mutLBSgeneDB |
Gene summary for MTR |
Gene summary |
Basic gene Info. | Gene symbol | MTR |
Gene name | 5-methyltetrahydrofolate-homocysteine methyltransferase | |
Synonyms | HMAG|MS|cblG | |
Cytomap | UCSC genome browser: 1q43 | |
Type of gene | protein-coding | |
RefGenes | NM_000254.2, NM_001291939.1,NM_001291940.1, | |
Description | 5-methyltetrahydrofolate-homocysteine methyltransferase 1cobalamin-dependent methionine synthasemethionine synthasevitamin-B12 dependent methionine synthase | |
Modification date | 20141219 | |
dbXrefs | MIM : 156570 | |
HGNC : HGNC | ||
Ensembl : ENSG00000116984 | ||
HPRD : 01136 | ||
Vega : OTTHUMG00000040060 | ||
Protein | UniProt: Q99707 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_MTR | |
BioGPS: 4548 | ||
Pathway | NCI Pathway Interaction Database: MTR | |
KEGG: MTR | ||
REACTOME: MTR | ||
Pathway Commons: MTR | ||
Context | iHOP: MTR | |
ligand binding site mutation search in PubMed: MTR | ||
UCL Cancer Institute: MTR | ||
Assigned class in mutLBSgeneDB | C: This gene just belongs to mutLBSgenes. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO Term | PubMed ID |
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Ligand binding site mutations for MTR |
Cancer type specific mutLBS sorted by frequency |
LBS | AAchange of nsSNV | Cancer type | # samples | N470 | V469A | STAD | 2 | S578 | S578F | BRCA | 1 | R591 | R591Q | COAD | 1 | G382,R384 | S383L | SKCM | 1 |
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. |
LBS | AAchange of nsSNV | Relative stability change | S578 | S578F | 0.40996365 | N470 | V469A | -1.4426222 | R591 | R591Q | -0.53628394 | G382 | S383L | -0.035005096 | R384 | S383L | -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 ID | PDB title | PDB structure | 4CCZ | Crystal 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) |
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Phenotype information for MTR |
Gene level disease information (DisGeNet) |
Disease ID | Disease name | # PubMed | Association type |
umls:C0013080 | Down Syndrome | 17 | Biomarker, GeneticVariation |
umls:C0024299 | Lymphoma | 9 | Biomarker, GeneticVariation |
umls:C0008924 | Cleft Lip | 6 | Biomarker, GeneticVariation |
umls:C0008925 | Cleft Palate | 6 | Biomarker, GeneticVariation |
umls:C1458155 | Breast Neoplasms | 3 | Biomarker, GeneticVariation |
umls:C0024301 | Lymphoma, Follicular | 3 | Biomarker, GeneticVariation |
umls:C1855128 | Methylcobalamin Deficiency, CblG Type | 2 | Biomarker, GeneticVariation |
umls:C3658338 | Drug-Related Side Effects and Adverse Reactions | 2 | Biomarker |
umls:C0021364 | Infertility, Male | 1 | Biomarker, GeneticVariation |
umls:C0017178 | Gastrointestinal Diseases | 1 | Biomarker, GeneticVariation |
umls:C0018939 | Hematologic Diseases | 1 | Biomarker, GeneticVariation |
umls:C0162429 | Malnutrition | 1 | Biomarker, GeneticVariation |
umls:C0270612 | Leukoencephalopathies | 1 | Biomarker |
umls:C0031117 | Peripheral Nervous System Diseases | 1 | Biomarker |
Mutation level pathogenic information (ClinVar annotation) |
Allele ID | AA change | Clinical significance | Origin | Phenotype 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 status | DrugBank ID | Name | Type | Drug structure |
Approved|nutraceutical | DB00115 | Cyanocobalamin | Small molecule | |
Approved|nutraceutical | DB00116 | Tetrahydrofolic acid | Small molecule | |
Approved|nutraceutical | DB00134 | L-Methionine | Small molecule | |
Approved | DB00200 | Hydroxocobalamin | Small molecule |
Gene-centered ligand-gene interaction network |
Ligands binding to mutated ligand binding site of MTR go to BioLip |
Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | THG | (6S)-5,6,7,8-TETRAHYDROFOLATE(2-) | 4ccz | A | G382 R384 N470 S578 R591 |
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Conservation information for LBS of MTR |
Multiple alignments for Q99707 in multiple species |
LBS | AA sequence | # species | Species | D449 | VPLCIDSSNFA | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | D449 | IPVCIDSSDFD | 1 | Caenorhabditis elegans | D537 | NDIIFDPNILT | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | D537 | NDIIFDANILT | 1 | Caenorhabditis elegans | E376 | FVNIGERCNVA | 5 | Homo sapiens, Caenorhabditis elegans, Bos taurus, Mus musculus, Rattus norvegicus | F582 | LSNLSFSFRGM | 3 | Homo sapiens, Bos taurus, Mus musculus | F582 | VSNISFSFRGM | 1 | Caenorhabditis elegans | F582 | LSNLSFAFRGM | 1 | Rattus norvegicus | G382 | RCNVAGSRKFA | 2 | Homo sapiens, Mus musculus | G382 | RCNVAGSRRFC | 1 | Caenorhabditis elegans | G382 | RCNVAGSRRFA | 1 | Bos taurus | G382 | RCNVAGSKKFA | 1 | Rattus norvegicus | G576 | VRISGGLSNLS | 2 | Mus musculus, Rattus norvegicus | G576 | ARISGGLSNLS | 1 | Homo sapiens | G576 | AHVSGGVSNIS | 1 | Caenorhabditis elegans | G576 | AKVSGGLSNLS | 1 | Bos taurus | I611 | GMDMGIVNAGN | 2 | Homo sapiens, Mus musculus | I611 | GMDMGIVNAGS | 2 | Bos taurus, Rattus norvegicus | I611 | GMDMGIVNAGA | 1 | Caenorhabditis elegans | M498 | AAVVVMAFDEE | 3 | Bos taurus, Mus musculus, Rattus norvegicus | M498 | AAMVVMAFDEE | 1 | Homo sapiens | M498 | AAVVVMAFDEQ | 1 | Caenorhabditis elegans | N379 | IGERCNVAGSR | 4 | Homo sapiens, Caenorhabditis elegans, Bos taurus, Mus musculus | N379 | IGERCNVAGSK | 1 | Rattus norvegicus | N470 | GKCIVNSISLK | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | N470 | GKCVVNSISLK | 1 | Caenorhabditis elegans | N579 | SGGLSNLSFSF | 3 | Homo sapiens, Bos taurus, Mus musculus | N579 | SGGVSNISFSF | 1 | Caenorhabditis elegans | N579 | SGGLSNLSFAF | 1 | Rattus norvegicus | R384 | NVAGSRKFAKL | 2 | Homo sapiens, Mus musculus | R384 | NVAGSRRFCNL | 1 | Caenorhabditis elegans | R384 | NVAGSRRFAKL | 1 | Bos taurus | R384 | NVAGSKKFAKL | 1 | Rattus norvegicus | R585 | LSFSFRGMEAI | 3 | Homo sapiens, Bos taurus, Mus musculus | R585 | ISFSFRGMEAI | 1 | Caenorhabditis elegans | R585 | LSFAFRGMDAI | 1 | Rattus norvegicus | R591 | GMEAIREAMHG | 3 | Homo sapiens, Bos taurus, Mus musculus | R591 | GMEAIREAMHS | 1 | Caenorhabditis elegans | R591 | GMDAIREAMHG | 1 | Rattus norvegicus | S578 | ISGGLSNLSFS | 2 | Homo sapiens, Mus musculus | S578 | VSGGVSNISFS | 1 | Caenorhabditis elegans | S578 | VSGGLSNLSFS | 1 | Bos taurus | S578 | ISGGLSNLSFA | 1 | Rattus norvegicus |
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