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mutLBSgeneDB |
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| Gene summary for APP |
 Gene summary |
| Basic gene Info. | Gene symbol | APP |
| Gene name | amyloid beta (A4) precursor protein | |
| Synonyms | AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2 | |
| Cytomap | UCSC genome browser: 21q21.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000484.3, NM_001136016.3,NM_001136129.2,NM_001136130.2,NM_001136131.2, NM_001204301.1,NM_001204302.1,NM_001204303.1,NM_201413.2, NM_201414.2, | |
| Description | alzheimer disease amyloid proteinamyloid beta A4 proteinbeta-amyloid peptidebeta-amyloid peptide(1-40)beta-amyloid peptide(1-42)cerebral vascular amyloid peptidepeptidase nexin-IIpreA4protease nexin-II | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 104760 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000142192 | ||
| HPRD : 00100 | ||
| Vega : OTTHUMG00000078438 | ||
| Protein | UniProt: P05067 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_APP | |
| BioGPS: 351 | ||
| Pathway | NCI Pathway Interaction Database: APP | |
| KEGG: APP | ||
| REACTOME: APP | ||
| Pathway Commons: APP | ||
| Context | iHOP: APP | |
| ligand binding site mutation search in PubMed: APP | ||
| UCL Cancer Institute: APP | ||
| Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. | |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO Term | PubMed ID | GO:0010951 | negative regulation of endopeptidase activity | 10652580 |
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| Ligand binding site mutations for APP |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | E443 | S441Y | UCEC | 2 | S159 | C158Y | COAD | 1 | P173 | P173L | SKCM | 1 | H684 | H684Q | UCEC | 1 | G700 | A701V | UCEC | 1 | H147 | E145K | UCEC | 1 | Q686,H684 | H685R | 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 APP |
| 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 | P173 | P173L | -0.94178008 | G700 | A701V | -0.7898473 | E443 | S441Y | -0.48397963 | S159 | C158Y | -0.45235528 | H684 | H684Q | -0.44959145 | H147 | E145K | -0.44824076 | Q686 | H685R | -0.041854024 | H684 | H685R | -0.041854024 |
| (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 APP from PDB |
| PDB ID | PDB title | PDB structure | 1AAP | X-RAY CRYSTAL STRUCTURE OF THE PROTEASE INHIBITOR DOMAIN OF ALZHEIMER'S AMYLOID BETA-PROTEIN PRECURSOR |  |
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| Differential gene expression and gene-gene network for APP |
| 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 APP |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0002395 | Alzheimer Disease | 215 | AlteredExpression, Biomarker, GeneticVariation, PostTranslationalModification |
| umls:C2936349 | Plaque, Amyloid | 73 | Biomarker, GeneticVariation |
| umls:C0497327 | Dementia | 30 | AlteredExpression, Biomarker, GeneticVariation |
| umls:C0085220 | Cerebral Amyloid Angiopathy | 20 | Biomarker, GeneticVariation |
| umls:C0027746 | Nerve Degeneration | 9 | Biomarker |
| umls:C0025261 | Memory Disorders | 7 | Biomarker |
| umls:C0524851 | Neurodegenerative Diseases | 6 | Biomarker |
| umls:C0003469 | Anxiety Disorders | 4 | Biomarker |
| umls:C0002622 | Amnesia | 4 | Biomarker |
| umls:C0023186 | Learning Disorders | 4 | Biomarker |
| umls:C0522224 | Paralysis | 4 | Biomarker |
| umls:C0009241 | Cognition Disorders | 3 | Biomarker |
| umls:C0016667 | Fragile X Syndrome | 2 | Biomarker, Therapeutic |
| umls:C2931672 | Cerebral hemorrhage with amyloidosis, hereditary, Dutch type | 2 | Biomarker |
| umls:C0012644 | Disease Models, Animal | 2 | Biomarker |
| umls:C0231341 | Aging, Premature | 1 | Biomarker |
| umls:C0006111 | Brain Diseases | 1 | Biomarker |
| umls:C0027540 | Necrosis | 1 | Biomarker |
| umls:C0600467 | Neurogenic Inflammation | 1 | Biomarker |
| umls:C0037928 | Spinal Cord Diseases | 1 | Biomarker |
| umls:C0043094 | Weight Gain | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for APP |
| 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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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Experimental | DB02235 | L-methionine (R)-S-oxide | Small molecule |  |
| Investigational | DB05150 | CAD106 | Small molecule |  |
| Investigational | DB05846 | Mito-4509 | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of APP go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | CU | COPPER(2+) | 2fk1 | A | H147 | CU1 | COPPER(1+) | 2fk2 | A | H147 | BU4 | (R)-BUTANE-1,3-DIOL | 3ktm | A | P173 | BU4 | (R)-BUTANE-1,3-DIOL | 3ktm | G | P173 | CU | COPPER(2+) | 2fk3 | F | S159 |
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| Conservation information for LBS of APP |
| Multiple alignments for P05067 in multiple species |
| LBS | AA sequence | # species | Species | C174 | GMLLPCGIDKF | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | C174 | AVLEPCALDMF | 1 | Caenorhabditis elegans | D504 | RAEQKDRQHTL | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | D504 | RAEEKDRMHTL | 1 | Caenorhabditis elegans | E139 | KFLHQERMDVC | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | E139 | QFSHVNSRDQC | 1 | Caenorhabditis elegans | E443 | KVESLEQEAAN | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | E443 | TVSSLEEEHKR | 1 | Caenorhabditis elegans | E462 | HMARVEAMLND | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | E462 | HEERVQAMLNE | 1 | Caenorhabditis elegans | E682 | HDSGYEVHHQK | 2 | Homo sapiens, Pan troglodytes | E682 | HDSGFEVRHQK | 2 | Mus musculus, Rattus norvegicus | E682 | IDEPASFYRHD | 1 | Caenorhabditis elegans | F690 | HQKLVFFAEDV | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | F690 | RHDKLIQSPEV | 1 | Caenorhabditis elegans | G175 | MLLPCGIDKFR | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | G175 | VLEPCALDMFT | 1 | Caenorhabditis elegans | G680 | FRHDSGYEVHH | 2 | Homo sapiens, Pan troglodytes | G680 | FGHDSGFEVRH | 2 | Mus musculus, Rattus norvegicus | G680 | PIIDEPASFYR | 1 | Caenorhabditis elegans | G700 | VGSNKGAIIG- | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | G700 | VERSASSVFQP | 1 | Caenorhabditis elegans | H108 | KQCKTHPHFVI | 2 | Homo sapiens, Pan troglodytes | H108 | KQCKTHTHIVI | 2 | Mus musculus, Rattus norvegicus | H108 | SPCK-WTHSVR | 1 | Caenorhabditis elegans | H110 | CKTHPHFVIPY | 2 | Homo sapiens, Pan troglodytes | H110 | CKTHTHIVIPY | 2 | Mus musculus, Rattus norvegicus | H110 | CK-WTHSVRPY | 1 | Caenorhabditis elegans | H137 | KCKFLHQERMD | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H137 | DCQFSHVNSRD | 1 | Caenorhabditis elegans | H147 | DVCETHLHWHT | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H147 | DQCNDYQHWKD | 1 | Caenorhabditis elegans | H151 | THLHWHTVAKE | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H151 | DYQHWKDEAGK | 1 | Caenorhabditis elegans | H166 | ----LHDYGML | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H166 | KDMIVRSFAVL | 1 | Caenorhabditis elegans | H388 | GDENEHAHFQK | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H388 | NWTNEHDDFKK | 1 | Caenorhabditis elegans | H402 | RLEAKHRERMS | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H402 | RMDEKHRKKVD | 1 | Caenorhabditis elegans | H457 | QLVETHMARVE | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H457 | EIEAVHEERVQ | 1 | Caenorhabditis elegans | H507 | QKDRQHTLKHF | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H507 | EKDRMHTLNRY | 1 | Caenorhabditis elegans | H511 | QHTLKHFEHVR | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H511 | MHTLNRYRHLL | 1 | Caenorhabditis elegans | H533 | SQVMTHLRVIY | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | H533 | PTVIHRLRYID | 1 | Caenorhabditis elegans | H684 | SGYEVHHQKLV | 2 | Homo sapiens, Pan troglodytes | H684 | SGFEVRHQKLV | 2 | Mus musculus, Rattus norvegicus | H684 | EPASFYRHDKL | 1 | Caenorhabditis elegans | I176 | LLPCGIDKFRG | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | I176 | LEPCALDMFTG | 1 | Caenorhabditis elegans | K699 | DVGSNKGAIIG | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | K699 | EVERSASSVFQ | 1 | Caenorhabditis elegans | L165 | -----LHDYGM | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | L165 | NKDMIVRSFAV | 1 | Caenorhabditis elegans | N164 | SEKSTN----- | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | N164 | KTKKSKGNKDM | 1 | Caenorhabditis elegans | N466 | VEAMLNDRRRL | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | N466 | VQAMLNEKKRD | 1 | Caenorhabditis elegans | N84 | ELQITNVVEAN | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | N84 | SMNITNIVEYS | 1 | Caenorhabditis elegans | P173 | YGMLLPCGIDK | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | P173 | FAVLEPCALDM | 1 | Caenorhabditis elegans | Q686 | YEVHHQKLVFF | 2 | Homo sapiens, Pan troglodytes | Q686 | FEVRHQKLVFF | 2 | Mus musculus, Rattus norvegicus | Q686 | ASFYRHDKLIQ | 1 | Caenorhabditis elegans | R40 | AMFCGRLNMHM | 2 | Homo sapiens, Pan troglodytes | R40 | AMFCGKLNMHM | 2 | Mus musculus, Rattus norvegicus | R40 | AFSCGYRNQYM | 1 | Caenorhabditis elegans | S159 | AKETCSEKSTN | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | S159 | AGKQCKTKKSK | 1 | Caenorhabditis elegans | S697 | AEDVGSNKGAI | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | S697 | SPEVERSASSV | 1 | Caenorhabditis elegans | T163 | CSEKSTN---- | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | T163 | CKTKKSKGNKD | 1 | Caenorhabditis elegans | T83 | PELQITNVVEA | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | T83 | PSMNITNIVEY | 1 | Caenorhabditis elegans | V683 | DSGYEVHHQKL | 2 | Homo sapiens, Pan troglodytes | V683 | DSGFEVRHQKL | 2 | Mus musculus, Rattus norvegicus | V683 | DEPASFYRHDK | 1 | Caenorhabditis elegans | Y168 | --LHDYGMLLP | 4 | Homo sapiens, Pan troglodytes, Mus musculus, Rattus norvegicus | Y168 | MIVRSFAVLEP | 1 | Caenorhabditis elegans | Y681 | RHDSGYEVHHQ | 2 | Homo sapiens, Pan troglodytes | Y681 | GHDSGFEVRHQ | 2 | Mus musculus, Rattus norvegicus | Y681 | IIDEPASFYRH | 1 | Caenorhabditis elegans |
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