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 TTPA
Gene summary
Basic gene Info.Gene symbolTTPA
Gene nametocopherol (alpha) transfer protein
SynonymsATTP|AVED|TTP1|alphaTTP
CytomapUCSC genome browser: 8q12.3
Type of geneprotein-coding
RefGenesNM_000370.3,
Descriptionalpha-TTPalpha-tocopherol transfer proteintocopherol (alpha) transfer protein (ataxia (Friedreich-like) with vitamin E deficiency)
Modification date20141219
dbXrefs MIM : 600415
HGNC : HGNC
Ensembl : ENSG00000137561
HPRD : 02685
Vega : OTTHUMG00000164367
ProteinUniProt: P49638
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_TTPA
BioGPS: 7274
PathwayNCI Pathway Interaction Database: TTPA
KEGG: TTPA
REACTOME: TTPA
Pathway Commons: TTPA
ContextiHOP: TTPA
ligand binding site mutation search in PubMed: TTPA
UCL Cancer Institute: TTPA
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 TTPA
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
W122W122CBRCA1
W163G162VBRCA1
V182T184MCOAD1
L47D49ECOAD1
S140E141DLUAD1
I171I171MLUSC1
I222R221LLUSC1
V206V206ALUSC1
F187S186LSKCM1
W122P124SSKCM1
S140S140YSKCM1
L137L137ISTAD1
I143L142IUCEC1
F133R134QUCEC1
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 TTPA
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
W122P124S-1.5055826
I143L142I-1.3228886
V206V206A-1.2074604
S140E141D-0.90968195
F133R134Q-0.89200711
I171I171M-0.82676357
W163G162V-0.79886356
L137L137I-0.67825685
I222R221L-0.66335534
W122W122C-0.35369984
L47D49E-0.33126229
F187S186L-0.29034838
V182T184M-0.26346943
S140S140Y-0.11925747
(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 TTPA from PDB

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Differential gene expression and gene-gene network for TTPA
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 TTPA and the right PPI network was created from samples without mutations in the LBS of TTPA. 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 TTPA
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1848533Ataxia with vitamin E deficiency25Biomarker, GeneticVariation
umls:C0042875Vitamin E Deficiency11Biomarker, GeneticVariation
umls:C0035334Retinitis Pigmentosa6Biomarker, GeneticVariation
umls:C0035309Retinal Diseases2Biomarker, GeneticVariation
umls:C0027765Nervous System Diseases2Biomarker
umls:C0012644Disease Models, Animal2Biomarker
umls:C0004153Atherosclerosis1Biomarker
umls:C0260662Hearing Disorders1Biomarker
umls:C0026846Muscular Atrophy1Biomarker
umls:C0034933Reflex, Abnormal1Biomarker
umls:C0752262Somatosensory Disorders1Biomarker
umls:C0037822Speech Disorders1Biomarker
umls:C0042035Urination Disorders1Biomarker
umls:C0042790Vision Disorders1Biomarker

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

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Pharmacological information for TTPA
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 TTPA go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
VIV(+)-ALPHA-TOCOPHEROL1oipAF133 L137 S140 I171 V182 F187
TRT1-[2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY]-4-(2,4,4-TRIMETHYLPENTAN-2-YL)BENZENE1oizAF133 S140 I143 V182
TRT1-[2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY]-4-(2,4,4-TRIMETHYLPENTAN-2-YL)BENZENE1oizBF133 S140 I171 V182
TRT1-[2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY]-4-(2,4,4-TRIMETHYLPENTAN-2-YL)BENZENE1oizBI171 V206
TRT1-[2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY]-4-(2,4,4-TRIMETHYLPENTAN-2-YL)BENZENE1oizBV206 I222
VIV(+)-ALPHA-TOCOPHEROL1r5lAW122 F133 S140 W163 I171 V182 F187
TRT1-[2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY]-4-(2,4,4-TRIMETHYLPENTAN-2-YL)BENZENE1oizAW163 I171
TRT1-[2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY]-4-(2,4,4-TRIMETHYLPENTAN-2-YL)BENZENE1oizAW163 V206 I222


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Conservation information for LBS of TTPA
Multiple alignments for P49638 in multiple species
LBSAA sequence# speciesSpecies
A129PKVFTAYDVFR3Homo sapiens, Mus musculus, Rattus norvegicus
A156RNGVKAIFDLE2Mus musculus, Rattus norvegicus
A156RNGIKAIFDLE1Homo sapiens
A168WQFSHAFQITP1Homo sapiens
A168WQVSHAFQITP1Mus musculus
A168WQISHAFQITP1Rattus norvegicus
F133TAYDVFRVSLI3Homo sapiens, Mus musculus, Rattus norvegicus
F158GVKAIFDLEGW2Mus musculus, Rattus norvegicus
F158GIKAIFDLEGW1Homo sapiens
F165LEGWQFSHAFQ1Homo sapiens
F165LEGWQVSHAFQ1Mus musculus
F165LEGWQISHAFQ1Rattus norvegicus
F187VLTDSFPLKVR2Homo sapiens, Mus musculus
F187VVTDSFPLKVR1Rattus norvegicus
F203NEPVIFHAVFS3Homo sapiens, Mus musculus, Rattus norvegicus
F207IFHAVFSMIKP3Homo sapiens, Mus musculus, Rattus norvegicus
I119VLIYRIAHWDP1Homo sapiens
I119VLIYRIAYWDP1Mus musculus
I119VLIYRISYWDP1Rattus norvegicus
I143ITSELIVQEVE3Homo sapiens, Mus musculus, Rattus norvegicus
I154TQRNGVKAIFD2Mus musculus, Rattus norvegicus
I154TQRNGIKAIFD1Homo sapiens
I171SHAFQITPSVA3Homo sapiens, Mus musculus, Rattus norvegicus
I179SVAKKIAAVLT2Homo sapiens, Mus musculus
I179SVAKKIAAVVT1Rattus norvegicus
I194LKVRGIHLINE3Homo sapiens, Mus musculus, Rattus norvegicus
I202INEPVIFHAVF3Homo sapiens, Mus musculus, Rattus norvegicus
I210AVFSMIKPFLT3Homo sapiens, Mus musculus, Rattus norvegicus
I222KIKERIHMHGN1Homo sapiens
I222KIKDRIHLHGN1Mus musculus
I222KIKGRIHLHGN1Rattus norvegicus
L115TGSKVLIYRIA1Homo sapiens
L115TGSRVLIYRIA1Mus musculus
L115TGSRVLIYRIS1Rattus norvegicus
L137VFRVSLITSEL3Homo sapiens, Mus musculus, Rattus norvegicus
L160KAIFDLEGWQF1Homo sapiens
L160KAIFDLEGWQV1Mus musculus
L160KAIFDLEGWQI1Rattus norvegicus
L189TDSFPLKVRGI3Homo sapiens, Mus musculus, Rattus norvegicus
L214MIKPFLTEKIK3Homo sapiens, Mus musculus, Rattus norvegicus
L47LAPLPLTDSFL1Homo sapiens
L47QTPQPLTDAFL1Mus musculus
L47ETPQPLTDAFL1Rattus norvegicus
M224KERIHMHGNNY1Homo sapiens
M224KDRIHLHGNNY1Mus musculus
M224KGRIHLHGNNY1Rattus norvegicus
S136DVFRVSLITSE3Homo sapiens, Mus musculus, Rattus norvegicus
S140VSLITSELIVQ3Homo sapiens, Mus musculus, Rattus norvegicus
V132FTAYDVFRVSL3Homo sapiens, Mus musculus, Rattus norvegicus
V182KKIAAVLTDSF2Homo sapiens, Mus musculus
V182KKIAAVVTDSF1Rattus norvegicus
V191SFPLKVRGIHL3Homo sapiens, Mus musculus, Rattus norvegicus
V206VIFHAVFSMIK3Homo sapiens, Mus musculus, Rattus norvegicus
W122YRIAHWDPKVF1Homo sapiens
W122YRIAYWDPKVF1Mus musculus
W122YRISYWDPKVF1Rattus norvegicus
W163FDLEGWQFSHA1Homo sapiens
W163FDLEGWQVSHA1Mus musculus
W163FDLEGWQISHA1Rattus norvegicus
Y100LLKAGYHGVLR3Homo sapiens, Mus musculus, Rattus norvegicus
Y117SKVLIYRIAHW1Homo sapiens
Y117SRVLIYRIAYW1Mus musculus
Y117SRVLIYRISYW1Rattus norvegicus


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