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 MRPL4
Gene summary
Basic gene Info.Gene symbolMRPL4
Gene namemitochondrial ribosomal protein L4
SynonymsCGI-28|L4mt
CytomapUCSC genome browser: 19p13.2
Type of geneprotein-coding
RefGenesNM_015956.2,
NM_146387.1,NM_146388.1,
Description39S ribosomal protein L4, mitochondrialMRP-L4
Modification date20141207
dbXrefs MIM : 611823
HGNC : HGNC
Ensembl : ENSG00000105364
HPRD : 14759
Vega : OTTHUMG00000180400
ProteinUniProt: Q9BYD3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MRPL4
BioGPS: 51073
PathwayNCI Pathway Interaction Database: MRPL4
KEGG: MRPL4
REACTOME: MRPL4
Pathway Commons: MRPL4
ContextiHOP: MRPL4
ligand binding site mutation search in PubMed: MRPL4
UCL Cancer Institute: MRPL4
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


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Ligand binding site mutations for MRPL4

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
P155R156WCOAD1
H97I95LCOAD1
P155R156LLUAD1
R125R125QSKCM1
P144P144LSTAD1
A152A152TSTAD1
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 MRPL4
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
P155R156L0.13756184
R125R125Q-0.98768721
H97I95L-0.82123388
A152A152T-0.50128443
P144P144L-0.48415526
P155R156W-0.18201481
(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 MRPL4 from PDB

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Differential gene expression and gene-gene network for MRPL4
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 MRPL4 and the right PPI network was created from samples without mutations in the LBS of MRPL4. 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 MRPL4
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 MRPL4
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 MRPL4 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
NUCNucleic Acids3j7yFH97 R125 P144 A152 P155


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Conservation information for LBS of MRPL4
Multiple alignments for Q9BYD3 in multiple species
LBSAA sequence# speciesSpecies
A112KRISYAKTKTR2Homo sapiens, Bos taurus
A112KRISYANVKTR1Danio rerio
A112RRISYANTKTR1Mus musculus
A118KTKTRAEVRGG2Homo sapiens, Bos taurus
A118NVKTRAEVRGG1Danio rerio
A118NTKTRAEVSGG1Mus musculus
A136KGSGRARHGSI2Mus musculus, Bos taurus
A136KGTGRARHGSI1Homo sapiens
A136KRTGRARHGSI1Danio rerio
A152RGGGVAHGPRG3Homo sapiens, Mus musculus, Bos taurus
A152RGGGIIHGPRG1Danio rerio
G123AEVRGGGRKPW3Homo sapiens, Danio rerio, Bos taurus
G123AEVSGGGRKPW1Mus musculus
G134QQKGSGRARHG2Mus musculus, Bos taurus
G134PQKGTGRARHG1Homo sapiens
G134QQKRTGRARHG1Danio rerio
G139GRARHGSIRSP4Homo sapiens, Danio rerio, Mus musculus, Bos taurus
G148SPLWRGGGVAH2Homo sapiens, Mus musculus
G148SPLWRGGGIIH1Danio rerio
G148SPIWRGGGVAH1Bos taurus
G154GGVAHGPRGPT3Homo sapiens, Mus musculus, Bos taurus
G154GGIIHGPRGPT1Danio rerio
H138TGRARHGSIRS2Homo sapiens, Danio rerio
H138SGRARHGSIRS2Mus musculus, Bos taurus
H153GGGVAHGPRGP3Homo sapiens, Mus musculus, Bos taurus
H153GGGIIHGPRGP1Danio rerio
H97RLDILHQVAMW1Homo sapiens
H97RLDILHAVEVW1Danio rerio
H97RLDIVHQVAIW1Mus musculus
H97RLDILHQVAIW1Bos taurus
K104VAMWQKNFKRI1Homo sapiens
K104VEVWQRNFKRI1Danio rerio
K104VAIWQRNFRRI1Mus musculus
K104VAIWQKNFKRI1Bos taurus
K113RISYAKTKTRA2Homo sapiens, Bos taurus
K113RISYANVKTRA1Danio rerio
K113RISYANTKTRA1Mus musculus
K126RGGGRKPWQQK2Danio rerio, Bos taurus
K126RGGGRKPWPQK1Homo sapiens
K126SGGGRKPWQQK1Mus musculus
K131KPWQQKGSGRA2Mus musculus, Bos taurus
K131KPWPQKGTGRA1Homo sapiens
K131KPWQQKRTGRA1Danio rerio
K168YMLPMKVRALG2Homo sapiens, Mus musculus
K168YMLPMKVRVQG2Danio rerio, Bos taurus
K255VHSMLKHQTLV2Homo sapiens, Bos taurus
K255VHSLLKHESLV1Danio rerio
K255VYSMLKHQTLV1Mus musculus
L145SIRSPLWRGGG3Homo sapiens, Danio rerio, Mus musculus
L145SIRSPIWRGGG1Bos taurus
L165SYYYMLPMKVR4Homo sapiens, Danio rerio, Mus musculus, Bos taurus
L172MKVRALGLKVA2Homo sapiens, Mus musculus
L172MKVRVQGLKIA1Danio rerio
L172MKVRVQGLKVA1Bos taurus
M101LHQVAMWQKNF1Homo sapiens
M101LHAVEVWQRNF1Danio rerio
M101VHQVAIWQRNF1Mus musculus
M101LHQVAIWQKNF1Bos taurus
M164TSYYYMLPMKV4Homo sapiens, Danio rerio, Mus musculus, Bos taurus
M167YYMLPMKVRAL2Homo sapiens, Mus musculus
M167YYMLPMKVRVQ2Danio rerio, Bos taurus
N105AMWQKNFKRIS1Homo sapiens
N105EVWQRNFKRIS1Danio rerio
N105AIWQRNFRRIS1Mus musculus
N105AIWQKNFKRIS1Bos taurus
P144GSIRSPLWRGG3Homo sapiens, Danio rerio, Mus musculus
P144GSIRSPIWRGG1Bos taurus
P155GVAHGPRGPTS3Homo sapiens, Mus musculus, Bos taurus
P155GIIHGPRGPTS1Danio rerio
P158HGPRGPTSYYY4Homo sapiens, Danio rerio, Mus musculus, Bos taurus
P166YYYMLPMKVRA2Homo sapiens, Mus musculus
P166YYYMLPMKVRV2Danio rerio, Bos taurus
P282DSRYTPLYPFR2Mus musculus, Bos taurus
P282DSRYRPLYPFS1Homo sapiens
P282DVRYTPLYPFK1Danio rerio
P285YTPLYPFRLPY2Mus musculus, Bos taurus
P285YRPLYPFSLPY1Homo sapiens
P285YTPLYPFKLPY1Danio rerio
Q130RKPWQQKGSGR2Mus musculus, Bos taurus
Q130RKPWPQKGTGR1Homo sapiens
Q130RKPWQQKRTGR1Danio rerio
R108QKNFKRISYAK2Homo sapiens, Bos taurus
R108QRNFKRISYAN1Danio rerio
R108QRNFRRISYAN1Mus musculus
R117AKTKTRAEVRG2Homo sapiens, Bos taurus
R117ANVKTRAEVRG1Danio rerio
R117ANTKTRAEVSG1Mus musculus
R121TRAEVRGGGRK3Homo sapiens, Danio rerio, Bos taurus
R121TRAEVSGGGRK1Mus musculus
R125VRGGGRKPWQQ2Danio rerio, Bos taurus
R125VRGGGRKPWPQ1Homo sapiens
R125VSGGGRKPWQQ1Mus musculus
R135QKGSGRARHGS2Mus musculus, Bos taurus
R135QKGTGRARHGS1Homo sapiens
R135QKRTGRARHGS1Danio rerio
R137GSGRARHGSIR2Mus musculus, Bos taurus
R137GTGRARHGSIR1Homo sapiens
R137RTGRARHGSIR1Danio rerio
R142RHGSIRSPLWR3Homo sapiens, Danio rerio, Mus musculus
R142RHGSIRSPIWR1Bos taurus
R147RSPLWRGGGVA2Homo sapiens, Mus musculus
R147RSPLWRGGGII1Danio rerio
R147RSPIWRGGGVA1Bos taurus
R170LPMKVRALGLK2Homo sapiens, Mus musculus
R170LPMKVRVQGLK2Danio rerio, Bos taurus
R281QDSRYRPLYPF1Homo sapiens
R281HDVRYTPLYPF1Danio rerio
R281QDSRYTPLYPF1Mus musculus
R281HDSRYTPLYPF1Bos taurus
R92FATAPRLDILH1Homo sapiens
R92FSVPIRLDILH1Danio rerio
R92FATAPRLDIVH1Mus musculus
R92FSTAPRLDILH1Bos taurus
S143HGSIRSPLWRG3Homo sapiens, Danio rerio, Mus musculus
S143HGSIRSPIWRG1Bos taurus
T114ISYAKTKTRAE2Homo sapiens, Bos taurus
T114ISYANVKTRAE1Danio rerio
T114ISYANTKTRAE1Mus musculus
T116YAKTKTRAEVR2Homo sapiens, Bos taurus
T116YANVKTRAEVR1Danio rerio
T116YANTKTRAEVS1Mus musculus
T133WQQKGSGRARH2Mus musculus, Bos taurus
T133WPQKGTGRARH1Homo sapiens
T133WQQKRTGRARH1Danio rerio
V120KTRAEVRGGGR3Homo sapiens, Danio rerio, Bos taurus
V120KTRAEVSGGGR1Mus musculus
V151WRGGGVAHGPR3Homo sapiens, Mus musculus, Bos taurus
V151WRGGGIIHGPR1Danio rerio
V169MLPMKVRALGL2Homo sapiens, Mus musculus
V169MLPMKVRVQGL2Danio rerio, Bos taurus
W146IRSPLWRGGGV2Homo sapiens, Mus musculus
W146IRSPLWRGGGI1Danio rerio
W146IRSPIWRGGGV1Bos taurus
Y111FKRISYAKTKT2Homo sapiens, Bos taurus
Y111FKRISYANVKT1Danio rerio
Y111FRRISYANTKT1Mus musculus
Y161RGPTSYYYMLP4Homo sapiens, Danio rerio, Mus musculus, Bos taurus
Y163PTSYYYMLPMK4Homo sapiens, Danio rerio, Mus musculus, Bos taurus


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