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mutLBSgeneDB |
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| Gene summary for LCMT1 |
 Gene summary |
| Basic gene Info. | Gene symbol | LCMT1 |
| Gene name | leucine carboxyl methyltransferase 1 | |
| Synonyms | LCMT|PPMT1 | |
| Cytomap | UCSC genome browser: 16p12.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001032391.1, NM_016309.2, | |
| Description | [Phosphatase 2A protein]-leucine-carboxy methyltransferase 1protein phosphatase methyltransferase 1protein-leucine O-methyltransferase | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 610286 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000205629 | ||
| HPRD : 17266 | ||
| Vega : OTTHUMG00000177182 | ||
| Protein | UniProt: Q9UIC8 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_LCMT1 | |
| BioGPS: 51451 | ||
| Pathway | NCI Pathway Interaction Database: LCMT1 | |
| KEGG: LCMT1 | ||
| REACTOME: LCMT1 | ||
| Pathway Commons: LCMT1 | ||
| Context | iHOP: LCMT1 | |
| ligand binding site mutation search in PubMed: LCMT1 | ||
| UCL Cancer Institute: LCMT1 | ||
| 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:0006481 | C-terminal protein methylation | 10600115 |
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| Ligand binding site mutations for LCMT1 |
| Lollipop-style diagram of mutations at LBS in amino-acid sequence. We represented ligand binding site mutations only. (You can see big image via clicking.)  : non-synonymous mutation on LBS, Circle size denotes number of samples. |
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| Cancer type specific mutLBS sorted by frequency |
| LBS | AAchange of nsSNV | Cancer type | # samples | G98 | L97H | COAD | 1 | R73 | R73Q | GBM | 1 | G100 | G100S | LUAD | 1 | G98 | G98V | LUAD | 1 | E198 | E198Q | LUAD | 1 | F123 | P124S | SKCM | 1 | V26 | V26A | STAD | 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 LCMT1 |
| 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 | F123 | P124S | -1.7940582 | V26 | V26A | -1.320869 | E198 | E198Q | -1.3024104 | R73 | R73Q | -1.1635929 | G100 | G100S | -0.90305657 | G98 | L97H | -0.81731822 | G98 | G98V | -0.53969748 |
| (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 LCMT1 from PDB |
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| Differential gene expression and gene-gene network for LCMT1 |
| 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 LCMT1 |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C0752351 | Embryo Loss | 1 | Biomarker |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
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| Pharmacological information for LCMT1 |
| 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 | DB00149 | L-Leucine | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of LCMT1 go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | SAM | S-ADENOSYL-L-METHIONINE | 3o7w | A | R73 G98 F123 E198 | AN6 | 5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL](ETHYL)AMINO}-5'-DEOXYADENOSINE | 3p71 | T | V26 R73 G98 F123 E198 | SAH | S-ADENOSYL-L-HOMOCYSTEINE | 3iei | A | V26 R73 G98 G100 F123 E198 | SAH | S-ADENOSYL-L-HOMOCYSTEINE | 3iei | B | V26 R73 G98 G100 F123 E198 | SAH | S-ADENOSYL-L-HOMOCYSTEINE | 3iei | C | V26 R73 G98 G100 F123 E198 | SAH | S-ADENOSYL-L-HOMOCYSTEINE | 3iei | D | V26 R73 G98 G100 F123 E198 | SAH | S-ADENOSYL-L-HOMOCYSTEINE | 3iei | E | V26 R73 G98 G100 F123 E198 | SAH | S-ADENOSYL-L-HOMOCYSTEINE | 3iei | F | V26 R73 G98 G100 F123 E198 | SAH | S-ADENOSYL-L-HOMOCYSTEINE | 3iei | G | V26 R73 G98 G100 F123 E198 | SAH | S-ADENOSYL-L-HOMOCYSTEINE | 3iei | H | V26 R73 G98 G100 F123 E198 |
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| Conservation information for LBS of LCMT1 |
| Multiple alignments for Q9UIC8 in multiple species |
| LBS | AA sequence | # species | Species | A170 | YAVIGADLRDL | 1 | Homo sapiens | A170 | YHLIGADLRQA | 1 | Caenorhabditis elegans | A170 | YAIIGADLRDI | 1 | Bos taurus | A170 | YAIIGADLRDL | 1 | Rattus norvegicus | A33 | GTCEDASLCKR | 2 | Homo sapiens, Rattus norvegicus | A33 | RTNDDATQCKY | 1 | Caenorhabditis elegans | A33 | GTCEDASICKR | 1 | Bos taurus | A99 | ILNLGAGMDTT | 2 | Bos taurus, Rattus norvegicus | A99 | IVNLGAGMDTT | 1 | Homo sapiens | A99 | VVSLGCGFDTL | 1 | Caenorhabditis elegans | C199 | LLIAECVLVYM | 2 | Homo sapiens, Bos taurus | C199 | IFIAECVLVYM | 1 | Caenorhabditis elegans | C199 | LLITECVLVYM | 1 | Rattus norvegicus | C30 | GVRGTCEDASL | 2 | Homo sapiens, Rattus norvegicus | C30 | SVQRTNDDATQ | 1 | Caenorhabditis elegans | C30 | GVRGTCEDASI | 1 | Bos taurus | D122 | KYFEVDFPMIV | 2 | Homo sapiens, Rattus norvegicus | D122 | KYVEVDFSSVT | 1 | Caenorhabditis elegans | D122 | KYFEIDFPMIV | 1 | Bos taurus | D171 | AVIGADLRDLS | 1 | Homo sapiens | D171 | HLIGADLRQAN | 1 | Caenorhabditis elegans | D171 | AIIGADLRDIA | 1 | Bos taurus | D171 | AIIGADLRDLS | 1 | Rattus norvegicus | E198 | TLLIAECVLVY | 2 | Homo sapiens, Bos taurus | E198 | TIFIAECVLVY | 1 | Caenorhabditis elegans | E198 | TLLITECVLVY | 1 | Rattus norvegicus | F123 | YFEVDFPMIVT | 2 | Homo sapiens, Rattus norvegicus | F123 | YVEVDFSSVTS | 1 | Caenorhabditis elegans | F123 | YFEIDFPMIVT | 1 | Bos taurus | G100 | LNLGAGMDTTF | 2 | Bos taurus, Rattus norvegicus | G100 | VNLGAGMDTTF | 1 | Homo sapiens | G100 | VSLGCGFDTLF | 1 | Caenorhabditis elegans | G98 | QILNLGAGMDT | 2 | Bos taurus, Rattus norvegicus | G98 | QIVNLGAGMDT | 1 | Homo sapiens | G98 | QVVSLGCGFDT | 1 | Caenorhabditis elegans | I126 | VDFPMIVTRKL | 2 | Homo sapiens, Rattus norvegicus | I126 | VDFSSVTSKKI | 1 | Caenorhabditis elegans | I126 | IDFPMIVTRKL | 1 | Bos taurus | K37 | DASLCKRFAVS | 2 | Homo sapiens, Rattus norvegicus | K37 | DATQCKYFATQ | 1 | Caenorhabditis elegans | K37 | DASICKRFAVS | 1 | Bos taurus | L172 | VIGADLRDLSE | 1 | Homo sapiens | L172 | LIGADLRQANE | 1 | Caenorhabditis elegans | L172 | IIGADLRDIAD | 1 | Bos taurus | L172 | IIGADLRDLSE | 1 | Rattus norvegicus | R173 | IGADLRDLSEL | 2 | Homo sapiens, Rattus norvegicus | R173 | IGADLRQANEL | 1 | Caenorhabditis elegans | R173 | IGADLRDIADL | 1 | Bos taurus | R73 | RGYFARVHGVS | 3 | Homo sapiens, Bos taurus, Rattus norvegicus | R73 | MGYWARTAAIE | 1 | Caenorhabditis elegans | T29 | EGVRGTCEDAS | 3 | Homo sapiens, Bos taurus, Rattus norvegicus | T29 | YSVQRTNDDAT | 1 | Caenorhabditis elegans | V200 | LIAECVLVYMT | 2 | Homo sapiens, Bos taurus | V200 | FIAECVLVYMS | 1 | Caenorhabditis elegans | V200 | LITECVLVYMT | 1 | Rattus norvegicus | V26 | ADDEGVRGTCE | 1 | Homo sapiens | V26 | SDDYSVQRTND | 1 | Caenorhabditis elegans | V26 | TDDEGVRGTCE | 1 | Bos taurus | V26 | FDDEGVRGTCE | 1 | Rattus norvegicus | Y203 | ECVLVYMTPEQ | 3 | Homo sapiens, Bos taurus, Rattus norvegicus | Y203 | ECVLVYMSADS | 1 | Caenorhabditis elegans |
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