKLSIQCYLS4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
I222DGKLSQTCYLM1Arabidopsis thaliana
I222DGHFSLTCYVK1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
I222DGHFSLECYVK1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K269HSPYCKLVQKS4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K269HSPYNKLVQKS1Arabidopsis thaliana
K269HVPTCKLVTKS1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K269HAPTCKQVQKA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K273CKLVQKSLARM3Homo sapiens, Mus musculus, Rattus norvegicus
K273NKLVQKSFARL1Arabidopsis thaliana
K273CKLVQKSVARL1Gallus gallus
K273CKLVTKSYGRL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K273CKQVQKAYARL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
K46GVDAGKYTIGL4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
K46GASKGKYTIGL1Arabidopsis thaliana
K46GVSQGKYTIGL1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
K46GVSTGKYTIGL1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
L270SPYCKLVQKSL3Homo sapiens, Mus musculus, Rattus norvegicus
L270SPYNKLVQKSF1Arabidopsis thaliana
L270SPYCKLVQKSV1Gallus gallus
L270VPTCKLVTKSY1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
L270APTCKQVQKAY1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
N167VYATGNARPTG2Homo sapiens, Gallus gallus
N167VYAEGPARPTG1Arabidopsis thaliana
N167IYATGNARPTG1Mus musculus
N167IYASGNARPTG1Rattus norvegicus
N167IYDKGAARPTG1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
N167LYAKGNARPTG1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
P266MIFHSPYCKLV4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
P266IVFHSPYNKLV1Arabidopsis thaliana
P266NVFHVPTCKLV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
P266CIFHAPTCKQV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
S221VDGKLSIQCYL4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
S221VDGKLSQTCYL1Arabidopsis thaliana
S221VDGHFSLTCYV1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
S221VDGHFSLECYV1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
T171GNARPTGGVGA3Homo sapiens, Mus musculus, Rattus norvegicus
T171GPARPTGGAAA1Arabidopsis thaliana
T171GNARPTGGAGA1Gallus gallus
T171GAARPTGGAGT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
T171GNARPTGGAGC1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V216SEYPVVDGKLS4Arabidopsis thaliana, Gallus gallus, Mus musculus, Rattus norvegicus
V216SEYPYVDGHFS2Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Schizosaccharomyces pombe (strain 972 / ATCC 24843)
V216SEYPIVDGKLS1Homo sapiens
Y163GDIAVYATGNA2Homo sapiens, Gallus gallus
Y163TDSAVYAEGPA1Arabidopsis thaliana
Y163GDIAIYATGNA1Mus musculus
Y163GDIAIYASGNA1Rattus norvegicus
Y163GDIAIYDKGAA1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y163GDIALYAKGNA1Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Y267IFHSPYCKLVQ4Homo sapiens, Gallus gallus, Mus musculus, Rattus norvegicus
Y267VFHSPYNKLVQ1Arabidopsis thaliana
Y267VFHVPTCKLVT1Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Y267IFHAPTCKQVQ1Schizosaccharomyces pombe (strain 972 / ATCC 24843)

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