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mutLBSgeneDB |
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| Gene summary for BHMT |
 Gene summary |
| Basic gene Info. | Gene symbol | BHMT |
| Gene name | betaine--homocysteine S-methyltransferase | |
| Synonyms | BHMT1|HEL-S-61p | |
| Cytomap | UCSC genome browser: 5q14.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001713.2, | |
| Description | betaine--homocysteine S-methyltransferase 1epididymis secretory sperm binding protein Li 61p | |
| Modification date | 20141211 | |
| dbXrefs | MIM : 602888 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000145692 | ||
| HPRD : 04200 | ||
| Vega : OTTHUMG00000108157 | ||
| Protein | UniProt: Q93088 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_BHMT | |
| BioGPS: 635 | ||
| Pathway | NCI Pathway Interaction Database: BHMT | |
| KEGG: BHMT | ||
| REACTOME: BHMT | ||
| Pathway Commons: BHMT | ||
| Context | iHOP: BHMT | |
| ligand binding site mutation search in PubMed: BHMT | ||
| UCL Cancer Institute: BHMT | ||
| 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 | GO:0006577 | amino-acid betaine metabolic process | 18230605 | GO:0046500 | S-adenosylmethionine metabolic process | 18230605 | GO:0071267 | L-methionine salvage | 18230605 |
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| Ligand binding site mutations for BHMT |
| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | Q72 | Q72P | BRCA | 1 | Y160 | E162Q | LUAD | 1 | F267 | P268T | LUAD | 1 | F267 | P265S | SKCM | 1 | W44 | P46L | SKCM | 1 | F267 | P268S | 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 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 |
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| 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 | W44 | P46L | 0.19537816 | Y160 | E162Q | -1.2844784 | F267 | P265S | -1.2008734 | F267 | P268S | -1.0930432 | F267 | P268T | -0.99960723 | Q72 | Q72P | -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) |
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| Phenotype information for BHMT |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0027794 | Neural Tube Defects | 2 | Biomarker, GeneticVariation |
| umls:C0000832 | Abruptio Placentae | 1 | Biomarker, GeneticVariation |
| umls:C0024305 | Lymphoma, Non-Hodgkin | 1 | Biomarker, GeneticVariation |
| umls:C0011860 | Diabetes Mellitus, Type 2 | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype 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. |
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| Gene-centered drug-gene interaction network |
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| Drug information targeting mutLBSgene (Approved drugs only) |
| Drug status | DrugBank ID | Name | Type | Drug structure |
| Approved|nutraceutical | DB00134 | L-Methionine | Small molecule |  |
| Experimental | DB02337 | S-(D-Carboxybutyl)-L-Homocysteine | Small molecule |  |
| Nutraceutical|vet_approved | DB04272 | Citric Acid | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of BHMT go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | K | POTASSIUM(1+) | 4m3p | A | Q72 | K | POTASSIUM(1+) | 4m3p | B | Q72 | K | POTASSIUM(1+) | 4m3p | C | Q72 | K | POTASSIUM(1+) | 4m3p | D | Q72 | CBH | S-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE | 1lt8 | B | W44 Q72 Y160 F267 | CBH | S-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE | 1lt8 | A | W44 Y160 F267 |
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| Conservation information for LBS of BHMT |
| Multiple alignments for Q93088 in multiple species |
| LBS | AA sequence | # species | Species | C217 | IVGVNCHFDPS | 2 | Mus musculus, Rattus norvegicus | C217 | IIGVNCHFDPT | 1 | Homo sapiens | C217 | IVGVNCHFDPL | 1 | Danio rerio | C217 | VVGVNCHFDPM | 1 | Xenopus tropicalis | C217 | IVGVNCHFDPT | 1 | Bos taurus | C299 | RYIGGCCGFEP | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | C300 | YIGGCCGFEPY | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | D26 | EVVIGDGGFVF | 4 | Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus | D26 | EIVIGDGGFVF | 1 | Homo sapiens | D26 | EVIIGDGGFVF | 1 | Bos taurus | E159 | DFLIAEYFEHV | 5 | Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | E159 | DLLIAEYFEHV | 1 | Danio rerio | F267 | IDLPEFPFGLE | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F267 | IDLPEFPFALE | 2 | Danio rerio, Xenopus tropicalis | F29 | IGDGGFVFALE | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | F76 | MQTFTFYASED | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | F76 | MQTFTFYASDD | 2 | Danio rerio, Xenopus tropicalis | G27 | VVIGDGGFVFA | 4 | Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus | G27 | IVIGDGGFVFA | 1 | Homo sapiens | G27 | VIIGDGGFVFA | 1 | Bos taurus | G28 | VIGDGGFVFAL | 5 | Homo sapiens, Danio rerio, Xenopus tropicalis, Mus musculus, Rattus norvegicus | G28 | IIGDGGFVFAL | 1 | Bos taurus | G298 | VRYIGGCCGFE | 5 | Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | G298 | IRYIGGCCGFE | 1 | Danio rerio | I262 | GKQGFIDLPEF | 4 | Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | I262 | NKQGFIDLPEF | 1 | Homo sapiens | I262 | SCQGFIDLPEF | 1 | Danio rerio | Q247 | AHLMSQPLAYH | 2 | Homo sapiens, Bos taurus | Q247 | AHYMTQPLAYH | 1 | Danio rerio | Q247 | AHLMTQPLAYH | 1 | Xenopus tropicalis | Q247 | AYLMSQPLAYH | 1 | Mus musculus | Q247 | AYLMSHALAYH | 1 | Rattus norvegicus | Q72 | GSNVMQTFTFY | 5 | Homo sapiens, Danio rerio, Bos taurus, Mus musculus, Rattus norvegicus | Q72 | GANVMQTFTFY | 1 | Xenopus tropicalis | V30 | GDGGFVFALEK | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | W44 | VKAGPWTPEAA | 6 | Homo sapiens, Danio rerio, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | Y160 | FLIAEYFEHVE | 5 | Homo sapiens, Xenopus tropicalis, Bos taurus, Mus musculus, Rattus norvegicus | Y160 | LLIAEYFEHVE | 1 | Danio rerio | Y77 | QTFTFYASEDK | 4 | Homo sapiens, Bos taurus, Mus musculus, Rattus norvegicus | Y77 | QTFTFYASDDK | 2 | Danio rerio, Xenopus tropicalis |
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