mutLBSgeneDB |
Gene summary for NDP |
Gene summary |
Basic gene Info. | Gene symbol | NDP |
Gene name | Norrie disease (pseudoglioma) | |
Synonyms | EVR2|FEVR|ND | |
Cytomap | UCSC genome browser: Xp11.4 | |
Type of gene | protein-coding | |
RefGenes | NM_000266.3, | |
Description | X-linked exudative vitreoretinopathy 2 proteinnorrie disease proteinnorrin | |
Modification date | 20141219 | |
dbXrefs | MIM : 300658 | |
HGNC : HGNC | ||
Ensembl : ENSG00000124479 | ||
HPRD : 02404 | ||
Vega : OTTHUMG00000021391 | ||
Protein | UniProt: Q00604 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_NDP | |
BioGPS: 4693 | ||
Pathway | NCI Pathway Interaction Database: NDP | |
KEGG: NDP | ||
REACTOME: NDP | ||
Pathway Commons: NDP | ||
Context | iHOP: NDP | |
ligand binding site mutation search in PubMed: NDP | ||
UCL Cancer Institute: NDP | ||
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:0016055 | Wnt signaling pathway | 17955262 | GO:0045893 | positive regulation of transcription, DNA-templated | 15035989 | GO:0060070 | canonical Wnt signaling pathway | 15035989 |
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Ligand binding site mutations for NDP |
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. |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | R107 | R109Q | LUAD | 1 | R107 | R107L | LUSC | 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 NDP |
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 |
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 | R107 | R109Q | -1.1517799 | R107 | R107L | -0.31976177 |
(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 NDP from PDB |
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Differential gene expression and gene-gene network for NDP |
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 NDP |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0266526 | Norrie disease | 23 | Biomarker, GeneticVariation |
umls:C1844579 | Exudative Vitreoretinopathy, Familial, X-Linked Recessive | 1 | Biomarker, GeneticVariation |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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Pharmacological information for NDP |
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. |
Drug information targeting mutLBSgene (Approved drugs only) |
Drug status | DrugBank ID | Name | Type | Drug structure |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of NDP go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | SCR | SUCROSE OCTASULFATE | 5bqc | A | R107 |
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Conservation information for LBS of NDP |
Multiple alignments for Q00604 in multiple species |
LBS | AA sequence | # species | Species | A72 | GHCSQASRSEP | 3 | Homo sapiens, Bos taurus, Mus musculus | C126 | RYILSCHCEEC | 3 | Homo sapiens, Bos taurus, Mus musculus | C128 | ILSCHCEECSS | 2 | Bos taurus, Mus musculus | C128 | ILSCHCEECNS | 1 | Homo sapiens | C39 | SDPRRCMRHHY | 1 | Homo sapiens | C39 | SDPQRCMRHHY | 1 | Bos taurus | C39 | S--QRCMRHHY | 1 | Mus musculus | C69 | RCEGHCSQASR | 3 | Homo sapiens, Bos taurus, Mus musculus | H127 | YILSCHCEECS | 2 | Bos taurus, Mus musculus | H127 | YILSCHCEECN | 1 | Homo sapiens | H43 | RCMRHHYVDSI | 3 | Homo sapiens, Bos taurus, Mus musculus | K58 | YKCSSKMVLLA | 3 | Homo sapiens, Bos taurus, Mus musculus | L106 | SKLKALRLRCS | 3 | Homo sapiens, Bos taurus, Mus musculus | L124 | TYRYILSCHCE | 3 | Homo sapiens, Bos taurus, Mus musculus | M40 | DPRRCMRHHYV | 1 | Homo sapiens | M40 | DPQRCMRHHYV | 1 | Bos taurus | M40 | --QRCMRHHYV | 1 | Mus musculus | Q71 | EGHCSQASRSE | 3 | Homo sapiens, Bos taurus, Mus musculus | R107 | KLKALRLRCSG | 3 | Homo sapiens, Bos taurus, Mus musculus | R115 | CSGGMRLTATY | 3 | Homo sapiens, Bos taurus, Mus musculus | R38 | DSDPRRCMRHH | 1 | Homo sapiens | R38 | DSDPQRCMRHH | 1 | Bos taurus | R38 | DS--QRCMRHH | 1 | Mus musculus | R41 | PRRCMRHHYVD | 1 | Homo sapiens | R41 | PQRCMRHHYVD | 1 | Bos taurus | R41 | -QRCMRHHYVD | 1 | Mus musculus | S125 | YRYILSCHCEE | 3 | Homo sapiens, Bos taurus, Mus musculus | S70 | CEGHCSQASRS | 3 | Homo sapiens, Bos taurus, Mus musculus | Y122 | TATYRYILSCH | 3 | Homo sapiens, Bos taurus, Mus musculus |
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