mutLBSgeneDB

mutLBSgeneDB
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 NSUN4
Gene summary
Basic gene Info.Gene symbolNSUN4
Gene nameNOP2/Sun domain family, member 4
SynonymsSHTAP
CytomapUCSC genome browser: 1p34
Type of geneprotein-coding
RefGenesNM_001256127.1,
NM_001256128.1,NM_199044.3,NR_045789.1,NR_045790.1,
NR_045791.1,
Description5-methylcytosine rRNA methyltransferase NSUN4NOL1/NOP2/Sun domain family member 4putative methyltransferase NSUN4sperm head and tail associated protein
Modification date20141207
dbXrefs MIM : 615394
HGNC : HGNC
HPRD : 14842
ProteinUniProt: Q96CB9
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NSUN4
BioGPS: 387338
PathwayNCI Pathway Interaction Database: NSUN4
KEGG: NSUN4
REACTOME: NSUN4
Pathway Commons: NSUN4
ContextiHOP: NSUN4
ligand binding site mutation search in PubMed: NSUN4
UCL Cancer Institute: NSUN4
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO TermPubMed ID
GO:0031167rRNA methylation23022348


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Ligand binding site mutations for NSUN4
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
P184P184SLUSC1
V256V256AUCEC1
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 NSUN4
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
V256V256A-2.0070709
P184P184S-0.94431425
(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 NSUN4 from PDB

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Differential gene expression and gene-gene network for NSUN4
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 NSUN4 and the right PPI network was created from samples without mutations in the LBS of NSUN4. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


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Phenotype information for NSUN4
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type

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

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Pharmacological information for NSUN4
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 NSUN4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
SAMS-ADENOSYL-L-METHIONINE4fp9AP184 V256
SAMS-ADENOSYL-L-METHIONINE4fp9CP184 V256
SAMS-ADENOSYL-L-METHIONINE4fp9DP184 V256
SAMS-ADENOSYL-L-METHIONINE4fp9FP184 V256
SAMS-ADENOSYL-L-METHIONINE4fzvAV256


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Conservation information for LBS of NSUN4
Multiple alignments for Q96CB9 in multiple species
LBSAA sequence# speciesSpecies
A182VLDLCAAPGGK4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus
A183LDLCAAPGGKT4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus
C181TVLDLCAAPGG2Bos taurus, Mus musculus
C181IVLDLCAAPGG1Homo sapiens
C181SVLDLCAAPGG1Xenopus tropicalis
D204NLAANDLSTSR2Bos taurus, Mus musculus
D204NLAANDLSPSR1Homo sapiens
D204YLAANDLSTSR1Xenopus tropicalis
D237RVTSWDGRKWG3Homo sapiens, Bos taurus, Mus musculus
D237CITSQDGRLWG1Xenopus tropicalis
D255DRVLVDVPCTT4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus
G185LCAAPGGKTLA4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus
G186CAAPGGKTLAL4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus
G238VTSWDGRKWGE3Homo sapiens, Bos taurus, Mus musculus
G238ITSQDGRLWGD1Xenopus tropicalis
K187AAPGGKTLALL4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus
L180DTVLDLCAAPG2Bos taurus, Mus musculus
L180DIVLDLCAAPG1Homo sapiens
L180HSVLDLCAAPG1Xenopus tropicalis
L205LAANDLSTSRT2Bos taurus, Mus musculus
L205LAANDLSPSRI1Homo sapiens
L205LAANDLSTSRS1Xenopus tropicalis
L291VLQVQLLAAGL2Homo sapiens, Bos taurus
L291LLQAELLVAGL1Xenopus tropicalis
L291MLQVQLLAAGL1Mus musculus
N203RNLAANDLSTS2Bos taurus, Mus musculus
N203RNLAANDLSPS1Homo sapiens
N203QYLAANDLSTS1Xenopus tropicalis
P184DLCAAPGGKTL4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus
P257VLVDVPCTTDR4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus
R209DLSPSRIARLQ1Homo sapiens
R209DLSTSRSSRLH1Xenopus tropicalis
R209DLSTSRTSRLQ1Bos taurus
R209DLSTSRTGRLQ1Mus musculus
S206AANDLSPSRIA1Homo sapiens
S206AANDLSTSRSS1Xenopus tropicalis
S206AANDLSTSRTS1Bos taurus
S206AANDLSTSRTG1Mus musculus
V256RVLVDVPCTTD4Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus


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