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mutLBSgeneDB |
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| Gene summary for APEX1 |
 Gene summary |
| Basic gene Info. | Gene symbol | APEX1 |
| Gene name | APEX nuclease (multifunctional DNA repair enzyme) 1 | |
| Synonyms | APE|APE1|APEN|APEX|APX|HAP1|REF1 | |
| Cytomap | UCSC genome browser: 14q11.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001244249.1, NM_001641.3,NM_080648.2,NM_080649.2, | |
| Description | AP endonuclease class IAP lyaseDNA-(apurinic or apyrimidinic site) lyaseapurinic-apyrimidinic endonuclease 1apurinic/apyrimidinic (abasic) endonucleasedeoxyribonuclease (apurinic or apyrimidinic)protein REF-1redox factor-1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 107748 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000100823 | ||
| HPRD : 00136 | ||
| Vega : OTTHUMG00000029544 | ||
| Protein | UniProt: P27695 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_APEX1 | |
| BioGPS: 328 | ||
| Pathway | NCI Pathway Interaction Database: APEX1 | |
| KEGG: APEX1 | ||
| REACTOME: APEX1 | ||
| Pathway Commons: APEX1 | ||
| Context | iHOP: APEX1 | |
| ligand binding site mutation search in PubMed: APEX1 | ||
| UCL Cancer Institute: APEX1 | ||
| 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:0000737 | DNA catabolic process, endonucleolytic | 19188445 | GO:0006281 | DNA repair | 9560228 | GO:0045739 | positive regulation of DNA repair | 9207062 | GO:0055114 | oxidation-reduction process | 12524539 | GO:0080111 | DNA demethylation | 21496894 |
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| Ligand binding site mutations for APEX1 |
| 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. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | A230 | A230D | COAD | 1 | Y128 | G130D | COAD | 1 | N222 | R221H | COAD | 1 | A273 | R274Q | COAD | 1 | A230 | A230T | COAD | 1 | E101 | N102I | STAD | 1 | N222 | R221H | 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 APEX1 |
| 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 | A273 | R274Q | -1.5322079 | N222 | R221H | -1.2885176 | A230 | A230D | -0.82875275 | A230 | A230T | -0.73454076 | E101 | N102I | -0.59660768 | Y128 | G130D | -0.2813466 |
| (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 APEX1 from PDB |
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| Differential gene expression and gene-gene network for APEX1 |
| 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 APEX1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0025202 | Melanoma | 8 | Biomarker, GeneticVariation |
| umls:C0038356 | Stomach Neoplasms | 4 | Biomarker, GeneticVariation |
| umls:C0036572 | Seizures | 2 | Biomarker |
| umls:C0270611 | Brain Injuries | 1 | Biomarker |
| umls:C0242656 | Disease Progression | 1 | Biomarker |
| umls:C0018799 | Heart Diseases | 1 | Biomarker |
| umls:C1449861 | Micronuclei, Chromosome-Defective | 1 | Biomarker |
| umls:C0033578 | Prostatic Neoplasms | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for APEX1 |
| 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 |
| Approved|investigational | DB04967 | Lucanthone | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of APEX1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | NUC | Nucleic Acids | 4iem | A | A230 | NUC | Nucleic Acids | 4iem | C | A230 | NUC | Nucleic Acids | 4iem | D | A230 | NUC | Nucleic Acids | 4iem | B | A230 A273 | NUC | Nucleic Acids | 1de9 | A | E101 | NUC | Nucleic Acids | 1de9 | A | N222 A230 | NUC | Nucleic Acids | 1de9 | B | N222 A230 | NUC | Nucleic Acids | 5dff | A | N222 A230 | NUC | Nucleic Acids | 5dfh | A | N222 A230 | NUC | Nucleic Acids | 1de9 | A | Y128 | NUC | Nucleic Acids | 1de9 | B | Y128 | NUC | Nucleic Acids | 4iem | A | Y128 | NUC | Nucleic Acids | 4iem | B | Y128 | NUC | Nucleic Acids | 4iem | C | Y128 | NUC | Nucleic Acids | 4iem | D | Y128 | NUC | Nucleic Acids | 5dff | A | Y128 | NUC | Nucleic Acids | 5dfh | A | Y128 | NUC | Nucleic Acids | 1de8 | A | Y128 A230 | NUC | Nucleic Acids | 5dfj | A | Y128 N222 | NUC | Nucleic Acids | 1de8 | B | Y128 N222 A230 | NUC | Nucleic Acids | 1dew | A | Y128 N222 A230 | NUC | Nucleic Acids | 1dew | B | Y128 N222 A230 | NUC | Nucleic Acids | 5dfi | A | Y128 N222 A230 | NUC | Nucleic Acids | 5dg0 | A | Y128 N222 A230 |
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| Conservation information for LBS of APEX1 |
| Multiple alignments for P27695 in multiple species |
| LBS | AA sequence | # species | Species | A230 | GNKKNAGFTPQ | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | A230 | GNKRSAGFTIE | 1 | Arabidopsis thaliana | A230 | GNRKNAGFTPE | 1 | Danio rerio | A273 | TYMMNARSKNV | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | A273 | GYRHGGRKTNK | 1 | Arabidopsis thaliana | A74 | VDGLRAWIKKK | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | A74 | VNGLRGLLKFE | 1 | Arabidopsis thaliana | A74 | VDGLRAWVKKN | 1 | Danio rerio | D210 | LVLCGDLNVAH | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | D210 | VVLTGDLNCAH | 1 | Arabidopsis thaliana | D308 | KALGSDHCPIT | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | D308 | DINGSDHCPIG | 1 | Arabidopsis thaliana | D308 | TAMGSDHCPIT | 1 | Danio rerio | D70 | CSWNVDGLRAW | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | D70 | MTWNVNGLRGL | 1 | Arabidopsis thaliana | D70 | TSWNVDGLRAW | 1 | Danio rerio | E101 | ETKCSENKL-P | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | E101 | ETKLQVKDVEE | 1 | Arabidopsis thaliana | E101 | ETKCAEKAL-P | 1 | Danio rerio | E126 | APSDKEGYSGV | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | E126 | CSVSKLGYSGT | 1 | Arabidopsis thaliana | E126 | GSEDKEGYSGV | 1 | Danio rerio | E96 | ILCLQETKCSE | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | E96 | ILCLQETKLQV | 1 | Arabidopsis thaliana | E96 | ILCLQETKCAE | 1 | Danio rerio | F266 | AYAYTFWTYMM | 4 | Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus | F266 | PYAYTFWTYMM | 2 | Homo sapiens, Pan troglodytes | F266 | V-GYTYWGYRH | 1 | Arabidopsis thaliana | G127 | PSDKEGYSGVG | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | G127 | SVSKLGYSGTA | 1 | Arabidopsis thaliana | G127 | SEDKEGYSGVA | 1 | Danio rerio | G178 | PNAGRGLVRLE | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | G178 | PNSGDGLKRLS | 1 | Arabidopsis thaliana | G178 | PNASRGLVRLD | 1 | Danio rerio | G225 | LRNPKGNKKNA | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | G225 | IFNPAGNKRSA | 1 | Arabidopsis thaliana | G225 | LKNPKGNRKNA | 1 | Danio rerio | G71 | SWNVDGLRAWI | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | G71 | TWNVNGLRGLL | 1 | Arabidopsis thaliana | G71 | SWNVDGLRAWV | 1 | Danio rerio | H309 | ALGSDHCPITL | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | H309 | INGSDHCPIGL | 1 | Arabidopsis thaliana | H309 | AMGSDHCPITL | 1 | Danio rerio | K224 | DLRNPKGNKKN | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | K224 | DIFNPAGNKRS | 1 | Arabidopsis thaliana | K224 | DLKNPKGNRKN | 1 | Danio rerio | K228 | PKGNKKNAGFT | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | K228 | PAGNKRSAGFT | 1 | Arabidopsis thaliana | K228 | PKGNRKNAGFT | 1 | Danio rerio | K276 | MNARSKNVGWR | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | K276 | HGGRKTNKGWR | 1 | Arabidopsis thaliana | K78 | RAWIKKK---G | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | K78 | RGLLKFESFSA | 1 | Arabidopsis thaliana | K78 | RAWVKKN---G | 1 | Danio rerio | K98 | CLQETKCSENK | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | K98 | CLQETKLQVKD | 1 | Arabidopsis thaliana | K98 | CLQETKCAEKA | 1 | Danio rerio | L179 | NAGRGLVRLEY | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | L179 | NSGDGLKRLSY | 1 | Arabidopsis thaliana | L179 | NASRGLVRLDY | 1 | Danio rerio | L282 | NVGWRLDYFLL | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | L282 | NKGWRLDYFLV | 1 | Arabidopsis thaliana | L282 | NVGWRLDYFVL | 1 | Danio rerio | M270 | TFWTYMMNARS | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | M270 | TYWGYRHGGRK | 1 | Arabidopsis thaliana | M271 | FWTYMMNARSK | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | M271 | YWGYRHGGRKT | 1 | Arabidopsis thaliana | N174 | TAYVPNAGRGL | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | N174 | NTYVPNSGDGL | 1 | Arabidopsis thaliana | N174 | TAYVPNASRGL | 1 | Danio rerio | N212 | LCGDLNVAHEE | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | N212 | LTGDLNCAHEE | 1 | Arabidopsis thaliana | N212 | LCGDLNVAHQE | 1 | Danio rerio | N222 | EIDLRNPKGNK | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | N222 | EIDIFNPAGNK | 1 | Arabidopsis thaliana | N222 | EIDLKNPKGNR | 1 | Danio rerio | N226 | RNPKGNKKNAG | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | N226 | FNPAGNKRSAG | 1 | Arabidopsis thaliana | N226 | KNPKGNRKNAG | 1 | Danio rerio | N229 | KGNKKNAGFTP | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | N229 | AGNKRSAGFTI | 1 | Arabidopsis thaliana | N229 | KGNRKNAGFTP | 1 | Danio rerio | N68 | KICSWNVDGLR | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | N68 | KVMTWNVNGLR | 1 | Arabidopsis thaliana | N68 | KITSWNVDGLR | 1 | Danio rerio | R177 | VPNAGRGLVRL | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | R177 | VPNSGDGLKRL | 1 | Arabidopsis thaliana | R177 | VPNASRGLVRL | 1 | Danio rerio | R181 | GRGLVRLEYR- | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | R181 | GDGLKRLSYRI | 1 | Arabidopsis thaliana | R181 | SRGLVRLDYR- | 1 | Danio rerio | R73 | NVDGLRAWIKK | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | R73 | NVNGLRGLLKF | 1 | Arabidopsis thaliana | R73 | NVDGLRAWVKK | 1 | Danio rerio | T268 | AYTFWTYMMNA | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | T268 | GYTYWGYRHGG | 1 | Arabidopsis thaliana | V278 | ARSKNVGWRLD | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | V278 | GRKTNKGWRLD | 1 | Arabidopsis thaliana | W280 | SKNVGWRLDYF | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | W280 | KTNKGWRLDYF | 1 | Arabidopsis thaliana | Y128 | SDKEGYSGVGL | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | Y128 | VSKLGYSGTAI | 1 | Arabidopsis thaliana | Y128 | EDKEGYSGVAM | 1 | Danio rerio | Y171 | VLVTAYVPNAG | 4 | Homo sapiens, Bos taurus, Mus musculus, Pan troglodytes | Y171 | YLINTYVPNSG | 1 | Arabidopsis thaliana | Y171 | FLVTAYVPNAS | 1 | Danio rerio | Y171 | ILVTAYVPNAG | 1 | Rattus norvegicus | Y269 | YTFWTYMMNAR | 6 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus, Pan troglodytes | Y269 | YTYWGYRHGGR | 1 | Arabidopsis thaliana |
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