mutLBSgeneDB

mutLBSgeneDB
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 IVD
Gene summary
Basic gene Info.Gene symbolIVD
Gene nameisovaleryl-CoA dehydrogenase
SynonymsACAD2
CytomapUCSC genome browser: 15q14-q15
Type of geneprotein-coding
RefGenesNM_001159508.1,
NM_002225.3,
Descriptionisovaleryl CoA dehydrogenaseisovaleryl Coenzyme A dehydrogenaseisovaleryl-CoA dehydrogenase, mitochondrial
Modification date20141211
dbXrefs MIM : 607036
HGNC : HGNC
Ensembl : ENSG00000128928
HPRD : 09516
Vega : OTTHUMG00000129984
ProteinUniProt: P26440
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_IVD
BioGPS: 3712
PathwayNCI Pathway Interaction Database: IVD
KEGG: IVD
REACTOME: IVD
Pathway Commons: IVD
ContextiHOP: IVD
ligand binding site mutation search in PubMed: IVD
UCL Cancer Institute: IVD
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 IVD
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
M322E322GCOAD1
C378G378WHNSC1
R309A308TLUAD1
S165N165SLUAD1
Q377G376RSKCM1
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 IVD
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 IVD from PDB

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Differential gene expression and gene-gene network for IVD
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 IVD and the right PPI network was created from samples without mutations in the LBS of IVD. 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 IVD
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0268575Acidemia, isovaleric17Biomarker, GeneticVariation

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

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Pharmacological information for IVD
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
ExperimentalDB04036Coenzyme a PersulfideSmall molecule

Gene-centered ligand-gene interaction network

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


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Conservation information for LBS of IVD
Multiple alignments for P26440 in multiple species
LBSAA sequence# speciesSpecies
A404LYEIGAGTSEV3Homo sapiens, Mus musculus, Bos taurus
A404LYEIGGGTSEV1Rattus norvegicus
A404LYEIGAGTSEI1Arabidopsis thaliana
A404LFEIGAGTSEI1Oryza sativa subsp. japonica
C378LDGIQCLGGNG3Mus musculus, Rattus norvegicus, Bos taurus
C378LQAIQCLGGNG2Arabidopsis thaliana, Oryza sativa subsp. japonica
C378LDGIQCFGGNG1Homo sapiens
D281LMSGLDLERLV5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Arabidopsis thaliana
D281MMSGLDLERLV1Oryza sativa subsp. japonica
E283SGLDLERLVLA6Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Arabidopsis thaliana, Oryza sativa subsp. japonica
E408GAGTSEVRRLV3Homo sapiens, Mus musculus, Bos taurus
E408GGGTSEVRRLV1Rattus norvegicus
E408GAGTSEIRRIV1Arabidopsis thaliana
E408GAGTSEIRRMI1Oryza sativa subsp. japonica
F312HVREAFGQKIG3Homo sapiens, Mus musculus, Rattus norvegicus
F312HMREAFGQKIG1Bos taurus
F312RQREQFGRPVG1Arabidopsis thaliana
F312RQREQFGRPIG1Oryza sativa subsp. japonica
F319QKIGHFQLMQG2Homo sapiens, Bos taurus
F319QKIGQFQLMQG2Mus musculus, Rattus norvegicus
F319RPVGEFQFIQG1Arabidopsis thaliana
F319RPIGEFQFIQG1Oryza sativa subsp. japonica
G170SEPNAGSDVVS4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
G170SEPNAGSDVVG1Arabidopsis thaliana
G170SEPNSGSDVVS1Oryza sativa subsp. japonica
G381IQCLGGNGYIN5Mus musculus, Rattus norvegicus, Bos taurus, Arabidopsis thaliana, Oryza sativa subsp. japonica
G381IQCFGGNGYIN1Homo sapiens
G403KLYEIGAGTSE4Homo sapiens, Mus musculus, Bos taurus, Arabidopsis thaliana
G403KLYEIGGGTSE1Rattus norvegicus
G403KLFEIGAGTSE1Oryza sativa subsp. japonica
G405YEIGAGTSEVR3Homo sapiens, Mus musculus, Bos taurus
G405YEIGGGTSEVR1Rattus norvegicus
G405YEIGAGTSEIR1Arabidopsis thaliana
G405FEIGAGTSEIR1Oryza sativa subsp. japonica
I196GNKFWITNGPD4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
I196GNKMWCTNGPS2Arabidopsis thaliana, Oryza sativa subsp. japonica
I316AFGQKIGHFQL2Homo sapiens, Bos taurus
I316AFGQKIGQFQL2Mus musculus, Rattus norvegicus
I316QFGRPVGEFQF1Arabidopsis thaliana
I316QFGRPIGEFQF1Oryza sativa subsp. japonica
I402AKLYEIGAGTS4Homo sapiens, Mus musculus, Bos taurus, Arabidopsis thaliana
I402AKLYEIGGGTS1Rattus norvegicus
I402AKLFEIGAGTS1Oryza sativa subsp. japonica
K242SKKLDKLGMRG4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
K242AQKLDKLGMRG2Arabidopsis thaliana, Oryza sativa subsp. japonica
L162EYIGALAMSEP2Homo sapiens, Bos taurus
L162EFIGALAMSEP2Mus musculus, Rattus norvegicus
L162EHVGALAMSEP2Arabidopsis thaliana, Oryza sativa subsp. japonica
L280VLMSGLDLERL5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Arabidopsis thaliana
L280VMMSGLDLERL1Oryza sativa subsp. japonica
L321IGHFQLMQGKM2Homo sapiens, Bos taurus
L321IGQFQLMQGKM2Mus musculus, Rattus norvegicus
L321VGEFQFIQGKV1Arabidopsis thaliana
L321IGEFQFIQGKL1Oryza sativa subsp. japonica
L399LRDAKLYEIGA4Homo sapiens, Mus musculus, Bos taurus, Arabidopsis thaliana
L399LRDAKLYEIGG1Rattus norvegicus
L399LRDAKLFEIGA1Oryza sativa subsp. japonica
L412SEVRRLVIGRA4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
L412SEIRRIVIGRE1Arabidopsis thaliana
L412SEIRRMIIGRE1Oryza sativa subsp. japonica
M164IGALAMSEPNA4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
M164VGALAMSEPNA1Arabidopsis thaliana
M164VGALAMSEPNS1Oryza sativa subsp. japonica
M277GVYVLMSGLDL5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Arabidopsis thaliana
M277GVYVMMSGLDL1Oryza sativa subsp. japonica
M322GHFQLMQGKMA2Homo sapiens, Bos taurus
M322GQFQLMQGKMA2Mus musculus, Rattus norvegicus
M322GEFQFIQGKVA1Arabidopsis thaliana
M322GEFQFIQGKLA1Oryza sativa subsp. japonica
Q377ALDGIQCLGGN3Mus musculus, Rattus norvegicus, Bos taurus
Q377ALQAIQCLGGN2Arabidopsis thaliana, Oryza sativa subsp. japonica
Q377ALDGIQCFGGN1Homo sapiens
R220AVPASRGITAF4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
R220A--GSKGITAF2Arabidopsis thaliana, Oryza sativa subsp. japonica
R284GLDLERLVLAG4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
R284GLDLERLVLAA2Arabidopsis thaliana, Oryza sativa subsp. japonica
R309PYLHVREAFGQ3Homo sapiens, Mus musculus, Rattus norvegicus
R309PYLHMREAFGQ1Bos taurus
R309PYIRQREQFGR1Arabidopsis thaliana
R309PYVRQREQFGR1Oryza sativa subsp. japonica
R416RLVIGRA-FNA4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
R416RIVIGRELFKE1Arabidopsis thaliana
R416RMIIGRELFKE1Oryza sativa subsp. japonica
S165GALAMSEPNAG5Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, Arabidopsis thaliana
S165GALAMSEPNSG1Oryza sativa subsp. japonica
S171EPNAGSDVVSM4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
S171EPNAGSDVVGM1Arabidopsis thaliana
S171EPNSGSDVVSM1Oryza sativa subsp. japonica
S219TAVPASRGITA3Mus musculus, Rattus norvegicus, Bos taurus
S219AAVPASRGITA1Homo sapiens
S219KA--GSKGITA1Arabidopsis thaliana
S219AA--GSKGITA1Oryza sativa subsp. japonica
T197NKFWITNGPDA4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
T197NKMWCTNGPSA2Arabidopsis thaliana, Oryza sativa subsp. japonica
T406EIGAGTSEVRR3Homo sapiens, Mus musculus, Bos taurus
T406EIGAGTSEIRR2Arabidopsis thaliana, Oryza sativa subsp. japonica
T406EIGGGTSEVRR1Rattus norvegicus
V173NAGSDVVSMKL3Homo sapiens, Mus musculus, Bos taurus
V173NAGSDVVSMRL1Rattus norvegicus
V173NAGSDVVGMKC1Arabidopsis thaliana
V173NSGSDVVSMKC1Oryza sativa subsp. japonica
V174AGSDVVSMKLK3Homo sapiens, Mus musculus, Bos taurus
V174AGSDVVSMRLK1Rattus norvegicus
V174AGSDVVGMKCK1Arabidopsis thaliana
V174SGSDVVSMKCK1Oryza sativa subsp. japonica
V273QESKGVYVLMS2Mus musculus, Rattus norvegicus
V273HENKGVYVLMS1Homo sapiens
V273HLGKGVYVLMS1Bos taurus
V273KEGKGVYVLMS1Arabidopsis thaliana
V273EEGKGVYVMMS1Oryza sativa subsp. japonica
V409AGTSEVRRLVI3Homo sapiens, Mus musculus, Bos taurus
V409GGTSEVRRLVI1Rattus norvegicus
V409AGTSEIRRIVI1Arabidopsis thaliana
V409AGTSEIRRMII1Oryza sativa subsp. japonica
V413EVRRLVIGRA-4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
V413EIRRIVIGREL1Arabidopsis thaliana
V413EIRRMIIGREL1Oryza sativa subsp. japonica
W195NGNKFWITNGP4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
W195NGNKMWCTNGP2Arabidopsis thaliana, Oryza sativa subsp. japonica
Y274ESKGVYVLMSG2Mus musculus, Rattus norvegicus
Y274ENKGVYVLMSG1Homo sapiens
Y274LGKGVYVLMSG1Bos taurus
Y274EGKGVYVLMSG1Arabidopsis thaliana
Y274EGKGVYVMMSG1Oryza sativa subsp. japonica


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