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 BHMT
Gene summary
Basic gene Info.Gene symbolBHMT
Gene namebetaine--homocysteine S-methyltransferase
SynonymsBHMT1|HEL-S-61p
CytomapUCSC genome browser: 5q14.1
Type of geneprotein-coding
RefGenesNM_001713.2,
Descriptionbetaine--homocysteine S-methyltransferase 1epididymis secretory sperm binding protein Li 61p
Modification date20141211
dbXrefs MIM : 602888
HGNC : HGNC
Ensembl : ENSG00000145692
HPRD : 04200
Vega : OTTHUMG00000108157
ProteinUniProt: Q93088
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BHMT
BioGPS: 635
PathwayNCI Pathway Interaction Database: BHMT
KEGG: BHMT
REACTOME: BHMT
Pathway Commons: BHMT
ContextiHOP: BHMT
ligand binding site mutation search in PubMed: BHMT
UCL Cancer Institute: BHMT
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:0006577amino-acid betaine metabolic process18230605
GO:0046500S-adenosylmethionine metabolic process18230605
GO:0071267L-methionine salvage18230605


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Ligand binding site mutations for BHMT

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
Q72Q72PBRCA1
Y160E162QLUAD1
F267P268TLUAD1
F267P265SSKCM1
W44P46LSKCM1
F267P268SSKCM1
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 BHMT
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
W44P46L0.19537816
Y160E162Q-1.2844784
F267P265S-1.2008734
F267P268S-1.0930432
F267P268T-0.99960723
Q72Q72P-0.64437385
(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 BHMT from PDB

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Differential gene expression and gene-gene network for BHMT
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 BHMT and the right PPI network was created from samples without mutations in the LBS of BHMT. 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 BHMT
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0027794Neural Tube Defects2Biomarker, GeneticVariation
umls:C0000832Abruptio Placentae1Biomarker, GeneticVariation
umls:C0024305Lymphoma, Non-Hodgkin1Biomarker, GeneticVariation
umls:C0011860Diabetes Mellitus, Type 21Biomarker

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

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Pharmacological information for BHMT
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
Approved|nutraceuticalDB00134L-MethionineSmall molecule
ExperimentalDB02337S-(D-Carboxybutyl)-L-HomocysteineSmall molecule
Nutraceutical|vet_approvedDB04272Citric AcidSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of BHMT go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
KPOTASSIUM(1+)4m3pAQ72
KPOTASSIUM(1+)4m3pBQ72
KPOTASSIUM(1+)4m3pCQ72
KPOTASSIUM(1+)4m3pDQ72
CBHS-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE1lt8BW44 Q72 Y160 F267
CBHS-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE1lt8AW44 Y160 F267


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Conservation information for LBS of BHMT
Multiple alignments for Q93088 in multiple species
LBSAA sequence# speciesSpecies
C217IVGVNCHFDPS2Mus musculus, Rattus norvegicus
C217IIGVNCHFDPT1Homo sapiens
C217IVGVNCHFDPL1Danio rerio
C217VVGVNCHFDPM1Xenopus tropicalis
C217IVGVNCHFDPT1Bos taurus
C299RYIGGCCGFEP6Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus
C300YIGGCCGFEPY6Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus
D26EVVIGDGGFVF4Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
D26EIVIGDGGFVF1Homo sapiens
D26EVIIGDGGFVF1Bos taurus
E159DFLIAEYFEHV5Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus
E159DLLIAEYFEHV1Danio rerio
F267IDLPEFPFGLE4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F267IDLPEFPFALE2Danio rerio, Xenopus tropicalis
F29IGDGGFVFALE6Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus
F76MQTFTFYASED4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
F76MQTFTFYASDD2Danio rerio, Xenopus tropicalis
G27VVIGDGGFVFA4Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
G27IVIGDGGFVFA1Homo sapiens
G27VIIGDGGFVFA1Bos taurus
G28VIGDGGFVFAL5Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus
G28IIGDGGFVFAL1Bos taurus
G298VRYIGGCCGFE5Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus
G298IRYIGGCCGFE1Danio rerio
I262GKQGFIDLPEF4Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus
I262NKQGFIDLPEF1Homo sapiens
I262SCQGFIDLPEF1Danio rerio
Q247AHLMSQPLAYH2Homo sapiens, Bos taurus
Q247AHYMTQPLAYH1Danio rerio
Q247AHLMTQPLAYH1Xenopus tropicalis
Q247AYLMSQPLAYH1Mus musculus
Q247AYLMSHALAYH1Rattus norvegicus
Q72GSNVMQTFTFY5Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus
Q72GANVMQTFTFY1Xenopus tropicalis
V30GDGGFVFALEK6Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus
W44VKAGPWTPEAA6Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus
Y160FLIAEYFEHVE5Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus
Y160LLIAEYFEHVE1Danio rerio
Y77QTFTFYASEDK4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
Y77QTFTFYASDDK2Danio rerio, Xenopus tropicalis


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