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mutLBSgeneDB |
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| Gene summary for YTHDC1 |
 Gene summary |
| Basic gene Info. | Gene symbol | YTHDC1 |
| Gene name | YTH domain containing 1 | |
| Synonyms | YT521|YT521-B | |
| Cytomap | UCSC genome browser: 4q13.2 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001031732.2, NM_133370.2, | |
| Description | YTH domain-containing protein 1putative splicing factor YT521splicing factor YT521-B | |
| Modification date | 20141207 | |
| dbXrefs | HGNC : HGNC | |
| Ensembl : ENSG00000083896 | ||
| HPRD : 11689 | ||
| Vega : OTTHUMG00000129306 | ||
| Protein | UniProt: Q96MU7 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_YTHDC1 | |
| BioGPS: 91746 | ||
| Pathway | NCI Pathway Interaction Database: YTHDC1 | |
| KEGG: YTHDC1 | ||
| REACTOME: YTHDC1 | ||
| Pathway Commons: YTHDC1 | ||
| Context | iHOP: YTHDC1 | |
| ligand binding site mutation search in PubMed: YTHDC1 | ||
| UCL Cancer Institute: YTHDC1 | ||
| 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:0006376 | mRNA splice site selection | 20167602 |
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| Ligand binding site mutations for YTHDC1 |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | M438 | K437E | KIRC | 1 | N367 | S369C | STAD | 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 YTHDC1 |
| 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 | M438 | K437E | -0.61797331 | N367 | S369C | -0.32746334 |
| (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 YTHDC1 from PDB |
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| Differential gene expression and gene-gene network for YTHDC1 |
| 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 YTHDC1 |
| 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 YTHDC1 |
| 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 YTHDC1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | NUC | Nucleic Acids | 4r3i | A | N367 M438 |
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| Conservation information for LBS of YTHDC1 |
| Multiple alignments for Q96MU7 in multiple species |
| LBS | AA sequence | # species | Species | D476 | VKIGRDGQEIE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | E405 | IFSVRESGKFQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | G474 | KPVKIGRDGQE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | I473 | HKPVKIGRDGQ | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K361 | RFFLIKSNNHE | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | K472 | EHKPVKIGRDG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | L380 | GVWSTLPVNEK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M434 | VLPAGMSAKML | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | M438 | GMSAKMLGGVF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N363 | FLIKSNNHENV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | N367 | SNNHENVSLAK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | P381 | VWSTLPVNEKK | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R404 | LIFSVRESGKF | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | R475 | PVKIGRDGQEI | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S362 | FFLIKSNNHEN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S378 | AKGVWSTLPVN | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | V382 | WSTLPVNEKKL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | W377 | KAKGVWSTLPV | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | W428 | GSPIHWVLPAG | 3 | Homo sapiens, Mus musculus, Rattus norvegicus |
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