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 COMP
Gene summary
Basic gene Info.Gene symbolCOMP
Gene namecartilage oligomeric matrix protein
SynonymsEDM1|EPD1|MED|PSACH|THBS5
CytomapUCSC genome browser: 19p13.1
Type of geneprotein-coding
RefGenesNM_000095.2,
DescriptionTSP5cartilage oligomeric matrix protein (pseudoachondroplasia, epiphyseal dysplasia 1, multiple)cartilage oligomeric matrix protein(pseudoachondroplasia, epiphyseal dysplasia 1, multiple)pseudoachondroplasia (epiphyseal dysplasia 1, multiple)thrombosp
Modification date20141219
dbXrefs MIM : 600310
HGNC : HGNC
Ensembl : ENSG00000105664
HPRD : 02632
Vega : OTTHUMG00000169318
ProteinUniProt: P49747
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_COMP
BioGPS: 1311
PathwayNCI Pathway Interaction Database: COMP
KEGG: COMP
REACTOME: COMP
Pathway Commons: COMP
ContextiHOP: COMP
ligand binding site mutation search in PubMed: COMP
UCL Cancer Institute: COMP
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:0043066negative regulation of apoptotic process17993464
GO:0060173limb development16542502


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Ligand binding site mutations for COMP
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
N338R337HBLCA1
D494Q492LBLCA1
D372,D374D373NBRCA1
P411P411LBRCA1
V390V390ICOAD1
D349D349NCOAD1
N415P416LCOAD1
F425F425ILUAD1
G309G309ELUSC1
G309G309RLUSC1
V390,P388R389MLUSC1
D678K680NOV1
P411P411SSKCM1
D595D595NSKCM1
D424D424NSKCM1
D361D361NSKCM1
T592T592MSTAD1
R367R367WSTAD1
N382,I380R381HUCEC1
D469D469GUCEC1
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 COMP
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
N338R337H-1.7606789
D595D595N-1.562534
V390V390I-1.261536
P411P411S-1.2213756
F425F425I-1.2184378
D424D424N-1.1264335
D372D373N-1.0435136
D374D373N-1.0435136
D678K680N-1.0310582
N382R381H-1.0292775
I380R381H-1.0292775
R367R367W-0.96455504
T592T592M-0.93645039
D469D469G-0.76125608
D349D349N-0.75774903
P388R389M-0.72441417
V390R389M-0.72441417
N415P416L-0.59320906
P411P411L-0.57328821
G309G309R-0.27596877
G309G309E-0.1551635
D361D361N-0.15251232
D494Q492L-0.040906649
(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 COMP from PDB

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Differential gene expression and gene-gene network for COMP
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 COMP and the right PPI network was created from samples without mutations in the LBS of COMP. 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 COMP
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0410538Pseudoachondroplasia60Biomarker, GeneticVariation
umls:C0029408Osteoarthritis13AlteredExpression, Biomarker, GeneticVariation
umls:C1838280Epiphyseal dysplasia, multiple, 12Biomarker, GeneticVariation
umls:C0022410Joint Instability1Biomarker

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

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Pharmacological information for COMP
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
NutraceuticalDB01373CalciumSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of COMP go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
CACALCIUM(2+)3fbyAD349
CACALCIUM(2+)3fbyBD349
CACALCIUM(2+)3fbyCD349
CACALCIUM(2+)3fbyAD361 R367 D372
CACALCIUM(2+)3fbyBD361 R367 D372
CACALCIUM(2+)3fbyCD361 R367 D372
CACALCIUM(2+)3fbyAD372 D374
CACALCIUM(2+)3fbyBD372 D374
CACALCIUM(2+)3fbyCD372 D374
CACALCIUM(2+)3fbyBD374 I380
CACALCIUM(2+)3fbyAD374 I380 N382 P388
CACALCIUM(2+)3fbyCD374 I380 P388
CACALCIUM(2+)3fbyAD424
CACALCIUM(2+)3fbyAD424
CACALCIUM(2+)3fbyBD424
CACALCIUM(2+)3fbyBD424
CACALCIUM(2+)3fbyCD424
CACALCIUM(2+)3fbyCD424 F425
CACALCIUM(2+)3fbyAD469
CACALCIUM(2+)3fbyAD469
CACALCIUM(2+)3fbyAD469
CACALCIUM(2+)3fbyBD469
CACALCIUM(2+)3fbyBD469
CACALCIUM(2+)3fbyBD469
CACALCIUM(2+)3fbyCD469
CACALCIUM(2+)3fbyCD469
CACALCIUM(2+)3fbyCD469
CACALCIUM(2+)3fbyAD494
CACALCIUM(2+)3fbyBD494
CACALCIUM(2+)3fbyCD494
CACALCIUM(2+)3fbyAD595
CACALCIUM(2+)3fbyAD595
CACALCIUM(2+)3fbyBD595
CACALCIUM(2+)3fbyBD595
CACALCIUM(2+)3fbyCD595
CACALCIUM(2+)3fbyCD595
CACALCIUM(2+)3fbyAN338 D349
CACALCIUM(2+)3fbyBN338 D349
CACALCIUM(2+)3fbyCN338 D349
CACALCIUM(2+)3fbyAN415
CACALCIUM(2+)3fbyCN415
CACALCIUM(2+)3fbyAP388 V390
CACALCIUM(2+)3fbyCP388 V390
CACALCIUM(2+)3fbyBP411 N415
CACALCIUM(2+)3fbyAT592 D678
CACALCIUM(2+)3fbyBT592 D678
CACALCIUM(2+)3fbyCT592 D678
CACALCIUM(2+)3fbyBV390


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Conservation information for LBS of COMP
Multiple alignments for P49747 in multiple species
LBSAA sequence# speciesSpecies
A316ACDPDADGDGV3Homo sapiens, Mus musculus, Rattus norvegicus
A524VCPENAEVTLT3Homo sapiens, Mus musculus, Rattus norvegicus
C292CRKDNCVTVPN3Homo sapiens, Mus musculus, Rattus norvegicus
C328NEQDNCPLVRN2Mus musculus, Rattus norvegicus
C328NEKDNCPLVRN1Homo sapiens
C351DACDNCRSQKN2Homo sapiens, Rattus norvegicus
C351DACDNCRSKKN1Mus musculus
C387NVADNCPRVPN2Mus musculus, Rattus norvegicus
C387NQADNCPRVPN1Homo sapiens
C410DACDNCPQKDN2Mus musculus, Rattus norvegicus
C410DACDNCPQKSN1Homo sapiens
C448DSRDNCPTVPN3Homo sapiens, Mus musculus, Rattus norvegicus
C520DKIDVCPENAE3Homo sapiens, Mus musculus, Rattus norvegicus
D269LLCGRDTDLDG2Mus musculus, Rattus norvegicus
D269ILCGRDTDLDG1Homo sapiens
D271CGRDTDLDGFP3Homo sapiens, Mus musculus, Rattus norvegicus
D273RDTDLDGFPDE3Homo sapiens, Mus musculus, Rattus norvegicus
D277LDGFPDEKLRC3Homo sapiens, Mus musculus, Rattus norvegicus
D290RQCRKDNCVTV3Homo sapiens, Mus musculus, Rattus norvegicus
D302NSGQEDVDRDG2Homo sapiens, Mus musculus
D302NSGQEDVDRDR1Rattus norvegicus
D304GQEDVDRDGIG2Homo sapiens, Mus musculus
D304GQEDVDRDRIG1Rattus norvegicus
D306EDVDRDGIGDA2Homo sapiens, Mus musculus
D306EDVDRDRIGDA1Rattus norvegicus
D310RDGIGDACDPD2Homo sapiens, Mus musculus
D310RDRIGDACDPD1Rattus norvegicus
D313IGDACDPDADG3Homo sapiens, Mus musculus, Rattus norvegicus
D315DACDPDADGDG3Homo sapiens, Mus musculus, Rattus norvegicus
D317CDPDADGDGVP3Homo sapiens, Mus musculus, Rattus norvegicus
D319PDADGDGVPNE3Homo sapiens, Mus musculus, Rattus norvegicus
D326VPNEQDNCPLV2Mus musculus, Rattus norvegicus
D326VPNEKDNCPLV1Homo sapiens
D340DQRNTDEDKWG1Homo sapiens
D340DQRNSDSDKWG1Mus musculus
D340DQRNSDKDKWG1Rattus norvegicus
D342RNTDEDKWGDA1Homo sapiens
D342RNSDSDKWGDA1Mus musculus
D342RNSDKDKWGDA1Rattus norvegicus
D346EDKWGDACDNC1Homo sapiens
D346SDKWGDACDNC1Mus musculus
D346KDKWGDACDNC1Rattus norvegicus
D349WGDACDNCRSQ2Homo sapiens, Rattus norvegicus
D349WGDACDNCRSK1Mus musculus
D361NDDQKDTDQDG1Homo sapiens
D361NDDQKDTDLDG1Mus musculus
D361NDDQKDTDRDG1Rattus norvegicus
D363DQKDTDQDGRG1Homo sapiens
D363DQKDTDLDGRG1Mus musculus
D363DQKDTDRDGQG1Rattus norvegicus
D365KDTDQDGRGDA1Homo sapiens
D365KDTDLDGRGDA1Mus musculus
D365KDTDRDGQGDA1Rattus norvegicus
D369QDGRGDACDDD1Homo sapiens
D369LDGRGDACDDD1Mus musculus
D369RDGQGDACDDD1Rattus norvegicus
D372RGDACDDDIDG2Homo sapiens, Mus musculus
D372QGDACDDDIDG1Rattus norvegicus
D374DACDDDIDGDR3Homo sapiens, Mus musculus, Rattus norvegicus
D376CDDDIDGDRIR3Homo sapiens, Mus musculus, Rattus norvegicus
D378DDIDGDRIRNV2Mus musculus, Rattus norvegicus
D378DDIDGDRIRNQ1Homo sapiens
D385IRNVADNCPRV2Mus musculus, Rattus norvegicus
D385IRNQADNCPRV1Homo sapiens
D397NFDQSDSDGDG2Mus musculus, Rattus norvegicus
D397NSDQKDSDGDG1Homo sapiens
D399DQSDSDGDGVG2Mus musculus, Rattus norvegicus
D399DQKDSDGDGIG1Homo sapiens
D408VGDACDNCPQK2Mus musculus, Rattus norvegicus
D408IGDACDNCPQK1Homo sapiens
D420NPDQRDVDHDF2Mus musculus, Rattus norvegicus
D420NPDQADVDHDF1Homo sapiens
D422DQRDVDHDFVG2Mus musculus, Rattus norvegicus
D422DQADVDHDFVG1Homo sapiens
D424RDVDHDFVGDA2Mus musculus, Rattus norvegicus
D424ADVDHDFVGDA1Homo sapiens
D428HDFVGDACDSD3Homo sapiens, Mus musculus, Rattus norvegicus
D431VGDACDSDQDQ3Homo sapiens, Mus musculus, Rattus norvegicus
D435CDSDQDQDGDG3Homo sapiens, Mus musculus, Rattus norvegicus
D437SDQDQDGDGHQ3Homo sapiens, Mus musculus, Rattus norvegicus
D439QDQDGDGHQDS3Homo sapiens, Mus musculus, Rattus norvegicus
D443GDGHQDSRDNC3Homo sapiens, Mus musculus, Rattus norvegicus
D446HQDSRDNCPTV3Homo sapiens, Mus musculus, Rattus norvegicus
D458NSAQQDSDHDG2Mus musculus, Rattus norvegicus
D458NSAQEDSDHDG1Homo sapiens
D460AQQDSDHDGKG2Mus musculus, Rattus norvegicus
D460AQEDSDHDGQG1Homo sapiens
D462QDSDHDGKGDA2Mus musculus, Rattus norvegicus
D462EDSDHDGQGDA1Homo sapiens
D469KGDACDDDDDN2Mus musculus, Rattus norvegicus
D469QGDACDDDDDN1Homo sapiens
D471DACDDDDDNDG3Homo sapiens, Mus musculus, Rattus norvegicus
D472ACDDDDDNDGV3Homo sapiens, Mus musculus, Rattus norvegicus
D473CDDDDDNDGVP3Homo sapiens, Mus musculus, Rattus norvegicus
D475DDDDNDGVPDS3Homo sapiens, Mus musculus, Rattus norvegicus
D482VPDSRDNCRLV3Homo sapiens, Mus musculus, Rattus norvegicus
D494NPGQEDNDRDG2Mus musculus, Rattus norvegicus
D494NPGQEDADRDG1Homo sapiens
D496GQEDNDRDGVG2Mus musculus, Rattus norvegicus
D496GQEDADRDGVG1Homo sapiens
D498EDNDRDGVGDA2Mus musculus, Rattus norvegicus
D498EDADRDGVGDV1Homo sapiens
D502RDGVGDACQGD2Mus musculus, Rattus norvegicus
D502RDGVGDVCQDD1Homo sapiens
D507DACQGDFDADK2Mus musculus, Rattus norvegicus
D507DVCQDDFDADK1Homo sapiens
D509CQGDFDADKVI2Mus musculus, Rattus norvegicus
D509CQDDFDADKVV1Homo sapiens
D511GDFDADKVIDK2Mus musculus, Rattus norvegicus
D511DDFDADKVVDK1Homo sapiens
D515ADKVIDKIDVC2Mus musculus, Rattus norvegicus
D515ADKVVDKIDVC1Homo sapiens
D518VIDKIDVCPEN2Mus musculus, Rattus norvegicus
D518VVDKIDVCPEN1Homo sapiens
D593VNTATDDDYAG2Mus musculus, Rattus norvegicus
D593VNTVTDDDYAG1Homo sapiens
D594NTATDDDYAGF2Mus musculus, Rattus norvegicus
D594NTVTDDDYAGF1Homo sapiens
D595TATDDDYAGFI2Mus musculus, Rattus norvegicus
D595TVTDDDYAGFI1Homo sapiens
D678NVGWKDKTSYR2Mus musculus, Rattus norvegicus
D678NVGWKDKKSYR1Homo sapiens
E236DGSPSPCHEKA2Mus musculus, Rattus norvegicus
E236DGSPSECHEHA1Homo sapiens
F275TDLDGFPDEKL3Homo sapiens, Mus musculus, Rattus norvegicus
F425DVDHDFVGDAC3Homo sapiens, Mus musculus, Rattus norvegicus
G309DRDGIGDACDP2Homo sapiens, Mus musculus
G309DRDRIGDACDP1Rattus norvegicus
G377DDDIDGDRIRN3Homo sapiens, Mus musculus, Rattus norvegicus
G476DDDNDGVPDSR3Homo sapiens, Mus musculus, Rattus norvegicus
G501DRDGVGDACQG2Mus musculus, Rattus norvegicus
G501DRDGVGDVCQD1Homo sapiens
H441QDGDGHQDSRD3Homo sapiens, Mus musculus, Rattus norvegicus
I308VDRDGIGDACD2Homo sapiens, Mus musculus
I308VDRDRIGDACD1Rattus norvegicus
I375ACDDDIDGDRI3Homo sapiens, Mus musculus, Rattus norvegicus
I380IDGDRIRNVAD2Mus musculus, Rattus norvegicus
I380IDGDRIRNQAD1Homo sapiens
K355NCRSQKNDDQK2Homo sapiens, Rattus norvegicus
K355NCRSKKNDDQK1Mus musculus
K413DNCPQKDNPDQ2Mus musculus, Rattus norvegicus
K413DNCPQKSNPDQ1Homo sapiens
N297CVTVPNSGQED3Homo sapiens, Mus musculus, Rattus norvegicus
N333CPLVRNPDQRN3Homo sapiens, Mus musculus, Rattus norvegicus
N338NPDQRNTDEDK1Homo sapiens
N338NPDQRNSDSDK1Mus musculus
N338NPDQRNSDKDK1Rattus norvegicus
N356CRSQKNDDQKD2Homo sapiens, Rattus norvegicus
N356CRSKKNDDQKD1Mus musculus
N382GDRIRNVADNC2Mus musculus, Rattus norvegicus
N382GDRIRNQADNC1Homo sapiens
N392CPRVPNFDQSD2Mus musculus, Rattus norvegicus
N392CPRVPNSDQKD1Homo sapiens
N415CPQKDNPDQRD2Mus musculus, Rattus norvegicus
N415CPQKSNPDQAD1Homo sapiens
N453CPTVPNSAQQD2Mus musculus, Rattus norvegicus
N453CPTVPNSAQED1Homo sapiens
N474DDDDDNDGVPD3Homo sapiens, Mus musculus, Rattus norvegicus
N523DVCPENAEVTL3Homo sapiens, Mus musculus, Rattus norvegicus
N565IVQTMNSDPGL3Homo sapiens, Mus musculus, Rattus norvegicus
P296NCVTVPNSGQE3Homo sapiens, Mus musculus, Rattus norvegicus
P388VADNCPRVPNF2Mus musculus, Rattus norvegicus
P388QADNCPRVPNS1Homo sapiens
P391NCPRVPNFDQS2Mus musculus, Rattus norvegicus
P391NCPRVPNSDQK1Homo sapiens
P411ACDNCPQKDNP2Mus musculus, Rattus norvegicus
P411ACDNCPQKSNP1Homo sapiens
P449SRDNCPTVPNS3Homo sapiens, Mus musculus, Rattus norvegicus
P478DNDGVPDSRDN3Homo sapiens, Mus musculus, Rattus norvegicus
P521KIDVCPENAEV3Homo sapiens, Mus musculus, Rattus norvegicus
Q226CQRRGQHFCPD2Mus musculus, Rattus norvegicus
Q226CQRRAQRFCPD1Homo sapiens
Q300VPNSGQEDVDR3Homo sapiens, Mus musculus, Rattus norvegicus
Q354DNCRSQKNDDQ2Homo sapiens, Rattus norvegicus
Q354DNCRSKKNDDQ1Mus musculus
Q359QKNDDQKDTDQ1Homo sapiens
Q359KKNDDQKDTDL1Mus musculus
Q359QKNDDQKDTDR1Rattus norvegicus
Q418KDNPDQRDVDH2Mus musculus, Rattus norvegicus
Q418KSNPDQADVDH1Homo sapiens
Q464SDHDGKGDACD2Mus musculus, Rattus norvegicus
Q464SDHDGQGDACD1Homo sapiens
Q505VGDACQGDFDA2Mus musculus, Rattus norvegicus
Q505VGDVCQDDFDA1Homo sapiens
Q616VVMWKQMEQTY3Homo sapiens, Mus musculus, Rattus norvegicus
Q619WKQMEQTYWQA3Homo sapiens, Mus musculus, Rattus norvegicus
R332NCPLVRNPDQR3Homo sapiens, Mus musculus, Rattus norvegicus
R352ACDNCRSQKND2Homo sapiens, Rattus norvegicus
R352ACDNCRSKKND1Mus musculus
R367TDQDGRGDACD1Homo sapiens
R367TDLDGRGDACD1Mus musculus
R367TDRDGQGDACD1Rattus norvegicus
S414NCPQKDNPDQR2Mus musculus, Rattus norvegicus
S414NCPQKSNPDQA1Homo sapiens
S728GVFCFSQENII3Homo sapiens, Mus musculus, Rattus norvegicus
T362DDQKDTDQDGR1Homo sapiens
T362DDQKDTDLDGR1Mus musculus
T362DDQKDTDRDGQ1Rattus norvegicus
T527ENAEVTLTDFR3Homo sapiens, Mus musculus, Rattus norvegicus
T592HVNTATDDDYA2Mus musculus, Rattus norvegicus
T592HVNTVTDDDYA1Homo sapiens
V293RKDNCVTVPNS3Homo sapiens, Mus musculus, Rattus norvegicus
V295DNCVTVPNSGQ3Homo sapiens, Mus musculus, Rattus norvegicus
V321ADGDGVPNEQD2Mus musculus, Rattus norvegicus
V321ADGDGVPNEKD1Homo sapiens
V331DNCPLVRNPDQ3Homo sapiens, Mus musculus, Rattus norvegicus
V390DNCPRVPNFDQ2Mus musculus, Rattus norvegicus
V390DNCPRVPNSDQ1Homo sapiens
V421PDQRDVDHDFV2Mus musculus, Rattus norvegicus
V421PDQADVDHDFV1Homo sapiens
V426VDHDFVGDACD3Homo sapiens, Mus musculus, Rattus norvegicus
V451DNCPTVPNSAQ3Homo sapiens, Mus musculus, Rattus norvegicus
V477DDNDGVPDSRD3Homo sapiens, Mus musculus, Rattus norvegicus
V500NDRDGVGDACQ2Mus musculus, Rattus norvegicus
V500ADRDGVGDVCQ1Homo sapiens
V513FDADKVIDKID2Mus musculus, Rattus norvegicus
V513FDADKVVDKID1Homo sapiens
V526PENAEVTLTDF3Homo sapiens, Mus musculus, Rattus norvegicus
V591FHVNTATDDDY2Mus musculus, Rattus norvegicus
V591FHVNTVTDDDY1Homo sapiens
W344TDEDKWGDACD1Homo sapiens
W344SDSDKWGDACD1Mus musculus
W344SDKDKWGDACD1Rattus norvegicus


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