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 GCDH
Gene summary
Basic gene Info.Gene symbolGCDH
Gene nameglutaryl-CoA dehydrogenase
SynonymsACAD5|GCD
CytomapUCSC genome browser: 19p13.2
Type of geneprotein-coding
RefGenesNM_000159.3,
NM_013976.3,NR_102316.1,NR_102317.1,
Descriptionglutaryl-CoA dehydrogenase, mitochondrialglutaryl-Coenzyme A dehydrogenase
Modification date20141211
dbXrefs MIM : 608801
HGNC : HGNC
Ensembl : ENSG00000105607
HPRD : 01977
Vega : OTTHUMG00000180561
ProteinUniProt: Q92947
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GCDH
BioGPS: 2639
PathwayNCI Pathway Interaction Database: GCDH
KEGG: GCDH
REACTOME: GCDH
Pathway Commons: GCDH
ContextiHOP: GCDH
ligand binding site mutation search in PubMed: GCDH
UCL Cancer Institute: GCDH
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 GCDH
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
LBSAAchange of nsSNVCancer type# samples
F434T435MCOAD1
S186S186TLUSC1
V143,L147S145FSKCM1
L179L179FSKCM1
R294R294QSTAD1
P364E365DUCEC1
S139A140VUCEC1
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 GCDH
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
R294R294Q-2.2101749
L179L179F-1.1658734
S186S186T-1.1299072
P364E365D-0.63058339
S139A140V-0.49716724
L147S145F-0.11002358
V143S145F-0.11002358
F434T435M-0.10419779
(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 GCDH from PDB

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Differential gene expression and gene-gene network for GCDH
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 GCDH and the right PPI network was created from samples without mutations in the LBS of GCDH. 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 GCDH
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0268595Glutaric aciduria 131Biomarker, GeneticVariation

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

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Pharmacological information for GCDH
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
ApprovedDB03147Flavin adenine dinucleotideSmall molecule
ExperimentalDB03245S-4-Nitrobutyryl-CoaSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of GCDH go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of GCDH
Multiple alignments for Q92947 in multiple species
LBSAA sequence# speciesSpecies
E414AVNTYEGTHDI2Homo sapiens, Mus musculus
E414PIYTYEGTYDI1Arabidopsis thaliana
E414TVNTYEGTHDV1Caenorhabditis elegans
E414SVNTYEGTHDI1Bos taurus
F177ELLGCFGLTEP3Homo sapiens, Mus musculus, Bos taurus
F177NTVACWALTEP1Arabidopsis thaliana
F177KKIGCFGLTEP1Caenorhabditis elegans
F287SLGGPFGCLNN1Homo sapiens
F287SFQDTSKVLAV1Arabidopsis thaliana
F287GLQGPFGCLNN1Caenorhabditis elegans
F287SLAGPFGCLNT1Mus musculus
F287GLAGPFGCLNN1Bos taurus
F434TGIQAFTASK-1Homo sapiens
F434TGIASFKPATR1Arabidopsis thaliana
F434TGLNGFC----1Caenorhabditis elegans
F434TGIQAFTVGK-1Mus musculus
F434TGIQAFVAGK-1Bos taurus
G185TEPNSGSDPSS1Homo sapiens
G185TEPDNGSDASG1Arabidopsis thaliana
G185TEPNHGSNPGG1Caenorhabditis elegans
G185TEPNHGSDPGG1Mus musculus
G185TEPNHGSDPSG1Bos taurus
G284GASSLGGPFGC1Homo sapiens
G284GVNSFQDTSKV1Arabidopsis thaliana
G284NAEGLQGPFGC1Caenorhabditis elegans
G284NVSSLAGPFGC1Mus musculus
G284GVSGLAGPFGC1Bos taurus
G288LGGPFGCLNNA1Homo sapiens
G288FQDTSKVLAVS1Arabidopsis thaliana
G288LQGPFGCLNNA1Caenorhabditis elegans
G288LAGPFGCLNTA1Mus musculus
G288LAGPFGCLNNA1Bos taurus
I213GTKTWITNSPM1Homo sapiens
I213GQKRWIGNSTF1Arabidopsis thaliana
I213GSKTWISNSPV1Caenorhabditis elegans
I213GTKTWITNSPV1Mus musculus
I213GSKTWITNSPV1Bos taurus
I419EGTHDIHALIL3Homo sapiens, Mus musculus, Bos taurus
I419EGTYDINTLVT1Arabidopsis thaliana
I419EGTHDVHALIL1Caenorhabditis elegans
I423DIHALILGRAI3Homo sapiens, Mus musculus, Bos taurus
I423DINTLVTGREV1Arabidopsis thaliana
I423DVHALILGRAI1Caenorhabditis elegans
L147SVQSSLVMHPI2Homo sapiens, Mus musculus
L147LVHSSLGMLTI1Arabidopsis thaliana
L147SVQTSLVIGPI1Caenorhabditis elegans
L147SVQSSLVMYPI1Bos taurus
L179LGCFGLTEPNH2Mus musculus, Bos taurus
L179LGCFGLTEPNS1Homo sapiens
L179VACWALTEPDN1Arabidopsis thaliana
L179IGCFGLTEPNH1Caenorhabditis elegans
L256QGKFSLRASAT1Homo sapiens
L256PNKIGLRMVQN1Arabidopsis thaliana
L256EGKLSLRASIT1Caenorhabditis elegans
L256EGKFSLRASAT1Mus musculus
L256EGKFSLRASST1Bos taurus
L290GPFGCLNNARY2Homo sapiens, Bos taurus
L290DTSKVLAVSRV1Arabidopsis thaliana
L290GPFGCLNNARL1Caenorhabditis elegans
L290GPFGCLNTARY1Mus musculus
N291PFGCLNNARYG2Homo sapiens, Bos taurus
N291TSKVLAVSRVM1Arabidopsis thaliana
N291PFGCLNNARLG1Caenorhabditis elegans
N291PFGCLNTARYG1Mus musculus
P188NSGSDPSSMET1Homo sapiens
P188DNGSDASGLGT1Arabidopsis thaliana
P188NHGSNPGGMET1Caenorhabditis elegans
P188NHGSDPGGMET1Mus musculus
P188NHGSDPSGMET1Bos taurus
P364QDKAAPEMVSL2Homo sapiens, Bos taurus
P364TGQMTPGQASL1Arabidopsis thaliana
P364EGKVQSEQISI1Caenorhabditis elegans
P364QDKATPEMVSM1Mus musculus
R138VDSGYRSAMSV2Homo sapiens, Bos taurus
R138VDASCSTFILV1Arabidopsis thaliana
R138VDSGYRSTMSV1Caenorhabditis elegans
R138VDSGYRSMMSV1Mus musculus
R294CLNNARYGIAW1Homo sapiens
R294VLAVSRVMVAW1Arabidopsis thaliana
R294CLNNARLGIAW1Caenorhabditis elegans
R294CLNTARYGITW1Mus musculus
R294CLNNARYGITW1Bos taurus
R426ALILGRAITGI3Homo sapiens, Mus musculus, Bos taurus
R426TLVTGREVTGI1Arabidopsis thaliana
R426ALILGRAITGL1Caenorhabditis elegans
S139DSGYRSAMSVQ2Homo sapiens, Bos taurus
S139DASCSTFILVH1Arabidopsis thaliana
S139DSGYRSTMSVQ1Caenorhabditis elegans
S139DSGYRSMMSVQ1Mus musculus
S142YRSAMSVQSSL2Homo sapiens, Bos taurus
S142CSTFILVHSSL1Arabidopsis thaliana
S142YRSTMSVQTSL1Caenorhabditis elegans
S142YRSMMSVQSSL1Mus musculus
S186EPNSGSDPSSM1Homo sapiens
S186EPDNGSDASGL1Arabidopsis thaliana
S186EPNHGSNPGGM1Caenorhabditis elegans
S186EPNHGSDPGGM1Mus musculus
S186EPNHGSDPSGM1Bos taurus
T180GCFGLTEPNHG3Caenorhabditis elegans, Mus musculus, Bos taurus
T180GCFGLTEPNSG1Homo sapiens
T180ACWALTEPDNG1Arabidopsis thaliana
T214TKTWITNSPMA1Homo sapiens
T214QKRWIGNSTFA1Arabidopsis thaliana
T214SKTWISNSPVS1Caenorhabditis elegans
T214TKTWITNSPVA1Mus musculus
T214SKTWITNSPVA1Bos taurus
T416NTYEGTHDIHA3Homo sapiens, Mus musculus, Bos taurus
T416YTYEGTYDINT1Arabidopsis thaliana
T416NTYEGTHDVHA1Caenorhabditis elegans
V143RSAMSVQSSLV2Homo sapiens, Bos taurus
V143STFILVHSSLG1Arabidopsis thaliana
V143RSTMSVQTSLV1Caenorhabditis elegans
V143RSMMSVQSSLV1Mus musculus
W212NGTKTWITNSP1Homo sapiens
W212NGQKRWIGNST1Arabidopsis thaliana
W212NGSKTWISNSP1Caenorhabditis elegans
W212SGTKTWITNSP1Mus musculus
W212SGSKTWITNSP1Bos taurus
Y413EAVNTYEGTHD2Homo sapiens, Mus musculus
Y413EPIYTYEGTYD1Arabidopsis thaliana
Y413ETVNTYEGTHD1Caenorhabditis elegans
Y413ESVNTYEGTHD1Bos taurus


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