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mutLBSgeneDB |
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| Gene summary for USH1C |
 Gene summary |
| Basic gene Info. | Gene symbol | USH1C |
| Gene name | Usher syndrome 1C (autosomal recessive, severe) | |
| Synonyms | AIE-75|DFNB18|DFNB18A|NY-CO-37|NY-CO-38|PDZ-45|PDZ-73|PDZ-73/NY-CO-38|PDZ73|PDZD7C|ush1cpst | |
| Cytomap | UCSC genome browser: 11p14.3 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001297764.1, NM_005709.3,NM_153676.3,NR_123738.1, | |
| Description | antigen NY-CO-38/NY-CO-37autoimmune enteropathy-related antigen AIE-75harmoninrenal carcinoma antigen NY-REN-3usher syndrome type-1C protein | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 605242 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000006611 | ||
| HPRD : 09241 | ||
| Vega : OTTHUMG00000166323 | ||
| Protein | UniProt: Q9Y6N9 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_USH1C | |
| BioGPS: 10083 | ||
| Pathway | NCI Pathway Interaction Database: USH1C | |
| KEGG: USH1C | ||
| REACTOME: USH1C | ||
| Pathway Commons: USH1C | ||
| Context | iHOP: USH1C | |
| ligand binding site mutation search in PubMed: USH1C | ||
| UCL Cancer Institute: USH1C | ||
| 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 |
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| Ligand binding site mutations for USH1C |
| 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 | I62 | D60H | LUAD | 1 | H34 | Q35R | LUSC | 1 | L222 | R220G | SKCM | 1 | R31 | R31L | SKCM | 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 USH1C |
| 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 | L222 | R220G | 0.000843559 | I62 | D60H | -0.71295505 | R31 | R31L | -0.37084703 | H34 | Q35R | -0.16241774 |
| (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 USH1C from PDB |
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| Differential gene expression and gene-gene network for USH1C |
| 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 USH1C |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C1848604 | Usher Syndrome, Type IC | 3 | Biomarker, GeneticVariation |
| umls:C2931207 | Usher syndrome, type 1C | 3 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for USH1C |
| 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 USH1C go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | III | Peptide ligand (ASP,ASP,ASP,ARG,TYR,LEU,ARG,GLU,ALA,ILE,GLN,GLU,TYR,ASP,ASN,ILE,ALA,LYS) | 2kbr | A | H34 | III | Peptide ligand (GLY,SER,LEU,LEU,LYS,GLU,VAL,LEU,GLU,ASP,TYR,LEU,ARG,LEU,LYS,LYS) | 2lsr | A | R31 H34 I62 |
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| Conservation information for LBS of USH1C |
| Multiple alignments for Q9Y6N9 in multiple species |
| LBS | AA sequence | # species | Species | A6 | MDRKVAREFRH | 3 | Homo sapiens, Mus musculus, Bos taurus | C224 | SRGLGCSISSG | 3 | Homo sapiens, Mus musculus, Bos taurus | D2 | 3 | Homo sapiens, Mus musculus, Bos taurus | D20 | FLIENDAEKDY | 3 | Homo sapiens, Mus musculus, Bos taurus | D24 | NDAEKDYLYDV | 3 | Homo sapiens, Mus musculus, Bos taurus | F9 | KVAREFRHKVD | 3 | Homo sapiens, Mus musculus, Bos taurus | G229 | CSISSGPIQKP | 3 | Homo sapiens, Mus musculus, Bos taurus | H11 | AREFRHKVDFL | 3 | Homo sapiens, Mus musculus, Bos taurus | H271 | FSNLDHKEAVN | 2 | Homo sapiens, Bos taurus | H271 | FTNLDHKEAVN | 1 | Mus musculus | H34 | VLRMYHQTMDV | 3 | Homo sapiens, Mus musculus, Bos taurus | I226 | GLGCSISSGPI | 3 | Homo sapiens, Mus musculus, Bos taurus | I62 | PLFDAIRPLIP | 3 | Homo sapiens, Mus musculus, Bos taurus | I66 | AIRPLIPLKHQ | 3 | Homo sapiens, Mus musculus, Bos taurus | K23 | ENDAEKDYLYD | 3 | Homo sapiens, Mus musculus, Bos taurus | K279 | AVNVLKSSRSL | 3 | Homo sapiens, Mus musculus, Bos taurus | L222 | VGSRGLGCSIS | 3 | Homo sapiens, Mus musculus, Bos taurus | L278 | EAVNVLKSSRS | 3 | Homo sapiens, Mus musculus, Bos taurus | L30 | YLYDVLRMYHQ | 3 | Homo sapiens, Mus musculus, Bos taurus | L65 | DAIRPLIPLKH | 3 | Homo sapiens, Mus musculus, Bos taurus | L68 | RPLIPLKHQVE | 3 | Homo sapiens, Mus musculus, Bos taurus | M37 | MYHQTMDVAVL | 3 | Homo sapiens, Mus musculus, Bos taurus | P230 | SISSGPIQKPG | 3 | Homo sapiens, Mus musculus, Bos taurus | P64 | FDAIRPLIPLK | 3 | Homo sapiens, Mus musculus, Bos taurus | P67 | IRPLIPLKHQV | 3 | Homo sapiens, Mus musculus, Bos taurus | R10 | VAREFRHKVDF | 3 | Homo sapiens, Mus musculus, Bos taurus | R3 | 3 | Homo sapiens, Mus musculus, Bos taurus | R31 | LYDVLRMYHQT | 3 | Homo sapiens, Mus musculus, Bos taurus | R7 | DRKVAREFRHK | 3 | Homo sapiens, Mus musculus, Bos taurus | S225 | RGLGCSISSGP | 3 | Homo sapiens, Mus musculus, Bos taurus | S227 | LGCSISSGPIQ | 3 | Homo sapiens, Mus musculus, Bos taurus | S228 | GCSISSGPIQK | 3 | Homo sapiens, Mus musculus, Bos taurus | S239 | PGIFISHVKPG | 2 | Homo sapiens, Bos taurus | S239 | PGIFVSHVKPG | 1 | Mus musculus | V13 | EFRHKVDFLIE | 3 | Homo sapiens, Mus musculus, Bos taurus | V275 | DHKEAVNVLKS | 3 | Homo sapiens, Mus musculus, Bos taurus | V5 | 3 | Homo sapiens, Mus musculus, Bos taurus | Y27 | EKDYLYDVLRM | 3 | Homo sapiens, Mus musculus, Bos taurus | Y33 | DVLRMYHQTMD | 3 | Homo sapiens, Mus musculus, Bos taurus |
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