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mutLBSgeneDB |
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| Gene summary for APAF1 |
 Gene summary |
| Basic gene Info. | Gene symbol | APAF1 |
| Gene name | apoptotic peptidase activating factor 1 | |
| Synonyms | APAF-1|CED4 | |
| Cytomap | UCSC genome browser: 12q23 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001160.2, NM_013229.2,NM_181861.1,NM_181868.1,NM_181869.1, | |
| Description | apoptotic protease-activating factor 1 | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 602233 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000120868 | ||
| HPRD : 03755 | ||
| Vega : OTTHUMG00000170214 | ||
| Protein | UniProt: O14727 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_APAF1 | |
| BioGPS: 317 | ||
| Pathway | NCI Pathway Interaction Database: APAF1 | |
| KEGG: APAF1 | ||
| REACTOME: APAF1 | ||
| Pathway Commons: APAF1 | ||
| Context | iHOP: APAF1 | |
| ligand binding site mutation search in PubMed: APAF1 | ||
| UCL Cancer Institute: APAF1 | ||
| 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:0006919 | activation of cysteine-type endopeptidase activity involved in apoptotic process | 21827945 | GO:0008635 | activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c | 9267021 |
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| Ligand binding site mutations for APAF1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | R129 | K131R | COAD | 5 | R265 | D266Y | COAD | 1 | R265 | D266Y | HNSC | 1 | E40 | E40V | HNSC | 1 | E78 | G79V | LUSC | 1 | D32,I30 | S31N | THCA | 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. |
| Clinical information for APAF1 from My Cancer Genome. |
| Apoptotic peptidase activating factor 1 (APAF1) is a gene that encodes a cytoplasmic protein that functions in the initiation of apoptosis. The protein also aids in the formation of an apoptosome that binds and cleaves procaspase 9 into its activated form. Missense mutations, nonsense mutations, silent mutations, and frameshift deletions and insertions are observed in cancers such as endometrial cancer, intestinal cancer, and stomach cancer. Related Pathways: Apoptosis. Modified: December 4, 2015 |
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| Protein structure related information for APAF1 |
| 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 | E78 | G79V | -1.5162605 | D32 | S31N | -1.3351166 | I30 | S31N | -1.3351166 | E40 | E40V | -0.9051498 | R129 | K131R | -0.85817444 | R265 | D266Y | -0.67974222 |
| (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 APAF1 from PDB |
| PDB ID | PDB title | PDB structure | 1C15 | SOLUTION STRUCTURE OF APAF-1 CARD |  |
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| Differential gene expression and gene-gene network for APAF1 |
| 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 APAF1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0007134 | Carcinoma, Renal Cell | 4 | Biomarker |
| umls:C0007138 | Carcinoma, Transitional Cell | 3 | Biomarker |
| umls:C0376634 | Craniofacial Abnormalities | 2 | Biomarker |
| umls:C0015393 | Eye Abnormalities | 1 | Biomarker |
| umls:C0035305 | Retinal Detachment | 1 | Biomarker |
| umls:C0037268 | Skin Abnormalities | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for APAF1 |
| 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|nutraceutical | DB00171 | Adenosine triphosphate | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of APAF1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | ZN | ZINC(2+) | 1cy5 | A | D32 | ZN | ZINC(2+) | 1cy5 | A | E78 | ZN | ZINC(2+) | 1cy5 | A | I30 E40 | ADP | ADP | 1z6t | A | R129 | ADP | ADP | 1z6t | D | R129 | ATP | ATP | 3j2t | A | R129 | ATP | ATP | 3j2t | B | R129 | ATP | ATP | 3j2t | C | R129 | ATP | ATP | 3j2t | D | R129 | ATP | ATP | 3j2t | E | R129 | ATP | ATP | 3j2t | F | R129 | ATP | ATP | 3j2t | G | R129 | ATP | ATP | 3iza | A | R129 R265 | ATP | ATP | 3iza | B | R129 R265 | ATP | ATP | 3iza | C | R129 R265 | ATP | ATP | 3iza | D | R129 R265 | ATP | ATP | 3iza | E | R129 R265 | ATP | ATP | 3iza | F | R129 R265 | ATP | ATP | 3iza | G | R129 R265 | DTP | DATP(4-) | 3jbt | A | R265 | DTP | DATP(4-) | 3jbt | C | R265 | DTP | DATP(4-) | 3jbt | E | R265 | DTP | DATP(4-) | 3jbt | G | R265 | DTP | DATP(4-) | 3jbt | I | R265 | DTP | DATP(4-) | 3jbt | K | R265 | DTP | DATP(4-) | 3jbt | M | R265 |
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| Conservation information for LBS of APAF1 |
| Multiple alignments for O14727 in multiple species |
| LBS | AA sequence | # species | Species | A156 | TIYGMAGCGKS | 2 | Mus musculus, Rattus norvegicus | A156 | TIHGMAGCGKS | 1 | Homo sapiens | A156 | TVFGMAGSGKS | 1 | Danio rerio | C158 | YGMAGCGKSVL | 2 | Mus musculus, Rattus norvegicus | C158 | HGMAGCGKSVL | 1 | Homo sapiens | C158 | FGMAGSGKSVM | 1 | Danio rerio | C8 | AKARNCLLQHR | 2 | Homo sapiens, Mus musculus | C8 | ERARSRLLRSK | 1 | Danio rerio | C8 | AKARNCLLQHK | 1 | Rattus norvegicus | D243 | SLLILDDVWDS | 2 | Homo sapiens, Danio rerio | D243 | SLLILDDVWDP | 2 | Mus musculus, Rattus norvegicus | D244 | LLILDDVWDPW | 2 | Mus musculus, Rattus norvegicus | D244 | LLILDDVWDSW | 1 | Homo sapiens | D244 | LLILDDVWDSS | 1 | Danio rerio | D27 | TSYIMDHMISN | 2 | Mus musculus, Rattus norvegicus | D27 | TSYIMDHMISD | 1 | Homo sapiens | D27 | ASYLMDHMISD | 1 | Danio rerio | D32 | DHMISDGFLTI | 1 | Homo sapiens | D32 | DHMISDGVLTN | 1 | Danio rerio | D32 | DHMISNGVLSV | 1 | Mus musculus | D32 | DHMISNGVLTV | 1 | Rattus norvegicus | D64 | MILKKDNDSYV | 1 | Homo sapiens | D64 | TLLRKDNRAYI | 1 | Danio rerio | D64 | MILNKDNCAYI | 1 | Mus musculus | D64 | MILNKDNYAYI | 1 | Rattus norvegicus | D66 | LKKDNDSYVSF | 1 | Homo sapiens | D66 | LRKDNRAYISF | 1 | Danio rerio | D66 | LNKDNCAYISF | 1 | Mus musculus | D66 | LNKDNYAYISF | 1 | Rattus norvegicus | D89 | AALLHDGIPVV | 1 | Homo sapiens | D89 | ASLLHSDLPLL | 1 | Danio rerio | D89 | AALLQSGLPLV | 1 | Mus musculus | D89 | AGLLHSGLPLV | 1 | Rattus norvegicus | E40 | LTISEEEKVRN | 1 | Homo sapiens | E40 | LTNDEEAKVLS | 1 | Danio rerio | E40 | LSVIEEEKVKS | 1 | Mus musculus | E40 | LTVVEEEKVKS | 1 | Rattus norvegicus | E78 | NALLHEGYKDL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E78 | NALIRESYGDL | 1 | Danio rerio | F126 | QRPVIFVTRKK | 2 | Mus musculus, Rattus norvegicus | F126 | QRPVVFVTRKK | 1 | Homo sapiens | F126 | QRPVVFVSRPP | 1 | Danio rerio | F425 | NKSLLFCNRNG | 2 | Mus musculus, Rattus norvegicus | F425 | NKSLLFCDRNG | 1 | Homo sapiens | F425 | NKSLLFRDCNQ | 1 | Danio rerio | G157 | IYGMAGCGKSV | 2 | Mus musculus, Rattus norvegicus | G157 | IHGMAGCGKSV | 1 | Homo sapiens | G157 | VFGMAGSGKSV | 1 | Danio rerio | G159 | GMAGCGKSVLA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G159 | GMAGSGKSVMA | 1 | Danio rerio | H28 | SYIMDHMISNG | 2 | Mus musculus, Rattus norvegicus | H28 | SYIMDHMISDG | 1 | Homo sapiens | H28 | SYLMDHMISDG | 1 | Danio rerio | H438 | FCYYLHDLQVD | 2 | Mus musculus, Rattus norvegicus | H438 | FRYYLHDLQVD | 1 | Homo sapiens | H438 | YRYYLHDLQLD | 1 | Danio rerio | I294 | EKGLEILSLFV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I294 | EKALEILALYV | 1 | Danio rerio | I30 | IMDHMISNGVL | 2 | Mus musculus, Rattus norvegicus | I30 | IMDHMISDGFL | 1 | Homo sapiens | I30 | LMDHMISDGVL | 1 | Danio rerio | K160 | MAGCGKSVLAA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K160 | MAGSGKSVMAA | 1 | Danio rerio | L322 | CKGSPLVVSLI | 3 | Homo sapiens, Danio rerio, Mus musculus | L322 | CKGSPLVVSLV | 1 | Rattus norvegicus | M155 | VTIYGMAGCGK | 2 | Mus musculus, Rattus norvegicus | M155 | VTIHGMAGCGK | 1 | Homo sapiens | M155 | VTVFGMAGSGK | 1 | Danio rerio | P123 | GVPQRPVIFVT | 2 | Mus musculus, Rattus norvegicus | P123 | GVPQRPVVFVT | 1 | Homo sapiens | P123 | GVPQRPVVFVS | 1 | Danio rerio | P321 | ECKGSPLVVSL | 4 | Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus | R129 | VVFVTRKKLVN | 1 | Homo sapiens | R129 | VVFVSRPPLLN | 1 | Danio rerio | R129 | VIFVTRKKLVH | 1 | Mus musculus | R129 | VIFVTRKKLVS | 1 | Rattus norvegicus | R265 | ILLTTRDKSVT | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R265 | VLLTTRNRALT | 1 | Danio rerio | S161 | AGCGKSVLAAE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S161 | AGSGKSVMAAE | 1 | Danio rerio | S325 | SPLVVSLIGAL | 3 | Homo sapiens, Danio rerio, Mus musculus | S325 | SPLVVSLVGAL | 1 | Rattus norvegicus | S358 | IRKSSSYDYEA | 4 | Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus | V125 | PQRPVIFVTRK | 2 | Mus musculus, Rattus norvegicus | V125 | PQRPVVFVTRK | 1 | Homo sapiens | V125 | PQRPVVFVSRP | 1 | Danio rerio | V127 | RPVIFVTRKKL | 2 | Mus musculus, Rattus norvegicus | V127 | RPVVFVTRKKL | 1 | Homo sapiens | V127 | RPVVFVSRPPL | 1 | Danio rerio | V162 | GCGKSVLAAEA | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V162 | GSGKSVMAAEV | 1 | Danio rerio | Y359 | RKSSSYDYEAL | 4 | Homo sapiens, Danio rerio, Mus musculus, Rattus norvegicus |
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