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 MTR
Gene summary
Basic gene Info.Gene symbolMTR
Gene name5-methyltetrahydrofolate-homocysteine methyltransferase
SynonymsHMAG|MS|cblG
CytomapUCSC genome browser: 1q43
Type of geneprotein-coding
RefGenesNM_000254.2,
NM_001291939.1,NM_001291940.1,
Description5-methyltetrahydrofolate-homocysteine methyltransferase 1cobalamin-dependent methionine synthasemethionine synthasevitamin-B12 dependent methionine synthase
Modification date20141219
dbXrefs MIM : 156570
HGNC : HGNC
Ensembl : ENSG00000116984
HPRD : 01136
Vega : OTTHUMG00000040060
ProteinUniProt: Q99707
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTR
BioGPS: 4548
PathwayNCI Pathway Interaction Database: MTR
KEGG: MTR
REACTOME: MTR
Pathway Commons: MTR
ContextiHOP: MTR
ligand binding site mutation search in PubMed: MTR
UCL Cancer Institute: MTR
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 MTR

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
N470V469ASTAD2
S578S578FBRCA1
R591R591QCOAD1
G382,R384S383LSKCM1
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 MTR
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
S578S578F0.40996365
N470V469A-1.4426222
R591R591Q-0.53628394
G382S383L-0.035005096
R384S383L-0.035005096
(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 MTR from PDB
PDB IDPDB titlePDB structure
4CCZCrystal structure of human 5-methyltetrahydrofolate-homocysteine methyltransferase, the homocysteine and folate binding domains

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Differential gene expression and gene-gene network for MTR
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 MTR and the right PPI network was created from samples without mutations in the LBS of MTR. 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 MTR
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0013080Down Syndrome17Biomarker, GeneticVariation
umls:C0024299Lymphoma9Biomarker, GeneticVariation
umls:C0008924Cleft Lip6Biomarker, GeneticVariation
umls:C0008925Cleft Palate6Biomarker, GeneticVariation
umls:C1458155Breast Neoplasms3Biomarker, GeneticVariation
umls:C0024301Lymphoma, Follicular3Biomarker, GeneticVariation
umls:C1855128Methylcobalamin Deficiency, CblG Type2Biomarker, GeneticVariation
umls:C3658338Drug-Related Side Effects and Adverse Reactions2Biomarker
umls:C0021364Infertility, Male1Biomarker, GeneticVariation
umls:C0017178Gastrointestinal Diseases1Biomarker, GeneticVariation
umls:C0018939Hematologic Diseases1Biomarker, GeneticVariation
umls:C0162429Malnutrition1Biomarker, GeneticVariation
umls:C0270612Leukoencephalopathies1Biomarker
umls:C0031117Peripheral Nervous System Diseases1Biomarker

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

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Pharmacological information for MTR
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|nutraceuticalDB00115CyanocobalaminSmall molecule
Approved|nutraceuticalDB00116Tetrahydrofolic acidSmall molecule
Approved|nutraceuticalDB00134L-MethionineSmall molecule
ApprovedDB00200HydroxocobalaminSmall molecule

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of MTR go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
THG(6S)-5,6,7,8-TETRAHYDROFOLATE(2-)4cczAG382 R384 N470 S578 R591


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Conservation information for LBS of MTR
Multiple alignments for Q99707 in multiple species
LBSAA sequence# speciesSpecies
D449VPLCIDSSNFA4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
D449IPVCIDSSDFD1Caenorhabditis elegans
D537NDIIFDPNILT4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
D537NDIIFDANILT1Caenorhabditis elegans
E376FVNIGERCNVA5Homo sapiens, Caenorhabditis elegans, Bos taurus, Mus musculus, Rattus norvegicus
F582LSNLSFSFRGM3Homo sapiens, Bos taurus, Mus musculus
F582VSNISFSFRGM1Caenorhabditis elegans
F582LSNLSFAFRGM1Rattus norvegicus
G382RCNVAGSRKFA2Homo sapiens, Mus musculus
G382RCNVAGSRRFC1Caenorhabditis elegans
G382RCNVAGSRRFA1Bos taurus
G382RCNVAGSKKFA1Rattus norvegicus
G576VRISGGLSNLS2Mus musculus, Rattus norvegicus
G576ARISGGLSNLS1Homo sapiens
G576AHVSGGVSNIS1Caenorhabditis elegans
G576AKVSGGLSNLS1Bos taurus
I611GMDMGIVNAGN2Homo sapiens, Mus musculus
I611GMDMGIVNAGS2Bos taurus, Rattus norvegicus
I611GMDMGIVNAGA1Caenorhabditis elegans
M498AAVVVMAFDEE3Bos taurus, Mus musculus, Rattus norvegicus
M498AAMVVMAFDEE1Homo sapiens
M498AAVVVMAFDEQ1Caenorhabditis elegans
N379IGERCNVAGSR4Homo sapiens, Caenorhabditis elegans, Bos taurus, Mus musculus
N379IGERCNVAGSK1Rattus norvegicus
N470GKCIVNSISLK4Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus
N470GKCVVNSISLK1Caenorhabditis elegans
N579SGGLSNLSFSF3Homo sapiens, Bos taurus, Mus musculus
N579SGGVSNISFSF1Caenorhabditis elegans
N579SGGLSNLSFAF1Rattus norvegicus
R384NVAGSRKFAKL2Homo sapiens, Mus musculus
R384NVAGSRRFCNL1Caenorhabditis elegans
R384NVAGSRRFAKL1Bos taurus
R384NVAGSKKFAKL1Rattus norvegicus
R585LSFSFRGMEAI3Homo sapiens, Bos taurus, Mus musculus
R585ISFSFRGMEAI1Caenorhabditis elegans
R585LSFAFRGMDAI1Rattus norvegicus
R591GMEAIREAMHG3Homo sapiens, Bos taurus, Mus musculus
R591GMEAIREAMHS1Caenorhabditis elegans
R591GMDAIREAMHG1Rattus norvegicus
S578ISGGLSNLSFS2Homo sapiens, Mus musculus
S578VSGGVSNISFS1Caenorhabditis elegans
S578VSGGLSNLSFS1Bos taurus
S578ISGGLSNLSFA1Rattus norvegicus


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