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 CD1D
Gene summary
Basic gene Info.Gene symbolCD1D
Gene nameCD1d molecule
SynonymsCD1A|R3
CytomapUCSC genome browser: 1q23.1
Type of geneprotein-coding
RefGenesNM_001766.3,
DescriptionCD1D antigen, d polypeptideHMC class I antigen-like glycoprotein CD1DR3G1T-cell surface glycoprotein CD1dantigen-presenting glycoprotein CD1ddifferentiation antigen CD1-alpha-3thymocyte antigen CD1D
Modification date20141222
dbXrefs MIM : 188410
HGNC : HGNC
HPRD : 01780
ProteinUniProt: P15813
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CD1D
BioGPS: 912
PathwayNCI Pathway Interaction Database: CD1D
KEGG: CD1D
REACTOME: CD1D
Pathway Commons: CD1D
ContextiHOP: CD1D
ligand binding site mutation search in PubMed: CD1D
UCL Cancer Institute: CD1D
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:0042102positive regulation of T cell proliferation19124746
GO:0048006antigen processing and presentation, endogenous lipid antigen via MHC class Ib10523605


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Ligand binding site mutations for CD1D
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
F132F131LBLCA1
Y91R92QBRCA1
L114V116AKIRC1
T172T172KKIRC1
I87I87TLUAD1
F136Q137HLUAD1
D61S62LLUAD1
T42T42KLUSC1
W149W149LLUSC1
L108S109CLUSC1
A37F36YOV1
L28P27LSKCM1
I141D140NSKCM1
C184,G182T183ISKCM1
V99V99MSTAD1
G46D45GSTAD1
W158L157PSTAD1
R43R43CSTAD1
L112P111LUCEC1
F187S189NUCEC1
F88,V90R89QUCEC1
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 CD1D
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
G46D45G0.085514086
L114V116A-1.2893188
T42T42K-1.2781487
W158L157P-1.2330798
F88R89Q-1.2245574
V90R89Q-1.2245574
V99V99M-1.1749305
I87I87T-1.1027935
T172T172K-0.95877618
L108S109C-0.927402
D61S62L-0.87310453
Y91R92Q-0.77313967
F136Q137H-0.76829698
G182T183I-0.73137377
C184T183I-0.73137377
F132F131L-0.71226937
A37F36Y-0.64415287
L112P111L-0.6088159
R43R43C-0.5687601
L28P27L-0.39006638
I141D140N-0.36653281
W149W149L-0.046222948
F187S189N-0.041279143
(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 CD1D from PDB

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Differential gene expression and gene-gene network for CD1D
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 CD1D and the right PPI network was created from samples without mutations in the LBS of CD1D. 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 CD1D
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0017661Glomerulonephritis, IGA1Biomarker

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

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Pharmacological information for CD1D
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
ExperimentalDB04661Cis-tetracosenoyl sulfatideSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of CD1D go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS


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Conservation information for LBS of CD1D
Multiple alignments for P15813 in multiple species
LBSAA sequence# speciesSpecies
A37QISSFANSSWT2Homo sapiens, Pan troglodytes
A37QMSSFANRSWS1Mus musculus
A37QISSFANRSWS1Rattus norvegicus
A48RTDGLAWLGEL2Homo sapiens, Pan troglodytes
A48RTDSVVWLGDL2Mus musculus, Rattus norvegicus
C184LLNGTCPQFVS2Homo sapiens, Pan troglodytes
C184LLNDTCPLFVR1Mus musculus
C184LLNDTCPQFVR1Rattus norvegicus
C30LFPLRCLQISS2Homo sapiens, Pan troglodytes
C30NYTFRCLQMSS1Mus musculus
C30NYTFGCLQISS1Rattus norvegicus
D169QVLNQDKWTRE2Homo sapiens, Pan troglodytes
D169KVLNADQGTSA1Mus musculus
D169KMLNADEGTRE1Rattus norvegicus
D61HSWSNDSDTVR2Homo sapiens, Pan troglodytes
D61HRWSNDSATIS1Mus musculus
D61HRWSNDSDTIS1Rattus norvegicus
D98SSFTRDVKEFA2Homo sapiens, Pan troglodytes
D98VSFTRDIQELV1Mus musculus
D98TSFTRDIKEIV1Rattus norvegicus
F102RDVKEFAKML-2Homo sapiens, Pan troglodytes
F102RDIQELVKMMS1Mus musculus
F102RDIKEIVKMMS1Rattus norvegicus
F132ASNNFFHVAFQ2Homo sapiens, Pan troglodytes
F132ASESFLHVAFQ2Mus musculus, Rattus norvegicus
F136FFHVAFQGKDI2Homo sapiens, Pan troglodytes
F136FLHVAFQGKYV1Mus musculus
F136FLHVAFQGEYV1Rattus norvegicus
F187GTCPQFVSGLL2Homo sapiens, Pan troglodytes
F187DTCPLFVRGLL1Mus musculus
F187DTCPQFVRGLL1Rattus norvegicus
F88TLQHIFRVYRS2Homo sapiens, Pan troglodytes
F88KLQHMFQVYRV1Mus musculus
F88KLQHMFQVYRT1Rattus norvegicus
F95VYRSSFTRDVK2Homo sapiens, Pan troglodytes
F95VYRVSFTRDIQ1Mus musculus
F95VYRTSFTRDIK1Rattus norvegicus
G182QWLLNGTCPQF2Homo sapiens, Pan troglodytes
G182QMLLNDTCPLF1Mus musculus
G182QILLNDTCPQF1Rattus norvegicus
G46WTRTDGLAWLG2Homo sapiens, Pan troglodytes
G46WSRTDSVVWLG2Mus musculus, Rattus norvegicus
H56GELQTHSWSND2Homo sapiens, Pan troglodytes
H56GDLQTHRWSND2Mus musculus, Rattus norvegicus
H86WETLQHIFRVY2Homo sapiens, Pan troglodytes
H86WEKLQHMFQVY2Mus musculus, Rattus norvegicus
I141FQGKDILSFQG2Homo sapiens, Pan troglodytes
I141FQGKYVVRFWG1Mus musculus
I141FQGEYVVRFHG1Rattus norvegicus
I87ETLQHIFRVYR2Homo sapiens, Pan troglodytes
I87EKLQHMFQVYR2Mus musculus, Rattus norvegicus
L108ML--RLSYPLE2Homo sapiens, Pan troglodytes
L108MMSPKEDYPIE2Mus musculus, Rattus norvegicus
L112RLSYPLELQVS2Homo sapiens, Pan troglodytes
L112KEDYPIEIQLS1Mus musculus
L112KEDYPIEVQLS1Rattus norvegicus
L114SYPLELQVSAG2Homo sapiens, Pan troglodytes
L114DYPIEIQLSAG1Mus musculus
L114DYPIEVQLSAG1Rattus norvegicus
L142QGKDILSFQGT2Homo sapiens, Pan troglodytes
L142QGKYVVRFWGT1Mus musculus
L142QGEYVVRFHGT1Rattus norvegicus
L166LAIQVLNQDKW2Homo sapiens, Pan troglodytes
L166LPIKVLNADQG1Mus musculus
L166LPIKMLNADEG1Rattus norvegicus
L179ETVQWLLNGTC2Homo sapiens, Pan troglodytes
L179ATVQMLLNDTC1Mus musculus
L179ETVQILLNDTC1Rattus norvegicus
L28QRLFPLRCLQI2Homo sapiens, Pan troglodytes
L28QKNYTFRCLQM1Mus musculus
L28Q-NYTFGCLQI1Rattus norvegicus
L31FPLRCLQISSF2Homo sapiens, Pan troglodytes
L31YTFRCLQMSSF1Mus musculus
L31YTFGCLQISSF1Rattus norvegicus
L47TRTDGLAWLGE2Homo sapiens, Pan troglodytes
L47SRTDSVVWLGD2Mus musculus, Rattus norvegicus
L84QQWETLQHIFR2Homo sapiens, Pan troglodytes
L84QQWEKLQHMFQ2Mus musculus, Rattus norvegicus
N181VQWLLNGTCPQ2Homo sapiens, Pan troglodytes
N181VQMLLNDTCPL1Mus musculus
N181VQILLNDTCPQ1Rattus norvegicus
N38ISSFANSSWTR2Homo sapiens, Pan troglodytes
N38MSSFANRSWSR1Mus musculus
N38ISSFANRSWSR1Rattus norvegicus
N60THSWSNDSDTV2Homo sapiens, Pan troglodytes
N60THRWSNDSATI1Mus musculus
N60THRWSNDSDTI1Rattus norvegicus
Q32PLRCLQISSFA2Homo sapiens, Pan troglodytes
Q32TFRCLQMSSFA1Mus musculus
Q32TFGCLQISSFA1Rattus norvegicus
R43NSSWTRTDGLA2Homo sapiens, Pan troglodytes
R43NRSWSRTDSVV2Mus musculus, Rattus norvegicus
R97RSSFTRDVKEF2Homo sapiens, Pan troglodytes
R97RVSFTRDIQEL1Mus musculus
R97RTSFTRDIKEI1Rattus norvegicus
S94RVYRSSFTRDV2Homo sapiens, Pan troglodytes
S94QVYRVSFTRDI1Mus musculus
S94QVYRTSFTRDI1Rattus norvegicus
T172NQDKWTRETVQ2Homo sapiens, Pan troglodytes
T172NADQGTSATVQ1Mus musculus
T172NADEGTRETVQ1Rattus norvegicus
T175KWTRETVQWLL2Homo sapiens, Pan troglodytes
T175QGTSATVQMLL1Mus musculus
T175EGTRETVQILL1Rattus norvegicus
T42ANSSWTRTDGL2Homo sapiens, Pan troglodytes
T42ANRSWSRTDSV2Mus musculus, Rattus norvegicus
V134NNFFHVAFQGK2Homo sapiens, Pan troglodytes
V134ESFLHVAFQGK1Mus musculus
V134ESFLHVAFQGE1Rattus norvegicus
V176WTRETVQWLLN2Homo sapiens, Pan troglodytes
V176GTSATVQMLLN1Mus musculus
V176GTRETVQILLN1Rattus norvegicus
V65NDSDTVRSLKP2Homo sapiens, Pan troglodytes
V65NDSATISFTKP1Mus musculus
V65NDSDTISFTKP1Rattus norvegicus
V90QHIFRVYRSSF2Homo sapiens, Pan troglodytes
V90QHMFQVYRVSF1Mus musculus
V90QHMFQVYRTSF1Rattus norvegicus
V99SFTRDVKEFAK2Homo sapiens, Pan troglodytes
V99SFTRDIQELVK1Mus musculus
V99SFTRDIKEIVK1Rattus norvegicus
W149FQGTSWEPTQE2Homo sapiens, Pan troglodytes
W149FWGTSWQTVPG1Mus musculus
W149FHGTSWQKVPE1Rattus norvegicus
W158QEAPLWVNLAI2Homo sapiens, Pan troglodytes
W158PGAPSWLDLPI1Mus musculus
W158PEAPSWLDLPI1Rattus norvegicus
W171LNQDKWTRETV2Homo sapiens, Pan troglodytes
W171LNADQGTSATV1Mus musculus
W171LNADEGTRETV1Rattus norvegicus
W41FANSSWTRTDG2Homo sapiens, Pan troglodytes
W41FANRSWSRTDS2Mus musculus, Rattus norvegicus
W58LQTHSWSNDSD2Homo sapiens, Pan troglodytes
W58LQTHRWSNDSA1Mus musculus
W58LQTHRWSNDSD1Rattus norvegicus
W81FSDQQWETLQH2Homo sapiens, Pan troglodytes
W81LSNQQWEKLQH1Mus musculus
W81FSNQQWEKLQH1Rattus norvegicus
Y91HIFRVYRSSFT2Homo sapiens, Pan troglodytes
Y91HMFQVYRVSFT1Mus musculus
Y91HMFQVYRTSFT1Rattus norvegicus


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