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 GPD1L
Gene summary
Basic gene Info.Gene symbolGPD1L
Gene nameglycerol-3-phosphate dehydrogenase 1-like
SynonymsGPD1-L
CytomapUCSC genome browser: 3p22.3
Type of geneprotein-coding
RefGenesNM_015141.3,
Descriptionglycerol-3-phosphate dehydrogenase 1-like protein
Modification date20141219
dbXrefs MIM : 611778
HGNC : HGNC
Ensembl : ENSG00000152642
HPRD : 10008
Vega : OTTHUMG00000155846
ProteinUniProt: Q8N335
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPD1L
BioGPS: 23171
PathwayNCI Pathway Interaction Database: GPD1L
KEGG: GPD1L
REACTOME: GPD1L
Pathway Commons: GPD1L
ContextiHOP: GPD1L
ligand binding site mutation search in PubMed: GPD1L
UCL Cancer Institute: GPD1L
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 GPD1L
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
P96H97NLUAD1
I121I121MLUSC1
T266I264FUCEC1
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 GPD1L
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
I121I121M-1.5792571
P96H97N-1.1952482
T266I264F-1.1551751
(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 GPD1L from PDB

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Differential gene expression and gene-gene network for GPD1L
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 GPD1L and the right PPI network was created from samples without mutations in the LBS of GPD1L. 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 GPD1L
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0038644Sudden Infant Death2Biomarker, GeneticVariation

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

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Pharmacological information for GPD1L
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 GPD1L go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NADNAD ZWITTERION2plaAP96 I121
NADNAD ZWITTERION2plaBP96 I121
PO4PHOSPHATE ION2plaAT266
PO4PHOSPHATE ION2plaBT266


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Conservation information for LBS of GPD1L
Multiple alignments for Q8N335 in multiple species
LBSAA sequence# speciesSpecies
A155MGANIANEVAA3Homo sapiens, Danio rerio, Xenopus tropicalis
A155MGANIANEIAV1Arabidopsis thaliana
A155MGANIASEVAA1Mus musculus
F43VKMWVFEETV-2Homo sapiens, Mus musculus
F43VRMWVFEEVLP1Arabidopsis thaliana
F43VKMWVYEEMV-1Danio rerio
F43VNMWVFEENI-1Xenopus tropicalis
F99VIPHQFIHKIC2Xenopus tropicalis, Mus musculus
F99VIPHQFIHRIC1Homo sapiens
F99VTPHQFMDGIC1Arabidopsis thaliana
F99VVPHQFIRKLC1Danio rerio
G14CIVGSGNWGSA4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
G14TVVGSGNWGSV1Arabidopsis thaliana
G17GSGNWGSAVAK3Homo sapiens, Xenopus tropicalis, Mus musculus
G17GSGNWGSVAAK1Arabidopsis thaliana
G17GSGNWGSAIAR1Danio rerio
G270TTCYGGRNRRV3Homo sapiens, Danio rerio, Mus musculus
G270TTCLGGRNRRV1Arabidopsis thaliana
G270TTCYGGRNRKV1Xenopus tropicalis
G296KEMLNGQKLQG3Homo sapiens, Danio rerio, Xenopus tropicalis
G296AEMLQGQKLQG1Arabidopsis thaliana
G296KELLNGQKLQG1Mus musculus
H69KYLPGHKLPEN2Homo sapiens, Mus musculus
H69KYLPGYKLPEN2Danio rerio, Xenopus tropicalis
H69KYLPGIKLGRN1Arabidopsis thaliana
I121LGITLIKGIDE3Homo sapiens, Xenopus tropicalis, Mus musculus
I121EAISLVKGMEV1Arabidopsis thaliana
I121RGITLIKGIDE1Danio rerio
I154LMGANIANEVA3Homo sapiens, Danio rerio, Xenopus tropicalis
I154LMGANIANEIA1Arabidopsis thaliana
I154LMGANIASEVA1Mus musculus
I95LLVFVIPHQFI2Homo sapiens, Mus musculus
I95MLVFVTPHQFM1Arabidopsis thaliana
I95LLVFVVPHQFI1Danio rerio
I95LLIFVIPHQFI1Xenopus tropicalis
K122GITLIKGIDEG4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
K122AISLVKGMEVK1Arabidopsis thaliana
K206LCGALKNIVAV4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
K206LCGTLKNVVAI1Arabidopsis thaliana
K22GSAVAKIIGNN1Homo sapiens
K22GSVAAKLIASN1Arabidopsis thaliana
K22GSAIARIIGSN1Danio rerio
K22GSAVAKIIGHN1Xenopus tropicalis
K22GSAVAKIIGSN1Mus musculus
K298MLNGQKLQGPQ2Homo sapiens, Xenopus tropicalis
K298MLQGQKLQGVS1Arabidopsis thaliana
K298MLNGQKLQGPL1Danio rerio
K298LLNGQKLQGPQ1Mus musculus
K70YLPGHKLPENV2Homo sapiens, Mus musculus
K70YLPGYKLPENV2Danio rerio, Xenopus tropicalis
K70YLPGIKLGRNV1Arabidopsis thaliana
L120ALGITLIKGID3Homo sapiens, Xenopus tropicalis, Mus musculus
L120VEAISLVKGME1Arabidopsis thaliana
L120ARGITLIKGID1Danio rerio
N15IVGSGNWGSAV3Homo sapiens, Xenopus tropicalis, Mus musculus
N15VVGSGNWGSVA1Arabidopsis thaliana
N15IVGSGNWGSAI1Danio rerio
N153VLMGANIANEV3Homo sapiens, Danio rerio, Xenopus tropicalis
N153VLMGANIANEI1Arabidopsis thaliana
N153VLMGANIASEV1Mus musculus
N272CYGGRNRRVAE3Homo sapiens, Danio rerio, Mus musculus
N272CLGGRNRRVAE1Arabidopsis thaliana
N272CYGGRNRKVSE1Xenopus tropicalis
P96LVFVIPHQFIH2Homo sapiens, Mus musculus
P96LVFVTPHQFMD1Arabidopsis thaliana
P96LVFVVPHQFIR1Danio rerio
P96LIFVIPHQFIH1Xenopus tropicalis
Q297EMLNGQKLQGP3Homo sapiens, Danio rerio, Xenopus tropicalis
Q297EMLQGQKLQGV1Arabidopsis thaliana
Q297ELLNGQKLQGP1Mus musculus
Q300NGQKLQGPQTS3Homo sapiens, Xenopus tropicalis, Mus musculus
Q300QGQKLQGVSTA1Arabidopsis thaliana
Q300NGQKLQGPLTS1Danio rerio
R102HQFIHRICDEI1Homo sapiens
R102HQFMDGICKKL1Arabidopsis thaliana
R102HQFIRKLCDEM1Danio rerio
R102HQFIHKICQEI1Xenopus tropicalis
R102HQFIHKICDEI1Mus musculus
R271TCYGGRNRRVA3Homo sapiens, Danio rerio, Mus musculus
R271TCLGGRNRRVA1Arabidopsis thaliana
R271TCYGGRNRKVS1Xenopus tropicalis
T266ADLITTCYGGR4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
T266ADVITTCLGGR1Arabidopsis thaliana
V94DLLVFVIPHQF2Homo sapiens, Mus musculus
V94NMLVFVTPHQF1Arabidopsis thaliana
V94DLLVFVVPHQF1Danio rerio
V94DLLIFVIPHQF1Xenopus tropicalis
W16VGSGNWGSAVA3Homo sapiens, Xenopus tropicalis, Mus musculus
W16VGSGNWGSVAA1Arabidopsis thaliana
W16VGSGNWGSAIA1Danio rerio
Y65HENVKYLPGHK2Homo sapiens, Mus musculus
Y65HENVKYLPGYK2Danio rerio, Xenopus tropicalis
Y65NENVKYLPGIK1Arabidopsis thaliana


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