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mutLBSgeneDB |
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| Gene summary for TARDBP |
 Gene summary |
| Basic gene Info. | Gene symbol | TARDBP |
| Gene name | TAR DNA binding protein | |
| Synonyms | ALS10|TDP-43 | |
| Cytomap | UCSC genome browser: 1p36.22 | |
| Type of gene | protein-coding | |
| RefGenes | NM_007375.3, | |
| Description | TAR DNA-binding protein 43TAR DNA-binding protein-43 | |
| Modification date | 20141222 | |
| dbXrefs | MIM : 605078 | |
| HGNC : HGNC | ||
| HPRD : 05466 | ||
| Protein | UniProt: Q13148 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_TARDBP | |
| BioGPS: 23435 | ||
| Pathway | NCI Pathway Interaction Database: TARDBP | |
| KEGG: TARDBP | ||
| REACTOME: TARDBP | ||
| Pathway Commons: TARDBP | ||
| Context | iHOP: TARDBP | |
| ligand binding site mutation search in PubMed: TARDBP | ||
| UCL Cancer Institute: TARDBP | ||
| 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:0008380 | RNA splicing | 11285240 | GO:0043922 | negative regulation by host of viral transcription | 7745706 | GO:0070935 | 3'-UTR-mediated mRNA stabilization | 17481916 |
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| Ligand binding site mutations for TARDBP |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | L139 | D138A | BLCA | 1 | D105 | D105N | COAD | 1 | R197 | R197C | 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 TARDBP |
| 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 | L139 | D138A | -1.4220217 | R197 | R197C | -0.93120767 | D105 | D105N | -0.87087178 |
| (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 TARDBP from PDB |
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| Differential gene expression and gene-gene network for TARDBP |
| 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 TARDBP |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0002736 | Amyotrophic Lateral Sclerosis | 283 | Biomarker, GeneticVariation, PostTranslationalModification |
| umls:C2677565 | AMYOTROPHIC LATERAL SCLEROSIS 10, WITH OR WITHOUT FRONTOTEMPORAL DEMENTIA | 9 | Biomarker, GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for TARDBP |
| 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 TARDBP go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | NUC | Nucleic Acids | 4iuf | A | D105 | NUC | Nucleic Acids | 4bs2 | A | D105 L139 R197 |
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| Conservation information for LBS of TARDBP |
| Multiple alignments for Q13148 in multiple species |
| LBS | AA sequence | # species | Species | A228 | PKPFRAFAFVT | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | A260 | VHISNAEPKHN | 3 | Homo sapiens, Mus musculus, Gallus gallus | A260 | VHVSTAEPKHN | 1 | Xenopus tropicalis | D105 | VQKTSDLIVLG | 3 | Homo sapiens, Mus musculus, Gallus gallus | D105 | VTKTSDLIVLG | 1 | Xenopus tropicalis | D174 | DGRWCDCKLPN | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | E261 | HISNAEPKHNS | 3 | Homo sapiens, Mus musculus, Gallus gallus | E261 | HVSTAEPKHNN | 1 | Xenopus tropicalis | F147 | GHSKGFGFVRF | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | F149 | SKGFGFVRFTE | 2 | Homo sapiens, Mus musculus | F149 | SKGFGFVRFAD | 1 | Xenopus tropicalis | F149 | SKGFGFVRFTD | 1 | Gallus gallus | F194 | RSRKVFVGRCT | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | F221 | EVVDVFIPKPF | 3 | Xenopus tropicalis, Mus musculus, Gallus gallus | F221 | DVMDVFIPKPF | 1 | Homo sapiens | F229 | KPFRAFAFVTF | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | F231 | FRAFAFVTFAD | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | G110 | DLIVLGLPWKT | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | G146 | TGHSKGFGFVR | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | I107 | KTSDLIVLGLP | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | K136 | LMVQVKKDLKT | 2 | Homo sapiens, Mus musculus | K136 | IMVQVKKDAKT | 1 | Xenopus tropicalis | K136 | LMVQVKKDIKT | 1 | Gallus gallus | K145 | KTGHSKGFGFV | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | K176 | RWCDCKLPNSK | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | K181 | KLPNSKQSPDE | 2 | Mus musculus, Gallus gallus | K181 | KLPNSKQSQDE | 1 | Homo sapiens | K181 | KLPNSK-SPDE | 1 | Xenopus tropicalis | K192 | PLRSRKVFVGR | 3 | Homo sapiens, Mus musculus, Gallus gallus | K192 | PMRSRKVFVGR | 1 | Xenopus tropicalis | K263 | SNAEPKHNSNR | 3 | Homo sapiens, Mus musculus, Gallus gallus | K263 | STAEPKHNNNR | 1 | Xenopus tropicalis | L109 | SDLIVLGLPWK | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | L111 | LIVLGLPWKTT | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | L139 | QVKKDLKTGHS | 2 | Homo sapiens, Mus musculus | L139 | QVKKDAKTGHS | 1 | Xenopus tropicalis | L139 | QVKKDIKTGHS | 1 | Gallus gallus | M132 | FGEVLMVQVKK | 3 | Homo sapiens, Mus musculus, Gallus gallus | M132 | FGEVIMVQVKK | 1 | Xenopus tropicalis | N12 | VTEDENDEPIE | 3 | Homo sapiens, Mus musculus, Gallus gallus | N12 | VAEDENEEPME | 1 | Xenopus tropicalis | N179 | DCKLPNSKQSP | 2 | Mus musculus, Gallus gallus | N179 | DCKLPNSKQSQ | 1 | Homo sapiens | N179 | DCKLPNSK-SP | 1 | Xenopus tropicalis | N259 | SVHISNAEPKH | 3 | Homo sapiens, Mus musculus, Gallus gallus | N259 | SVHVSTAEPKH | 1 | Xenopus tropicalis | P112 | IVLGLPWKTTE | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | P178 | CDCKLPNSKQS | 3 | Homo sapiens, Mus musculus, Gallus gallus | P178 | CDCKLPNSK-S | 1 | Xenopus tropicalis | Q134 | EVLMVQVKKDL | 2 | Homo sapiens, Mus musculus | Q134 | EVIMVQVKKDA | 1 | Xenopus tropicalis | Q134 | EVLMVQVKKDI | 1 | Gallus gallus | R171 | HMIDGRWCDCK | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | R197 | KVFVGRCTEDM | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | R227 | IPKPFRAFAFV | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus | S254 | IIKGISVHISN | 3 | Homo sapiens, Mus musculus, Gallus gallus | S254 | IIKGVSVHVST | 1 | Xenopus tropicalis | S258 | ISVHISNAEPK | 3 | Homo sapiens, Mus musculus, Gallus gallus | S258 | VSVHVSTAEPK | 1 | Xenopus tropicalis | W113 | VLGLPWKTTEQ | 4 | Homo sapiens, Xenopus tropicalis, Mus musculus, Gallus gallus |
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