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mutLBSgeneDB |
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| Gene summary for HMGCL |
 Gene summary |
| Basic gene Info. | Gene symbol | HMGCL |
| Gene name | 3-hydroxymethyl-3-methylglutaryl-CoA lyase | |
| Synonyms | HL | |
| Cytomap | UCSC genome browser: 1p36.1-p35 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000191.2, NM_001166059.1, | |
| Description | 3-hydroxy-3-methylglutarate-CoA lyase3-hydroxy-3-methylglutaryl-CoA lyase3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyaseHMG-CoA lyasehydroxymethylglutaricaciduriahydroxymethylglutaryl-CoA lyase, mitochondrialmitochondrial 3-hydroxy-3-methylglutary | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 613898 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000117305 | ||
| HPRD : 02003 | ||
| Vega : OTTHUMG00000002963 | ||
| Protein | UniProt: P35914 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_HMGCL | |
| BioGPS: 3155 | ||
| Pathway | NCI Pathway Interaction Database: HMGCL | |
| KEGG: HMGCL | ||
| REACTOME: HMGCL | ||
| Pathway Commons: HMGCL | ||
| Context | iHOP: HMGCL | |
| ligand binding site mutation search in PubMed: HMGCL | ||
| UCL Cancer Institute: HMGCL | ||
| 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:0046951 | ketone body biosynthetic process | 22847177 | GO:0051262 | protein tetramerization | 12464283 |
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| Ligand binding site mutations for HMGCL |
| 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 | R41 | R41Q | COAD | 1 | G112 | G112C | LUSC | 1 | C266 | P267S | SKCM | 1 | R41 | P40T | UCEC | 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 HMGCL |
| 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 | C266 | P267S | -0.91997779 | R41 | P40T | -0.90266154 | R41 | R41Q | -0.89239144 | G112 | G112C | -0.60216164 |
| (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 HMGCL from PDB |
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| Differential gene expression and gene-gene network for HMGCL |
| 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 HMGCL |
| Gene level disease information (DisGeNet) |
| Disease ID | Disease name | # PubMed | Association type |
| umls:C1415614 | 3-HYDROXY-3-METHYLGLUTARYL-CoA LYASE DEFICIENCY | 9 | GeneticVariation |
| umls:C0268601 | 3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency | 3 | Biomarker, GeneticVariation |
| Mutation level pathogenic information (ClinVar annotation) |
| Allele ID | AA change | Clinical significance | Origin | Phenotype IDs |
| 26996 | R41Q | Pathogenic | Germline | GeneReviews:NBK1134 MedGen:C0268601 OMIM:246450 Orphanet:ORPHA20 SNOMED CT:124611007 MedGen:CN221809 |
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| Pharmacological information for HMGCL |
| 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 |
| Experimental | DB04594 | 3-hydroxyglutaric acid | Small molecule |  |
| Gene-centered ligand-gene interaction network |
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| Ligands binding to mutated ligand binding site of HMGCL go to BioLip |
| Ligand ID | Ligand short name | Ligand long name | PDB ID | PDB name | mutLBS | HMG | (3S)-3-HYDROXY-3-METHYLGLUTARYL-COA(5-) | 3mp5 | B | C266 | 3HG | 3-HYDROXYGLUTARIC ACID | 2cw6 | A | R41 | 3HG | 3-HYDROXYGLUTARIC ACID | 3mp3 | A | R41 | HGG | 3-HYDROXYL GLUTARYL COA | 3mp3 | B | R41 G112 |
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| Conservation information for LBS of HMGCL |
| Multiple alignments for P35914 in multiple species |
| LBS | AA sequence | # species | Species | C266 | AGLGGCPYAKG | 3 | Arabidopsis thaliana, Mus musculus, Rattus norvegicus | C266 | AGLGGCPYAQG | 2 | Homo sapiens, Bos taurus | D42 | EVGPRDGLQNE | 5 | Homo sapiens, Arabidopsis thaliana, Mus musculus, Rattus norvegicus, Bos taurus | F127 | KEVVIFGAASE | 1 | Homo sapiens | F127 | KEVAIFASASE | 1 | Arabidopsis thaliana | F127 | KEVSVFGAVSE | 1 | Mus musculus | F127 | KEVSIFGAASE | 1 | Rattus norvegicus | F127 | KEVAIFGAASE | 1 | Bos taurus | F76 | VEATSFVSPKW | 2 | Arabidopsis thaliana, Bos taurus | F76 | IEATSFVSPKW | 2 | Mus musculus, Rattus norvegicus | F76 | IETTSFVSPKW | 1 | Homo sapiens | G112 | TPNMKGFEEAV | 2 | Mus musculus, Rattus norvegicus | G112 | TPNLKGFEAAV | 1 | Homo sapiens | G112 | TPNLKGFQAAV | 1 | Arabidopsis thaliana | G112 | TPNFKGFQAAV | 1 | Bos taurus | G203 | YEISLGDTIGV | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | G203 | FEISLGDTIGI | 1 | Arabidopsis thaliana | H233 | AALAVHCHDTY | 2 | Homo sapiens, Rattus norvegicus | H233 | TALAVHCHDTY | 2 | Mus musculus, Bos taurus | H233 | DKLAVHFHDTY | 1 | Arabidopsis thaliana | H235 | LAVHCHDTYGQ | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | H235 | LAVHFHDTYGQ | 1 | Arabidopsis thaliana | I139 | FTKKNINCSIE | 1 | Homo sapiens | I139 | FSLSNINCTIE | 1 | Arabidopsis thaliana | I139 | FTRKNANCSIE | 1 | Mus musculus | I139 | FTRKNVNCSIE | 1 | Rattus norvegicus | I139 | FTKKNINCSID | 1 | Bos taurus | K111 | LTPNMKGFEEA | 2 | Mus musculus, Rattus norvegicus | K111 | LTPNLKGFEAA | 1 | Homo sapiens | K111 | LTPNLKGFQAA | 1 | Arabidopsis thaliana | K111 | LTPNFKGFQAA | 1 | Bos taurus | K80 | SFVSPKWVPQM | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | K80 | SFVSPKWVPQL | 1 | Arabidopsis thaliana | L106 | INYPVLTPNMK | 2 | Mus musculus, Rattus norvegicus | L106 | INYPVLTPNLK | 1 | Homo sapiens | L106 | ARLPVLTPNLK | 1 | Arabidopsis thaliana | L106 | VNYPVLTPNFK | 1 | Bos taurus | N109 | PVLTPNMKGFE | 2 | Mus musculus, Rattus norvegicus | N109 | PVLTPNLKGFE | 1 | Homo sapiens | N109 | PVLTPNLKGFQ | 1 | Arabidopsis thaliana | N109 | PVLTPNFKGFQ | 1 | Bos taurus | N138 | LFTKKNINCSI | 2 | Homo sapiens, Bos taurus | N138 | SFSLSNINCTI | 1 | Arabidopsis thaliana | N138 | LFTRKNANCSI | 1 | Mus musculus | N138 | LFTRKNVNCSI | 1 | Rattus norvegicus | N140 | TKKNINCSIEE | 1 | Homo sapiens | N140 | SLSNINCTIEE | 1 | Arabidopsis thaliana | N140 | TRKNANCSIEE | 1 | Mus musculus | N140 | TRKNVNCSIEE | 1 | Rattus norvegicus | N140 | TKKNINCSIDE | 1 | Bos taurus | N275 | QGASGNLATED | 2 | Homo sapiens, Bos taurus | N275 | KGASGNLATED | 2 | Mus musculus, Rattus norvegicus | N275 | KGASGNVATED | 1 | Arabidopsis thaliana | P108 | YPVLTPNMKGF | 2 | Mus musculus, Rattus norvegicus | P108 | YPVLTPNLKGF | 1 | Homo sapiens | P108 | LPVLTPNLKGF | 1 | Arabidopsis thaliana | P108 | YPVLTPNFKGF | 1 | Bos taurus | P79 | TSFVSPKWVPQ | 5 | Homo sapiens, Arabidopsis thaliana, Mus musculus, Rattus norvegicus, Bos taurus | Q45 | PRDGLQNEKNI | 3 | Homo sapiens, Arabidopsis thaliana, Bos taurus | Q45 | PRDGLQNEKSI | 2 | Mus musculus, Rattus norvegicus | R149 | EESFQRFDAIL | 1 | Homo sapiens | R149 | EESLLRYRVVA | 1 | Arabidopsis thaliana | R149 | EESFQRFAGVM | 1 | Mus musculus | R149 | EESFQRFDGVM | 1 | Rattus norvegicus | R149 | DESLQRFDEIL | 1 | Bos taurus | R41 | VEVGPRDGLQN | 5 | Homo sapiens, Arabidopsis thaliana, Mus musculus, Rattus norvegicus, Bos taurus | S169 | VRGYVSCALGC | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | S169 | VRGYVSCVVGC | 1 | Arabidopsis thaliana | S169 | VRGYVSCVLGC | 1 | Bos taurus | S78 | ATSFVSPKWVP | 4 | Arabidopsis thaliana, Mus musculus, Rattus norvegicus, Bos taurus | S78 | TTSFVSPKWVP | 1 | Homo sapiens | T205 | ISLGDTIGVGT | 4 | Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus | T205 | ISLGDTIGIGT | 1 | Arabidopsis thaliana | V77 | EATSFVSPKWV | 4 | Arabidopsis thaliana, Mus musculus, Rattus norvegicus, Bos taurus | V77 | ETTSFVSPKWV | 1 | Homo sapiens | V82 | VSPKWVPQMAD | 3 | Mus musculus, Rattus norvegicus, Bos taurus | V82 | VSPKWVPQMGD | 1 | Homo sapiens | V82 | VSPKWVPQLAD | 1 | Arabidopsis thaliana | W81 | FVSPKWVPQMA | 3 | Mus musculus, Rattus norvegicus, Bos taurus | W81 | FVSPKWVPQMG | 1 | Homo sapiens | W81 | FVSPKWVPQLA | 1 | Arabidopsis thaliana | Y167 | ISVRGYVSCAL | 3 | Homo sapiens, Mus musculus, Rattus norvegicus | Y167 | VPVRGYVSCVV | 1 | Arabidopsis thaliana | Y167 | ISVRGYVSCVL | 1 | Bos taurus |
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