mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

Home

Download

 Statistics

Help

About Us
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 GMDS
Gene summary
Basic gene Info.Gene symbolGMDS
Gene nameGDP-mannose 4,6-dehydratase
SynonymsGMD|SDR3E1
CytomapUCSC genome browser: 6p25
Type of geneprotein-coding
RefGenesNM_001253846.1,
NM_001500.3,
DescriptionGDP-D-mannose dehydrataseGDP-mannose 4,6 dehydrataseshort chain dehydrogenase/reductase family 3E, member 1
Modification date20141222
dbXrefs MIM : 602884
HGNC : HGNC
Ensembl : ENSG00000112699
HPRD : 11925
Vega : OTTHUMG00000016143
ProteinUniProt: O60547
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GMDS
BioGPS: 2762
PathwayNCI Pathway Interaction Database: GMDS
KEGG: GMDS
REACTOME: GMDS
Pathway Commons: GMDS
ContextiHOP: GMDS
ligand binding site mutation search in PubMed: GMDS
UCL Cancer Institute: GMDS
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
GO:0019673GDP-mannose metabolic process9525924
GO:0042351'de novo' GDP-L-fucose biosynthetic process9525924


Top
Ligand binding site mutations for GMDS
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
D35G36ABRCA1
R56R56WCOAD1
R55R55WCOAD1
R56R56LLUAD1
R55V54LLUAD1
V281E283KLUAD1
V281E283KSKCM1
R325R325QSTAD1
V127G129RUCEC1
R56R56QUCEC1
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.


Top
Protein structure related information for GMDS
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
R325R325Q-1.3414763
V281E283K-0.83965273
V127G129R-0.77816049
R56R56Q-0.75310662
R55R55W-0.42593473
R56R56W-0.4128677
R55V54L-0.28960667
D35G36A-0.11054427
R56R56L-0.064947668
(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 GMDS from PDB

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


Top

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

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

Top
Pharmacological information for GMDS
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
ExperimentalDB02547Guanosine-5'-Diphosphate-RhamnoseSmall molecule
ExperimentalDB04315Guanosine-5'-DiphosphateSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of GMDS go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NDPNADPH1t2aAD35 R55 V127
NDPNADPH1t2aBD35 R55 V127
NDPNADPH1t2aCD35 R55 V127
NDPNADPH1t2aDD35 R55 V127
NDPNADPH1t2aAR56
NDPNADPH1t2aBR56
NDPNADPH1t2aCR56
NDPNADPH1t2aDR56
GDPGUANOSINE-5'-DIPHOSPHATE1t2aAV281 R325
GDPGUANOSINE-5'-DIPHOSPHATE1t2aBV281 R325
GDPGUANOSINE-5'-DIPHOSPHATE1t2aCV281 R325
GDPGUANOSINE-5'-DIPHOSPHATE1t2aDV281 R325


Top
Conservation information for LBS of GMDS
Multiple alignments for O60547 in multiple species
LBSAA sequence# speciesSpecies
A110IYNLGAQSHVK2Homo sapiens, Mus musculus
A110VYNLAAQSHVA2Arabidopsis thaliana, Arabidopsis thaliana
A110VYHLAAQSHVK1Caenorhabditis elegans
A110IYHLAAQSHVK1Caenorhabditis elegans
A110IYNLAAQSHVK1Drosophila melanogaster
A153VRFYQASTSEL3Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster
A153VKFYQASTSEL2Homo sapiens, Mus musculus
A153IKYYQAGSSEM1Arabidopsis thaliana
A153VKYYQAGSSEM1Arabidopsis thaliana
A245LGNLDAKRDWG2Homo sapiens, Mus musculus
A245LGNLSALRDWG2Caenorhabditis elegans, Caenorhabditis elegans
A245LGNIQASRDWG1Arabidopsis thaliana
A245LGNLQASRDWG1Arabidopsis thaliana
A245LGNLDSKRDWG1Drosophila melanogaster
D35GITGQDGSYLA4Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus
D35GITGQDGSYLT2Arabidopsis thaliana, Arabidopsis thaliana
D35GISGQDGSYLA1Caenorhabditis elegans
D86KLHYGDLTDST2Homo sapiens, Mus musculus
D86SLHYGDMTDSS2Caenorhabditis elegans, Caenorhabditis elegans
D86KLHYGDLSDAS1Arabidopsis thaliana
D86KLHYADLTDAS1Arabidopsis thaliana
D86KLHYGDMTDSS1Drosophila melanogaster
E157QASTSELYGKV5Homo sapiens, Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus
E157QAGSSEMFGST2Arabidopsis thaliana, Arabidopsis thaliana
E328YYRPTEVDFLQ2Homo sapiens, Mus musculus
E328YYRPTEVETLL2Caenorhabditis elegans, Caenorhabditis elegans
E328YFRPTEVDNLK1Arabidopsis thaliana
E328YFRPAEVDNLQ1Arabidopsis thaliana
E328YFRPTEVDLLQ1Drosophila melanogaster
F218RRGENFVTRKI3Arabidopsis thaliana, Arabidopsis thaliana, Drosophila melanogaster
F218RRGANFVTRKI2Homo sapiens, Mus musculus
F218RRGETFVTRKI2Caenorhabditis elegans, Caenorhabditis elegans
G109EIYNLGAQSHV2Homo sapiens, Mus musculus
G109EVYNLAAQSHV2Arabidopsis thaliana, Arabidopsis thaliana
G109EVYHLAAQSHV1Caenorhabditis elegans
G109EIYHLAAQSHV1Caenorhabditis elegans
G109EIYNLAAQSHV1Drosophila melanogaster
G241ECFSLGNLDAK2Homo sapiens, Mus musculus
G241TKLFLGNIQAS1Arabidopsis thaliana
G241TKLFLGNLQAS1Arabidopsis thaliana
G241ESIELGNLSAL1Caenorhabditis elegans
G241EHIELGNLSAL1Caenorhabditis elegans
G241EYFELGNLDSK1Drosophila melanogaster
G30VALITGITGQD4Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus
G30IALVTGITGQD1Arabidopsis thaliana
G30IALITGITGQD1Arabidopsis thaliana
G30VALITGISGQD1Caenorhabditis elegans
G33ITGITGQDGSY5Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus
G33VTGITGQDGSY1Arabidopsis thaliana
G33ITGISGQDGSY1Caenorhabditis elegans
H113LAAQSHVKVSF3Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster
H113LGAQSHVKISF2Homo sapiens, Mus musculus
H113LAAQSHVAVSF2Arabidopsis thaliana, Arabidopsis thaliana
H209GILFNHESPRR7Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus
K183PYGAAKLYAYW2Homo sapiens, Mus musculus
K183PYAASKCAAHW2Arabidopsis thaliana, Arabidopsis thaliana
K183PYAVAKMYGYW2Caenorhabditis elegans, Caenorhabditis elegans
K183PYACAKMYGFW1Drosophila melanogaster
K222NFVTRKISRSV2Homo sapiens, Mus musculus
K222NFVTRKITRAL2Arabidopsis thaliana, Arabidopsis thaliana
K222TFVTRKITRSV2Caenorhabditis elegans, Caenorhabditis elegans
K222NFVTRKITRSV1Drosophila melanogaster
L108TEIYNLGAQSH2Homo sapiens, Mus musculus
L108DEVYNLAAQSH2Arabidopsis thaliana, Arabidopsis thaliana
L108TEVYHLAAQSH1Caenorhabditis elegans
L108TEIYHLAAQSH1Caenorhabditis elegans
L108TEIYNLAAQSH1Drosophila melanogaster
L206ACNGILFNHES5Arabidopsis thaliana, Arabidopsis thaliana, Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster
L206AVNGILFNHES2Homo sapiens, Mus musculus
L240LECFSLGNLDA2Homo sapiens, Mus musculus
L240QTKLFLGNIQA1Arabidopsis thaliana
L240QTKLFLGNLQA1Arabidopsis thaliana
L240QESIELGNLSA1Caenorhabditis elegans
L240QEHIELGNLSA1Caenorhabditis elegans
L240MEYFELGNLDS1Drosophila melanogaster
L87LHYGDLTDSTC2Homo sapiens, Mus musculus
L87LHYGDMTDSSC2Caenorhabditis elegans, Caenorhabditis elegans
L87LHYGDLSDASS1Arabidopsis thaliana
L87LHYADLTDASS1Arabidopsis thaliana
L87LHYGDMTDSSS1Drosophila melanogaster
N208NGILFNHESPR7Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus
N217PRRGENFVTRK3Arabidopsis thaliana, Arabidopsis thaliana, Drosophila melanogaster
N217PRRGANFVTRK2Homo sapiens, Mus musculus
N217PRRGETFVTRK2Caenorhabditis elegans, Caenorhabditis elegans
N242CFSLGNLDAKR2Homo sapiens, Mus musculus
N242KLFLGNIQASR1Arabidopsis thaliana
N242KLFLGNLQASR1Arabidopsis thaliana
N242SIELGNLSALR1Caenorhabditis elegans
N242HIELGNLSALR1Caenorhabditis elegans
N242YFELGNLDSKR1Drosophila melanogaster
Q34TGITGQDGSYL6Homo sapiens, Arabidopsis thaliana, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus
Q34TGISGQDGSYL1Caenorhabditis elegans
R214HESPRRGENFV3Arabidopsis thaliana, Arabidopsis thaliana, Drosophila melanogaster
R214HESPRRGANFV2Homo sapiens, Mus musculus
R214HESPRRGETFV2Caenorhabditis elegans, Caenorhabditis elegans
R247NLDAKRDWGHA2Homo sapiens, Mus musculus
R247NLSALRDWGHA2Caenorhabditis elegans, Caenorhabditis elegans
R247NIQASRDWGFA1Arabidopsis thaliana
R247NLQASRDWGFA1Arabidopsis thaliana
R247NLDSKRDWGHA1Drosophila melanogaster
R325DLKYYRPTEVD2Homo sapiens, Mus musculus
R325SPKYYRPTEVE2Caenorhabditis elegans, Caenorhabditis elegans
R325DKRYFRPTEVD1Arabidopsis thaliana
R325DQRYFRPAEVD1Arabidopsis thaliana
R325NPKYFRPTEVD1Drosophila melanogaster
R55VHGIVRRSSSF2Homo sapiens, Mus musculus
R55VHGLIRRSSNF2Arabidopsis thaliana, Arabidopsis thaliana
R55VHGIIRRSSSF2Caenorhabditis elegans, Caenorhabditis elegans
R55VHGIIRRASTF1Drosophila melanogaster
R56HGIVRRSSSFN2Homo sapiens, Mus musculus
R56HGLIRRSSNFN2Arabidopsis thaliana, Arabidopsis thaliana
R56HGIIRRSSSFN2Caenorhabditis elegans, Caenorhabditis elegans
R56HGIIRRASTFN1Drosophila melanogaster
S112NLGAQSHVKIS2Homo sapiens, Mus musculus
S112NLAAQSHVAVS2Arabidopsis thaliana, Arabidopsis thaliana
S112HLAAQSHVKVS2Caenorhabditis elegans, Caenorhabditis elegans
S112NLAAQSHVKVS1Drosophila melanogaster
S154RFYQASTSELY3Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster
S154KFYQASTSELY2Homo sapiens, Mus musculus
S154KYYQAGSSEMF2Arabidopsis thaliana, Arabidopsis thaliana
S57GIVRRSSSFNT2Homo sapiens, Mus musculus
S57GLIRRSSNFNT2Arabidopsis thaliana, Arabidopsis thaliana
S57GIIRRSSSFNT2Caenorhabditis elegans, Caenorhabditis elegans
S57GIIRRASTFNT1Drosophila melanogaster
S58IVRRSSSFNTG2Homo sapiens, Mus musculus
S58LIRRSSNFNTQ2Arabidopsis thaliana, Arabidopsis thaliana
S58IIRRSSSFNTA2Caenorhabditis elegans, Caenorhabditis elegans
S58IIRRASTFNTT1Drosophila melanogaster
T155FYQASTSELYG5Homo sapiens, Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus
T155YYQAGSSEMFG2Arabidopsis thaliana, Arabidopsis thaliana
T32LITGITGQDGS5Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus
T32LVTGITGQDGS1Arabidopsis thaliana
T32LITGISGQDGS1Caenorhabditis elegans
V114AAQSHVKVSFD3Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster
V114GAQSHVKISFD2Homo sapiens, Mus musculus
V114AAQSHVAVSFE2Arabidopsis thaliana, Arabidopsis thaliana
V127EYTAEVDAVGT3Caenorhabditis elegans, Caenorhabditis elegans, Drosophila melanogaster
V127EYTADVDGVGT2Homo sapiens, Mus musculus
V127DYTADVVATGA2Arabidopsis thaliana, Arabidopsis thaliana
V219RGENFVTRKIT3Arabidopsis thaliana, Arabidopsis thaliana, Drosophila melanogaster
V219RGANFVTRKIS2Homo sapiens, Mus musculus
V219RGETFVTRKIT2Caenorhabditis elegans, Caenorhabditis elegans
V281GEVHSVREFVE2Homo sapiens, Mus musculus
V281GKQFSVREFCN2Caenorhabditis elegans, Caenorhabditis elegans
V281EESHTVKEFLD1Arabidopsis thaliana
V281EEGHTVEEFLD1Arabidopsis thaliana
V281GETHSVREFVE1Drosophila melanogaster
Y123FDLAEYTADVD2Homo sapiens, Mus musculus
Y123FEIPDYTADVV2Arabidopsis thaliana, Arabidopsis thaliana
Y123FDLPEYTAEVD2Caenorhabditis elegans, Caenorhabditis elegans
Y123FDLSEYTAEVD1Drosophila melanogaster
Y179YPRSPYGAAKL2Homo sapiens, Mus musculus
Y179HPRSPYAASKC2Arabidopsis thaliana, Arabidopsis thaliana
Y179YPRSPYAVAKM2Caenorhabditis elegans, Caenorhabditis elegans
Y179YPRSPYACAKM1Drosophila melanogaster
Y323TVDLKYYRPTE2Homo sapiens, Mus musculus
Y323KVSPKYYRPTE2Caenorhabditis elegans, Caenorhabditis elegans
Y323EIDKRYFRPTE1Arabidopsis thaliana
Y323EIDQRYFRPAE1Arabidopsis thaliana
Y323RINPKYFRPTE1Drosophila melanogaster


Copyright © 2016-Present - The University of Texas Health Science Center at Houston
Site Policies | State of Texas