mutated Ligand Binding Site gene DataBase





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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for NOTCH3
Gene summary
Basic gene Info.Gene symbolNOTCH3
Gene namenotch 3
CytomapUCSC genome browser: 19p13.2-p13.1
Type of geneprotein-coding
DescriptionNotch homolog 3neurogenic locus notch homolog protein 3
Modification date20141219
dbXrefs MIM : 600276
Ensembl : ENSG00000074181
HPRD : 02607
Vega : OTTHUMG00000183217
ProteinUniProt: Q9UM47
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NOTCH3
BioGPS: 4854
PathwayNCI Pathway Interaction Database: NOTCH3
Pathway Commons: NOTCH3
ContextiHOP: NOTCH3
ligand binding site mutation search in PubMed: NOTCH3
UCL Cancer Institute: NOTCH3
Assigned class in mutLBSgeneDBA: This gene has a literature evidence and it belongs to targetable_mutLBSgenes.
References showing study about ligand binding site mutation for NOTCH3.1. Lin, L., Mernaugh, R., Yi, F., Blum, D., Carbone, D. P., & Dang, T. P. (2010). Targeting specific regions of the Notch3 ligand-binding domain induces apoptosis and inhibits tumor growth in lung cancer. Cancer research, 70(2), 632-638. 20068176

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for NOTCH3

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for NOTCH3
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.
LBSAAchange of nsSNVRelative stability change
(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 NOTCH3 from PDB

Differential gene expression and gene-gene network for NOTCH3
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)
* Left PPI network was created from samples with mutations in the LBS of NOTCH3 and the right PPI network was created from samples without mutations in the LBS of NOTCH3. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for NOTCH3
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0751587CADASIL172Biomarker, GeneticVariation
umls:C1458155Breast Neoplasms5AlteredExpression, Biomarker
umls:C0007131Carcinoma, Non-Small-Cell Lung4Biomarker
umls:C0024121Lung Neoplasms2Biomarker
umls:C0887833Carcinoma, Pancreatic Ductal2Biomarker
umls:C0279626Esophageal Squamous Cell Carcinoma1Biomarker
umls:C0432284Fibromatosis, Congenital Generalized1Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for NOTCH3
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 statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of NOTCH3 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of NOTCH3
Multiple alignments for Q9UM47 in multiple species
LBSAA sequence# speciesSpecies
D1398QAKRGDQNCDR2Mus musculus, Rattus norvegicus
D1398QAKRGDQRCDR1Homo sapiens
D1402GDQRCDRECNS1Homo sapiens
D1402GDQNCDRECNT1Mus musculus
D1402GDQNCDRECNS1Rattus norvegicus
D1413PGCGWDGGDCS3Homo sapiens, Mus musculus, Rattus norvegicus
D1416GWDGGDCSLNV2Mus musculus, Rattus norvegicus
D1416GWDGGDCSLSV1Homo sapiens
D1443NNSRCDPACSS3Homo sapiens, Mus musculus, Rattus norvegicus
D1454PACLYDNFDCY2Mus musculus, Rattus norvegicus
D1454PACLYDNFDCH1Homo sapiens
D1457LYDNFDCYSGG2Mus musculus, Rattus norvegicus
D1457LYDNFDCHAGG1Homo sapiens
D1481ADHFADGRCDQ3Homo sapiens, Mus musculus, Rattus norvegicus
D1485ADGRCDQGCNT3Homo sapiens, Mus musculus, Rattus norvegicus
D1496EECGWDGLDCA3Homo sapiens, Mus musculus, Rattus norvegicus
D1499GWDGLDCASEV3Homo sapiens, Mus musculus, Rattus norvegicus
H1478KYCADHFADGR3Homo sapiens, Mus musculus, Rattus norvegicus
K1395AACQAKRGDQN2Mus musculus, Rattus norvegicus
K1395AACQAKRGDQR1Homo sapiens
L1436LQCWRLFNNSR3Homo sapiens, Mus musculus, Rattus norvegicus
N1439WRLFNNSRCDP3Homo sapiens, Mus musculus, Rattus norvegicus
R1400KRGDQNCDREC2Mus musculus, Rattus norvegicus
R1400KRGDQRCDREC1Homo sapiens
R1441LFNNSRCDPAC3Homo sapiens, Mus musculus, Rattus norvegicus
R1483HFADGRCDQGC3Homo sapiens, Mus musculus, Rattus norvegicus

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