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mutLBSgeneDB |
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| Gene summary for RAP1A |
 Gene summary |
| Basic gene Info. | Gene symbol | RAP1A |
| Gene name | RAP1A, member of RAS oncogene family | |
| Synonyms | C21KG|G-22K|KREV-1|KREV1|RAP1|SMGP21 | |
| Cytomap | UCSC genome browser: 1p13.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001010935.2, NM_001291896.1,NM_002884.3, | |
| Description | GTP-binding protein smg p21ARas-related protein Krev-1ras-related protein Rap-1A | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 179520 | |
| HGNC : HGNC | ||
| HPRD : 01545 | ||
| Protein | UniProt: P62834 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RAP1A | |
| BioGPS: 5906 | ||
| Pathway | NCI Pathway Interaction Database: RAP1A | |
| KEGG: RAP1A | ||
| REACTOME: RAP1A | ||
| Pathway Commons: RAP1A | ||
| Context | iHOP: RAP1A | |
| ligand binding site mutation search in PubMed: RAP1A | ||
| UCL Cancer Institute: RAP1A | ||
| 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:0015031 | protein transport | 17916086 | GO:0071320 | cellular response to cAMP | 21840392 |
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| Ligand binding site mutations for RAP1A |
| 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 | N116 | G115D | COAD | 1 | P34 | P34Q | LUAD | 1 | G12 | S11L | LUAD | 1 | N116 | G115D | 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 RAP1A |
| 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 | P34 | P34Q | -1.1385863 | N116 | G115D | -0.62662788 | G12 | S11L | -0.59068622 |
| (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 RAP1A from PDB |
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| Differential gene expression and gene-gene network for RAP1A |
| 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 RAP1A |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for RAP1A |
| 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 RAP1A go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | GTP | GTP | 1c1y | A | G12 P34 N116 | GNP | PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER | 1gua | A | G12 P34 N116 | GDP | GUANOSINE-5'-DIPHOSPHATE | 3kuc | A | N116 | GTP | GTP | 4kvg | A | P34 N116 | GTP | GTP | 4kvg | C | P34 N116 |
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| Conservation information for LBS of RAP1A |
| Multiple alignments for P62834 in multiple species |
| LBS | AA sequence | # species | Species | A148 | FLESSAKSKIN | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | A148 | FMETSAKAKVN | 1 | Drosophila melanogaster | A18 | GVGKSALTVQF | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | D119 | VGNKCDLEDER | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | D119 | VGNKCDLEEER | 1 | Drosophila melanogaster | E30 | QGIFVEKYDPT | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | E30 | QCIFVEKYDPT | 1 | Drosophila melanogaster | F28 | FVQGIFVEKYD | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F28 | FVQCIFVEKYD | 1 | Drosophila melanogaster | G12 | VVLGSGGVGKS | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | G13 | VLGSGGVGKSA | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | G15 | GSGGVGKSALT | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | G60 | ILDTAGTEQFT | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | K117 | ILVGNKCDLED | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | K117 | VLVGNKCDLEE | 1 | Drosophila melanogaster | K149 | LESSAKSKINV | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | K149 | METSAKAKVNV | 1 | Drosophila melanogaster | K16 | SGGVGKSALTV | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | L120 | GNKCDLEDERV | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | L120 | GNKCDLEEERV | 1 | Drosophila melanogaster | N116 | MILVGNKCDLE | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | N116 | MVLVGNKCDLE | 1 | Drosophila melanogaster | P34 | VEKYDPTIEDS | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | S147 | AFLESSAKSKI | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | S147 | AFMETSAKAKV | 1 | Drosophila melanogaster | S17 | GGVGKSALTVQ | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | T35 | EKYDPTIEDSY | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | V14 | LGSGGVGKSAL | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster | V29 | VQGIFVEKYDP | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | V29 | VQCIFVEKYDP | 1 | Drosophila melanogaster | Y32 | IFVEKYDPTIE | 5 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus, Drosophila melanogaster |
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