mutLBSgeneDB

mutLBSgeneDB
mutated Ligand Binding Site gene DataBase

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 CUBN
Gene summary
Basic gene Info.Gene symbolCUBN
Gene namecubilin (intrinsic factor-cobalamin receptor)
SynonymsIFCR|MGA1|gp280
CytomapUCSC genome browser: 10p12.31
Type of geneprotein-coding
RefGenesNM_001081.3,
Description460 kDa receptorcubilincubilin precursor variant 1cubilin precursor variant 2intestinal intrinsic factor receptorintrinsic factor-vitamin B12 receptor
Modification date20141207
dbXrefs MIM : 602997
HGNC : HGNC
Ensembl : ENSG00000107611
HPRD : 04296
Vega : OTTHUMG00000017741
ProteinUniProt: O60494
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CUBN
BioGPS: 8029
PathwayNCI Pathway Interaction Database: CUBN
KEGG: CUBN
REACTOME: CUBN
Pathway Commons: CUBN
ContextiHOP: CUBN
ligand binding site mutation search in PubMed: CUBN
UCL Cancer Institute: CUBN
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 CUBN
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
L1030L1030HBLCA1
D1146K1144RLUAD1
D1149D1149GLUAD1
D1221Y1222CLUSC1
V1375R1377LSTAD1
D1149D1149YUCEC1
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 CUBN
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
D1221Y1222C-1.2381057
L1030L1030H-1.1883998
D1146K1144R-0.55234717
D1149D1149G-0.47961446
V1375R1377L-0.23920147
D1149D1149Y-0.063019116
(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 CUBN from PDB

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Differential gene expression and gene-gene network for CUBN
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 CUBN and the right PPI network was created from samples without mutations in the LBS of CUBN. 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 CUBN
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C1306856Imerslund-Grasbeck syndrome9Biomarker, GeneticVariation
umls:C0236733Amphetamine-Related Disorders1Biomarker
umls:C0025202Melanoma1Biomarker

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

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Pharmacological information for CUBN
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.

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
ApprovedDB00200HydroxocobalaminSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CUBN go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
CACALCIUM(2+)3kq4BD1146 D1149
CACALCIUM(2+)3kq4DD1146 D1149
CACALCIUM(2+)3kq4FD1146 D1149
CACALCIUM(2+)3kq4BD1221
CACALCIUM(2+)3kq4DD1221
CACALCIUM(2+)3kq4FD1221
CACALCIUM(2+)3kq4BL1030
CACALCIUM(2+)3kq4DL1030
CACALCIUM(2+)3kq4FL1030
CACALCIUM(2+)3kq4BV1375
CACALCIUM(2+)3kq4DV1375
CACALCIUM(2+)3kq4FV1375


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Conservation information for LBS of CUBN
Multiple alignments for O60494 in multiple species
LBSAA sequence# speciesSpecies
D1027LIFVSDSALAH2Mus musculus, Rattus norvegicus
D1027LVFVTDSDLAY1Homo sapiens
D1027VVFVSDRSVAG1Caenorhabditis elegans
D1027LIFVADSDLAY1Canis lupus familiaris
D1029FVSDSALAHEG2Mus musculus, Rattus norvegicus
D1029FVTDSDLAYEG1Homo sapiens
D1029FVSDRSVAGPG1Caenorhabditis elegans
D1029FVADSDLAYEG1Canis lupus familiaris
D1105NYYT-DFLEIR1Homo sapiens
D1105--CDKSSLMFR1Caenorhabditis elegans
D1105PKCV-DFVEIR1Mus musculus
D1105SQCV-DFVEIR1Rattus norvegicus
D1105GQCVADFVEIR1Canis lupus familiaris
D1146LKFKSDQIDTR1Homo sapiens
D1146IVYKS---INS1Caenorhabditis elegans
D1146LRFKSDTALTA1Mus musculus
D1146LKFKSDAALTA1Rattus norvegicus
D1146LQFTSDFLGSG1Canis lupus familiaris
D1149KSDQIDTRSG-1Homo sapiens
D1149KS---INSEGS1Caenorhabditis elegans
D1149KSDTALTARG-1Mus musculus
D1149KSDAALTAKG-1Rattus norvegicus
D1149TSDFLGSGPG-1Canis lupus familiaris
D1221TL---DYLAVY2Homo sapiens, Canis lupus familiaris
D1221SL---DYLAVF2Mus musculus, Rattus norvegicus
D1221PLFAANRIDFF1Caenorhabditis elegans
D1262LKLRTDAGQQG2Mus musculus, Rattus norvegicus
D1262IKLRTDEGQQG1Homo sapiens
D1262IKYVQSGGFQS1Caenorhabditis elegans
D1262LKFRTDEDQQG1Canis lupus familiaris
D1336INCSTDYLEL-2Homo sapiens, Canis lupus familiaris
D1336INCITDMLKVD1Caenorhabditis elegans
D1336VNCSTDYLEL-1Mus musculus
D1336MNCSTDYVEL-1Rattus norvegicus
D1373VLLLTDGVGRR1Homo sapiens
D1373LTYSSQGDPTN1Caenorhabditis elegans
D1373VVFHTDGVDSG1Mus musculus
D1373VLFHTDGINSG1Rattus norvegicus
D1373VLFYTDGVGHQ1Canis lupus familiaris
D988YNCTNDYLEVY2Homo sapiens, Canis lupus familiaris
D988KSCEYDRVEIY1Caenorhabditis elegans
D988YNCANDYLEVY1Mus musculus
D988YNCTNDYLEIY1Rattus norvegicus
E1096TNFSLEEAIGN1Homo sapiens
E1096NNMSLP-----1Caenorhabditis elegans
E1096TDFALEDYFGP1Mus musculus
E1096TDFTLEDYFGS1Rattus norvegicus
E1096TNFALEEAIGG1Canis lupus familiaris
E1213KDFHLEHHPN-1Homo sapiens
E1213TALDDLNSSDS1Caenorhabditis elegans
E1213QDFHLEHHPN-1Mus musculus
E1213QDFHLEHHPS-1Rattus norvegicus
E1213EDFHLEHHPN-1Canis lupus familiaris
E1263KLRTDAGQQGR2Mus musculus, Rattus norvegicus
E1263KLRTDEGQQGR1Homo sapiens
E1263KYVQSGGFQSK1Caenorhabditis elegans
E1263KFRTDEDQQGG1Canis lupus familiaris
E1328-----EHHINC1Homo sapiens
E1328QKSYFEGGINC1Caenorhabditis elegans
E1328-----ENYVNC1Mus musculus
E1328-----ESYMNC1Rattus norvegicus
E1328-----ENHINC1Canis lupus familiaris
E980SSFYLEFH--Y2Mus musculus, Rattus norvegicus
E980ETFHLEFH--Y1Homo sapiens
E980DVFDLEVTPAK1Caenorhabditis elegans
E980RKFHLEFH--Y1Canis lupus familiaris
G1264LRTDAGQQGR-2Mus musculus, Rattus norvegicus
G1264LRTDEGQQGR-1Homo sapiens
G1264YVQSGGFQSKK1Caenorhabditis elegans
G1264FRTDEDQQGG-1Canis lupus familiaris
I1148FKSDQIDTRSG1Homo sapiens
I1148YKS---INSEG1Caenorhabditis elegans
I1148FKSDTALTARG1Mus musculus
I1148FKSDAALTAKG1Rattus norvegicus
I1148FTSDFLGSGPG1Canis lupus familiaris
L1030VSDSALAHEGF2Mus musculus, Rattus norvegicus
L1030VTDSDLAYEGF1Homo sapiens
L1030VSDRSVAGPGW1Caenorhabditis elegans
L1030VADSDLAYEGF1Canis lupus familiaris
Q1265RTDAGQQGR--2Mus musculus, Rattus norvegicus
Q1265RTDEGQQGR--1Homo sapiens
Q1265VQSGGFQSKKI1Caenorhabditis elegans
Q1265RTDEDQQGG--1Canis lupus familiaris
Q1266TDAGQQGR---2Mus musculus, Rattus norvegicus
Q1266TDEGQQGR---1Homo sapiens
Q1266QSGGFQSKKIF1Caenorhabditis elegans
Q1266TDEDQQGG---1Canis lupus familiaris
T1372QVLLLTDGVGR1Homo sapiens
T1372KLTYSSQGDPT1Caenorhabditis elegans
T1372IVVFHTDGVDS1Mus musculus
T1372HVLFHTDGINS1Rattus norvegicus
T1372QVLFYTDGVGH1Canis lupus familiaris
V1375LLTDGVGRREK1Homo sapiens
V1375YSSQGDPTNQ-1Caenorhabditis elegans
V1375FHTDGVDSGEK1Mus musculus
V1375FHTDGINSGEK1Rattus norvegicus
V1375FYTDGVGHQEK1Canis lupus familiaris
Y1300GYPNPYSENQH1Homo sapiens
Y1300GYPYKVYSNQF1Caenorhabditis elegans
Y1300NYPNPYDKDQR1Mus musculus
Y1300NYPNPYDKNQR1Rattus norvegicus
Y1300HYPNPYSDNQR1Canis lupus familiaris


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