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mutLBSgeneDB |
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| Gene summary for PSEN1 |
 Gene summary |
| Basic gene Info. | Gene symbol | PSEN1 |
| Gene name | presenilin 1 | |
| Synonyms | AD3|FAD|PS-1|PS1|S182 | |
| Cytomap | UCSC genome browser: 14q24.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000021.3, NM_007318.2,NM_007319.1, | |
| Description | presenilin-1 | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 104311 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000080815 | ||
| HPRD : 00087 | ||
| Vega : OTTHUMG00000141279 | ||
| Protein | UniProt: P49768 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_PSEN1 | |
| BioGPS: 5663 | ||
| Pathway | NCI Pathway Interaction Database: PSEN1 | |
| KEGG: PSEN1 | ||
| REACTOME: PSEN1 | ||
| Pathway Commons: PSEN1 | ||
| Context | iHOP: PSEN1 | |
| ligand binding site mutation search in PubMed: PSEN1 | ||
| UCL Cancer Institute: PSEN1 | ||
| Assigned class in mutLBSgeneDB | B: This gene belongs to targetable_mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0006509 | membrane protein ectodomain proteolysis | 15274632 | GO:0016485 | protein processing | 15274632 | GO:0032469 | endoplasmic reticulum calcium ion homeostasis | 17431506 | GO:0042325 | regulation of phosphorylation | 9689133 | GO:0043066 | negative regulation of apoptotic process | 10805794 | GO:0043085 | positive regulation of catalytic activity | 15274632 |
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| Ligand binding site mutations for PSEN1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | M233 | A234D | LUAD | 1 | Y240 | L241F | LUSC | 1 | F176 | F175L | UCEC | 1 |
| 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 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 |
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| 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. |
| LBS | AAchange of nsSNV | Relative stability change | Y240 | L241F | -1.4452558 | F176 | F175L | -1.1333863 | M233 | A234D | -0.70515764 |
| (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 |
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| 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) |
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| Phenotype information for PSEN1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0002395 | Alzheimer Disease | 177 | AlteredExpression, Biomarker, GeneticVariation |
| umls:C0236642 | Pick Disease of the Brain | 19 | Biomarker, GeneticVariation |
| umls:C0338451 | Frontotemporal Dementia | 17 | Biomarker, GeneticVariation |
| umls:C0007193 | Cardiomyopathy, Dilated | 3 | Biomarker, GeneticVariation |
| umls:C1843013 | Alzheimer disease, familial, type 3 | 1 | Biomarker, GeneticVariation |
| umls:C0004045 | Asphyxia Neonatorum | 1 | Biomarker |
| umls:C0012644 | Disease Models, Animal | 1 | Biomarker |
| umls:C0017661 | Glomerulonephritis, IGA | 1 | Biomarker |
| umls:C1840560 | Hidradenitis suppurativa, familial | 1 | Biomarker |
| umls:C0027746 | Nerve Degeneration | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| 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. |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of PSEN1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA) | 5fn3 | B | F176 M233 Y240 | III | Peptide ligand (ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA,ALA) | 5fn4 | B | F176 Y240 |
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| Conservation information for LBS of PSEN1 |
| Multiple alignments for P49768 in multiple species |
| LBS | AA sequence | # species | Species | F176 | LLLLFFFSFIY | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F176 | FLLLFLFTTIY | 1 | Caenorhabditis elegans | F176 | LLLLFFFSLIY | 1 | Danio rerio | F176 | FIVLGNLGGEI | 1 | Arabidopsis thaliana | F176 | FFVLGTMGGAI | 1 | Arabidopsis thaliana | F177 | LLLFFFSFIYL | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F177 | LLLFLFTTIYV | 1 | Caenorhabditis elegans | F177 | LLLFFFSLIYL | 1 | Danio rerio | F177 | IVLGNLGGEIL | 1 | Arabidopsis thaliana | F177 | FVLGTMGGAIF | 1 | Arabidopsis thaliana | F237 | LMALVFIKYLP | 6 | Homo sapiens, Caenorhabditis elegans, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus | F237 | LVAYFFTL-LP | 1 | Arabidopsis thaliana | F237 | VVAAWFTK-LP | 1 | Arabidopsis thaliana | F283 | RNETLFPALIY | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F283 | RNEPIFPALIY | 1 | Caenorhabditis elegans | F283 | RNEAIFPALIY | 1 | Danio rerio | F283 | RDEDI-PALVY | 1 | Arabidopsis thaliana | F283 | RDEEL-PAMVY | 1 | Arabidopsis thaliana | M139 | LNAAIMISVIV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M139 | GNALVMLCVVV | 1 | Caenorhabditis elegans | M139 | LNAIIMISVIV | 1 | Danio rerio | M139 | LNAVIMISVIV | 1 | Bos taurus | M139 | LNSVVFVAAIT | 1 | Arabidopsis thaliana | M139 | ANAIVFVVLIA | 1 | Arabidopsis thaliana | M146 | SVIVVMTILLV | 2 | Homo sapiens, Rattus norvegicus | M146 | SVIVIMTILLV | 2 | Bos taurus, Mus musculus | M146 | CVVVLMTVLLI | 1 | Caenorhabditis elegans | M146 | SVIVVMTLVLV | 1 | Danio rerio | M146 | AAITVATFVLV | 1 | Arabidopsis thaliana | M146 | VLIAAVTFILV | 1 | Arabidopsis thaliana | M233 | MISALMALVFI | 5 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus | M233 | TMSALMALVFI | 1 | Caenorhabditis elegans | M233 | WIGVLVAYFFT | 1 | Arabidopsis thaliana | M233 | VMGIVVAAWFT | 1 | Arabidopsis thaliana | Q112 | TRKDGQ-LIYT | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Q112 | SQNNGRHLLYT | 1 | Caenorhabditis elegans | Q112 | TQKDGQQLIYT | 1 | Danio rerio | Q112 | SSASFSSIATA | 1 | Arabidopsis thaliana | Q112 | SDPQIRSAANL | 1 | Arabidopsis thaliana | S169 | AWLIISSLLLL | 2 | Homo sapiens, Mus musculus | S169 | AWLIVSSLLLL | 2 | Bos taurus, Rattus norvegicus | S169 | GWLIVSSFLLL | 1 | Caenorhabditis elegans | S169 | AWLFFSNLLLL | 1 | Danio rerio | S169 | FYMGFSAFIVL | 1 | Arabidopsis thaliana | S169 | HYMRFSAFFVL | 1 | Arabidopsis thaliana | T147 | VIVVMTILLVV | 2 | Homo sapiens, Rattus norvegicus | T147 | VIVIMTILLVV | 2 | Bos taurus, Mus musculus | T147 | VVVLMTVLLIV | 1 | Caenorhabditis elegans | T147 | VIVVMTLVLVV | 1 | Danio rerio | T147 | AITVATFVLVL | 1 | Arabidopsis thaliana | T147 | LIAAVTFILVL | 1 | Arabidopsis thaliana | Y115 | GQ-LIYTPFTE | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Y115 | GRHLLYTPFVR | 1 | Caenorhabditis elegans | Y115 | GQQLIYTPFRE | 1 | Danio rerio | Y115 | FSSIATAAYSE | 1 | Arabidopsis thaliana | Y115 | IRSAANLIYIE | 1 | Arabidopsis thaliana | Y240 | LVFIKYLPEWT | 6 | Homo sapiens, Caenorhabditis elegans, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus | Y240 | YFFTL-LPEWT | 1 | Arabidopsis thaliana | Y240 | AWFTK-LPEWT | 1 | Arabidopsis thaliana |
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