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 PSEN1
Gene summary
Basic gene Info.Gene symbolPSEN1
Gene namepresenilin 1
CytomapUCSC genome browser: 14q24.3
Type of geneprotein-coding
Modification date20141222
dbXrefs MIM : 104311
Ensembl : ENSG00000080815
HPRD : 00087
Vega : OTTHUMG00000141279
ProteinUniProt: P49768
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PSEN1
BioGPS: 5663
PathwayNCI Pathway Interaction Database: PSEN1
Pathway Commons: PSEN1
ContextiHOP: PSEN1
ligand binding site mutation search in PubMed: PSEN1
UCL Cancer Institute: PSEN1
Assigned class in mutLBSgeneDBB: This gene belongs to targetable_mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO:0006509membrane protein ectodomain proteolysis15274632
GO:0016485protein processing15274632
GO:0032469endoplasmic reticulum calcium ion homeostasis17431506
GO:0042325regulation of phosphorylation9689133
GO:0043066negative regulation of apoptotic process10805794
GO:0043085positive regulation of catalytic activity15274632

Ligand binding site mutations for PSEN1

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for PSEN1
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 PSEN1 from PDB

Differential gene expression and gene-gene network for PSEN1
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 PSEN1 and the right PPI network was created from samples without mutations in the LBS of PSEN1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for PSEN1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0002395Alzheimer Disease177AlteredExpression, Biomarker, GeneticVariation
umls:C0236642Pick Disease of the Brain19Biomarker, GeneticVariation
umls:C0338451Frontotemporal Dementia17Biomarker, GeneticVariation
umls:C0007193Cardiomyopathy, Dilated3Biomarker, GeneticVariation
umls:C1843013Alzheimer disease, familial, type 31Biomarker, GeneticVariation
umls:C0004045Asphyxia Neonatorum1Biomarker
umls:C0012644Disease Models, Animal1Biomarker
umls:C0017661Glomerulonephritis, IGA1Biomarker
umls:C1840560Hidradenitis suppurativa, familial1Biomarker
umls:C0027746Nerve Degeneration1Biomarker

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

Pharmacological information for PSEN1
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 PSEN1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of PSEN1
Multiple alignments for P49768 in multiple species
LBSAA sequence# speciesSpecies
F176LLLLFFFSFIY4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F176FLLLFLFTTIY1Caenorhabditis elegans
F176LLLLFFFSLIY1Danio rerio
F176FIVLGNLGGEI1Arabidopsis thaliana
F176FFVLGTMGGAI1Arabidopsis thaliana
F177LLLFFFSFIYL4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F177LLLFLFTTIYV1Caenorhabditis elegans
F177LLLFFFSLIYL1Danio rerio
F177IVLGNLGGEIL1Arabidopsis thaliana
F177FVLGTMGGAIF1Arabidopsis thaliana
F237LMALVFIKYLP6Homo sapiens, Caenorhabditis elegans, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
F237LVAYFFTL-LP1Arabidopsis thaliana
F237VVAAWFTK-LP1Arabidopsis thaliana
F283RNETLFPALIY4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F283RNEPIFPALIY1Caenorhabditis elegans
F283RNEAIFPALIY1Danio rerio
F283RDEDI-PALVY1Arabidopsis thaliana
F283RDEEL-PAMVY1Arabidopsis thaliana
M139LNAAIMISVIV3Homo sapiens, Mus musculus, Rattus norvegicus
M139GNALVMLCVVV1Caenorhabditis elegans
M139LNAIIMISVIV1Danio rerio
M139LNAVIMISVIV1Bos taurus
M139LNSVVFVAAIT1Arabidopsis thaliana
M139ANAIVFVVLIA1Arabidopsis thaliana
M146SVIVVMTILLV2Homo sapiens, Rattus norvegicus
M146SVIVIMTILLV2Bos taurus, Mus musculus
M146CVVVLMTVLLI1Caenorhabditis elegans
M146SVIVVMTLVLV1Danio rerio
M146AAITVATFVLV1Arabidopsis thaliana
M146VLIAAVTFILV1Arabidopsis thaliana
M233MISALMALVFI5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
M233TMSALMALVFI1Caenorhabditis elegans
M233WIGVLVAYFFT1Arabidopsis thaliana
M233VMGIVVAAWFT1Arabidopsis thaliana
Q112TRKDGQ-LIYT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Q112SQNNGRHLLYT1Caenorhabditis elegans
Q112TQKDGQQLIYT1Danio rerio
Q112SSASFSSIATA1Arabidopsis thaliana
Q112SDPQIRSAANL1Arabidopsis thaliana
S169AWLIISSLLLL2Homo sapiens, Mus musculus
S169AWLIVSSLLLL2Bos taurus, Rattus norvegicus
S169GWLIVSSFLLL1Caenorhabditis elegans
S169AWLFFSNLLLL1Danio rerio
S169FYMGFSAFIVL1Arabidopsis thaliana
S169HYMRFSAFFVL1Arabidopsis thaliana
T147VIVVMTILLVV2Homo sapiens, Rattus norvegicus
T147VIVIMTILLVV2Bos taurus, Mus musculus
T147VVVLMTVLLIV1Caenorhabditis elegans
T147VIVVMTLVLVV1Danio rerio
T147AITVATFVLVL1Arabidopsis thaliana
T147LIAAVTFILVL1Arabidopsis thaliana
Y115GQ-LIYTPFTE4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Y115GRHLLYTPFVR1Caenorhabditis elegans
Y115GQQLIYTPFRE1Danio rerio
Y115FSSIATAAYSE1Arabidopsis thaliana
Y115IRSAANLIYIE1Arabidopsis thaliana
Y240LVFIKYLPEWT6Homo sapiens, Caenorhabditis elegans, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
Y240YFFTL-LPEWT1Arabidopsis thaliana
Y240AWFTK-LPEWT1Arabidopsis thaliana

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