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 AP4M1
Gene summary
Basic gene Info.Gene symbolAP4M1
Gene nameadaptor-related protein complex 4, mu 1 subunit
CytomapUCSC genome browser: 7q22.1
Type of geneprotein-coding
DescriptionAP-4 adaptor complex mu subunitAP-4 complex subunit mu-1adapter-related protein complex 4 mu-1 subunitadapter-related protein complex 4 subunit mu-1adaptor-related protein complex 4 subunit mu-1adaptor-related protein complex AP-4 mu4 subunitmu subu
Modification date20141207
dbXrefs MIM : 602296
Ensembl : ENSG00000221838
HPRD : 03803
Vega : OTTHUMG00000154722
ProteinUniProt: O00189
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_AP4M1
BioGPS: 9179
PathwayNCI Pathway Interaction Database: AP4M1
Pathway Commons: AP4M1
ContextiHOP: AP4M1
ligand binding site mutation search in PubMed: AP4M1
UCL Cancer Institute: AP4M1
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 AP4M1
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 AP4M1
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 AP4M1 from PDB

Differential gene expression and gene-gene network for AP4M1
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 AP4M1 and the right PPI network was created from samples without mutations in the LBS of AP4M1. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for AP4M1
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C3714756Intellectual Disability1Biomarker

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

Pharmacological information for AP4M1
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 AP4M1 go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
IIIPeptide ligand (THR,TYR,LYS,PHE,PHE,GLU,GLN)3l81AF264 T280
IIIPeptide ligand (THR,TYR,LYS,PHE,PHE,GLU,GLN)4mdrAT280

Conservation information for LBS of AP4M1
Multiple alignments for O00189 in multiple species
LBSAA sequence# speciesSpecies
E265NLDEFESHRIL3Homo sapiens, Mus musculus, Rattus norvegicus
E265RLDSFDSDRTL1Arabidopsis thaliana
E265YLDEFESHRIL1Bos taurus
F255VDEVSFHSSVN3Homo sapiens, Mus musculus, Rattus norvegicus
F255LDDCNFHESVR1Arabidopsis thaliana
F255VDEVSFHSSVY1Bos taurus
F264VNLDEFESHRI3Homo sapiens, Mus musculus, Rattus norvegicus
F264VRLDSFDSDRT1Arabidopsis thaliana
F264VYLDEFESHRI1Bos taurus
H256DEVSFHSSVNL3Homo sapiens, Mus musculus, Rattus norvegicus
H256DDCNFHESVRL1Arabidopsis thaliana
H256DEVSFHSSVYL1Bos taurus
L261HSSVNLDEFES3Homo sapiens, Mus musculus, Rattus norvegicus
L261HESVRLDSFDS1Arabidopsis thaliana
L261HSSVYLDEFES1Bos taurus
R283ELTVMRYQLSD4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
R283EFPVMNYRMTQ1Arabidopsis thaliana
S254RVDEVSFHSSV4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
S254ILDDCNFHESV1Arabidopsis thaliana
S257EVSFHSSVNLD3Homo sapiens, Mus musculus, Rattus norvegicus
S257DCNFHESVRLD1Arabidopsis thaliana
S257EVSFHSSVYLD1Bos taurus
T280PQGELTVMRYQ4Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus
T280PDGEFPVMNYR1Arabidopsis thaliana
V259SFHSSVNLDEF3Homo sapiens, Mus musculus, Rattus norvegicus
V259NFHESVRLDSF1Arabidopsis thaliana
V259SFHSSVYLDEF1Bos taurus

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