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 SEPSECS
Gene summary
Basic gene Info.Gene symbolSEPSECS
Gene nameSep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase
SynonymsLP|PCH2D|SLA|SLA/LP
CytomapUCSC genome browser: 4p15.2
Type of geneprotein-coding
RefGenesNM_016955.3,
NM_001159728.1,
DescriptionO-phosphoseryl-tRNA(Sec) selenium transferaseSLA-p35SLA/LP autoantigenUGA suppressor tRNA-associated proteinliver-pancreas antigensoluble liver antigensoluble liver antigen/liver pancreas antigentRNA(Ser/Sec)-associated antigenic protein
Modification date20141207
dbXrefs MIM : 613009
HGNC : HGNC
Ensembl : ENSG00000109618
HPRD : 11561
Vega : OTTHUMG00000128563
ProteinUniProt: Q9HD40
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SEPSECS
BioGPS: 51091
PathwayNCI Pathway Interaction Database: SEPSECS
KEGG: SEPSECS
REACTOME: SEPSECS
Pathway Commons: SEPSECS
ContextiHOP: SEPSECS
ligand binding site mutation search in PubMed: SEPSECS
UCL Cancer Institute: SEPSECS
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 SEPSECS

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
K40C41FBRCA1
K284F286VCOAD1
G99G99SCOAD1
Y255Y255CCOAD1
H368P367LLUAD1
R97R97QUCEC1
S174S174FUCEC1
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 SEPSECS
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
R97R97Q-1.5674934
K284F286V-1.1761142
Y255Y255C-1.0584624
H368P367L-0.86611203
G99G99S-0.59676837
K40C41F-0.56172859
S174S174F-0.21339274
(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 SEPSECS from PDB

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Differential gene expression and gene-gene network for SEPSECS
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 SEPSECS and the right PPI network was created from samples without mutations in the LBS of SEPSECS. 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 SEPSECS
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C3151140PONTOCEREBELLAR HYPOPLASIA, TYPE 2D1Biomarker, GeneticVariation
umls:C0043094Weight Gain1Biomarker

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

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Pharmacological information for SEPSECS

Gene-centered drug-gene interaction network
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure
NutraceuticalDB00114Pyridoxal PhosphateSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of SEPSECS go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
TS6PHOSPHOROTHIOIC O,O,S-ACID3hl2AH368
SEPO-PHOSPHO-L-SERINE RESIDUE3hl2BH368
SEPO-PHOSPHO-L-SERINE RESIDUE3hl2DH368
NUCNucleic Acids3hl2AK40
NUCNucleic Acids3hl2CK40
TS6PHOSPHOROTHIOIC O,O,S-ACID3hl2AR97
TS6PHOSPHOROTHIOIC O,O,S-ACID3hl2CR97
SEPO-PHOSPHO-L-SERINE RESIDUE3hl2BR97 G99
SEPO-PHOSPHO-L-SERINE RESIDUE3hl2DR97 G99
PLR(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE3hl2AS174 Y255 K284
PLR(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE3hl2BS174 Y255 K284
PLR(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE3hl2CS174 Y255 K284
PLR(5-HYDROXY-4,6-DIMETHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE3hl2DS174 Y255 K284


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Conservation information for LBS of SEPSECS
Multiple alignments for Q9HD40 in multiple species
LBSAA sequence# speciesSpecies
A143FVVPMATGMSL4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
A143IVVPLCTGMSL1Caenorhabditis elegans
A254HIVNNAYGVQS1Homo sapiens
A254HLVNNAYGLQS1Caenorhabditis elegans
A254HIVNNAYGVQP1Danio rerio
A254HVVNNAYGVQS1Xenopus tropicalis
A254HVVNNAYGLQS1Mus musculus
C175IDQKSCFKSMI2Homo sapiens, Xenopus tropicalis
C175IDQKSCFKSMV2Danio rerio, Mus musculus
C175IDQKSSLKSIY1Caenorhabditis elegans
E37IRLLLEKGKCP1Homo sapiens
E37LNSLWEKKQIP1Caenorhabditis elegans
E37IRRLLDQGKCP1Danio rerio
E37VRQLVEQGKCP1Xenopus tropicalis
E37IRLLLEQGKCP1Mus musculus
G145VPMATGMSLTL4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
G145VPLCTGMSLSL1Caenorhabditis elegans
G99GIGRSGDISAV2Homo sapiens, Mus musculus
G99GIGRSGNLLEI1Caenorhabditis elegans
G99GIGRSGDIAAV1Danio rerio
G99GIGRSGDISAI1Xenopus tropicalis
H132KLAGVHTVANC1Homo sapiens
H132HLLGLHAVKSC1Caenorhabditis elegans
H132KLTGVRSVSSC1Danio rerio
H132RLAGVRTASSC1Xenopus tropicalis
H132KLAGVHSVASC1Mus musculus
H264SSKCMHLIQQG3Homo sapiens, Xenopus tropicalis, Mus musculus
H264SEETIRKIAAA1Caenorhabditis elegans
H264PSKCMHLIQQG1Danio rerio
H30RRSHEHLIRLL1Homo sapiens
H30SKSSNKLLNSL1Caenorhabditis elegans
H30RRGHEQLIRRL1Danio rerio
H30RRMHEQLVRQL1Xenopus tropicalis
H30RRAHEHLIRLL1Mus musculus
H368LLHTPHNPISL1Homo sapiens
H368VYEVPENEISS1Caenorhabditis elegans
H368LLKTPHNPISL1Danio rerio
H368LLETPHNPISL1Xenopus tropicalis
H368LLQTPHNPISL1Mus musculus
I170IIWPRIDQKSC3Homo sapiens, Xenopus tropicalis, Mus musculus
I170VVWLRIDQKSS1Caenorhabditis elegans
I170ILWPRIDQKSC1Danio rerio
K261GVQSSKCMHLI2Homo sapiens, Xenopus tropicalis
K261GLQSEETIRKI1Caenorhabditis elegans
K261GVQPSKCMHLI1Danio rerio
K261GLQSSKCMHLI1Mus musculus
K284VQSLDKNFMVP3Homo sapiens, Xenopus tropicalis, Mus musculus
K284VQSLDKNFQVP1Caenorhabditis elegans
K284VQSLDKNFVVP1Danio rerio
K38RLLLEKGKCPE1Homo sapiens
K38NSLWEKKQIPE1Caenorhabditis elegans
K38RRLLDQGKCPE1Danio rerio
K38RQLVEQGKCPK1Xenopus tropicalis
K38RLLLEQGKCPE1Mus musculus
K40LLEKGKCPENG1Homo sapiens
K40LWEKKQIPEEG1Caenorhabditis elegans
K40LLDQGKCPEEG1Danio rerio
K40LVEQGKCPKEP1Xenopus tropicalis
K40LLEQGKCPEDG1Mus musculus
K452VDLFIKRLDRC1Homo sapiens
K452LEELFTRLTSS1Caenorhabditis elegans
K452VTVCMKRLGKC1Danio rerio
K452VDMFIKRLDKC1Xenopus tropicalis
K452VDLFIKRLDKC1Mus musculus
M394TQLGSMLFTRQ4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
M394TLFGSILFAKG1Caenorhabditis elegans
N252IPHIVNNAYGV2Homo sapiens, Danio rerio
N252VPHLVNNAYGL1Caenorhabditis elegans
N252IPHVVNNAYGV1Xenopus tropicalis
N252IPHVVNNAYGL1Mus musculus
Q105DISAVQPKAAG2Homo sapiens, Mus musculus
Q105NLLEIQPKALG1Caenorhabditis elegans
Q105DIAAVQPKAAG1Danio rerio
Q105DISAIQPKAAG1Xenopus tropicalis
Q172WPRIDQKSCFK4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
Q172WLRIDQKSSLK1Caenorhabditis elegans
Q399MLFTRQVSGAR4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
Q399ILFAKGITGAR1Caenorhabditis elegans
R199EGDELRTDLKA2Homo sapiens, Mus musculus
R199DRDSLITDVET1Caenorhabditis elegans
R199EGDELRTNLEE1Danio rerio
R199EGDELRTDLDA1Xenopus tropicalis
R26GCEARRSHEHL1Homo sapiens
R26---VSKSSNKL1Caenorhabditis elegans
R26GLDARRGHEQL1Danio rerio
R26GREARRMHEQL1Xenopus tropicalis
R26GCEARRAHEHL1Mus musculus
R271IQQGARVGRID4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
R271IAAAHECGRVD1Caenorhabditis elegans
R313KMYPGRASASP3Homo sapiens, Xenopus tropicalis, Mus musculus
R313QSYPGRASSVP1Caenorhabditis elegans
R313KIYPGRASASP1Danio rerio
R398SMLFTRQVSGA4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
R398SILFAKGITGA1Caenorhabditis elegans
R453DLFIKRLDRCL1Homo sapiens
R453EELFTRLTSSY1Caenorhabditis elegans
R453TVCMKRLGKCL1Danio rerio
R453DMFIKRLDKCL1Xenopus tropicalis
R453DLFIKRLDKCL1Mus musculus
R456IKRLDRCLKAV1Homo sapiens
R456FTRLTSSYAKF1Caenorhabditis elegans
R456MKRLGKCLKIL1Danio rerio
R456IKRLDKCLRLC1Xenopus tropicalis
R456IKRLDKCLNIV1Mus musculus
R97IHGIGRSGDIS3Homo sapiens, Xenopus tropicalis, Mus musculus
R97THGIGRSGNLL1Caenorhabditis elegans
R97IHGIGRSGDIA1Danio rerio
S174RIDQKSCFKSM4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
S174RIDQKSSLKSI1Caenorhabditis elegans
S260YGVQSSKCMHL2Homo sapiens, Xenopus tropicalis
S260YGLQSEETIRK1Caenorhabditis elegans
S260YGVQPSKCMHL1Danio rerio
S260YGLQSSKCMHL1Mus musculus
S27CEARRSHEHLI1Homo sapiens
S27--VSKSSNKLL1Caenorhabditis elegans
S27LDARRGHEQLI1Danio rerio
S27REARRMHEQLV1Xenopus tropicalis
S27CEARRAHEHLI1Mus musculus
S393VTQLGSMLFTR4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
S393-TLFGSILFAK1Caenorhabditis elegans
S98HGIGRSGDISA3Homo sapiens, Xenopus tropicalis, Mus musculus
S98HGIGRSGNLLE1Caenorhabditis elegans
S98HGIGRSGDIAA1Danio rerio
T133LAGVHTVANCF1Homo sapiens
T133LLGLHAVKSCI1Caenorhabditis elegans
T133LTGVRSVSSCF1Danio rerio
T133LAGVRTASSCF1Xenopus tropicalis
T133LAGVHSVASCF1Mus musculus
T144VVPMATGMSLT4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
T144VVPLCTGMSLS1Caenorhabditis elegans
T397GSMLFTRQVSG4Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus
T397GSILFAKGITG1Caenorhabditis elegans
Y255IVNNAYGVQSS1Homo sapiens
Y255LVNNAYGLQSE1Caenorhabditis elegans
Y255IVNNAYGVQPS1Danio rerio
Y255VVNNAYGVQSS1Xenopus tropicalis
Y255VVNNAYGLQSS1Mus musculus


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