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 FMR1
Gene summary
Basic gene Info.Gene symbolFMR1
Gene namefragile X mental retardation 1
CytomapUCSC genome browser: Xq27.3
Type of geneprotein-coding
Descriptionfragile X mental retardation protein 1
Modification date20141222
dbXrefs MIM : 309550
Ensembl : ENSG00000102081
HPRD : 02398
Vega : OTTHUMG00000022606
ProteinUniProt: Q06787
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FMR1
BioGPS: 2332
PathwayNCI Pathway Interaction Database: FMR1
Pathway Commons: FMR1
ContextiHOP: FMR1
ligand binding site mutation search in PubMed: FMR1
UCL Cancer Institute: FMR1
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

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

Ligand binding site mutations for FMR1
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
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 FMR1
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 FMR1 from PDB

Differential gene expression and gene-gene network for FMR1
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 FMR1 and the right PPI network was created from samples without mutations in the LBS of FMR1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for FMR1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0016667Fragile X Syndrome523AlteredExpression, Biomarker, GeneticVariation
umls:C1839780Fragile X Tremor Ataxia Syndrome118Biomarker, GeneticVariation
umls:C0085215Primary Ovarian Insufficiency71Biomarker, GeneticVariation
umls:C0004352Autistic Disorder35Biomarker, GeneticVariation
umls:C3714756Intellectual Disability25Biomarker, GeneticVariation
umls:C0000768Congenital Abnormalities4Biomarker
umls:C0009241Cognition Disorders3Biomarker
umls:C2749127Primary Ovarian Insufficiency, Fragile X-Associated2Biomarker
umls:C0376634Craniofacial Abnormalities2Biomarker
umls:C0018051Gonadal Dysgenesis1Biomarker

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

Pharmacological information for FMR1
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 FMR1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS

Conservation information for LBS of FMR1
Multiple alignments for Q06787 in multiple species
LBSAA sequence# speciesSpecies
E227QFIVREDLMGL3Homo sapiens, Xenopus tropicalis, Rattus norvegicus
E227EFRVRDDLMGL1Drosophila melanogaster
E257AIDLDEDTCTF3Homo sapiens, Xenopus tropicalis, Rattus norvegicus
E257NIELEEKSCTF1Drosophila melanogaster

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