|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for HMGCL |
Basic gene info. | Gene symbol | HMGCL |
Gene name | 3-hydroxymethyl-3-methylglutaryl-CoA lyase | |
Synonyms | HL | |
Cytomap | UCSC genome browser: 1p36.1-p35 | |
Genomic location | chr1 :24128366-24151949 | |
Type of gene | protein-coding | |
RefGenes | NM_000191.2, NM_001166059.1, | |
Ensembl id | ENSG00000117305 | |
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: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_HMGCL | |
BioGPS: 3155 | ||
Gene Expression Atlas: ENSG00000117305 | ||
The Human Protein Atlas: ENSG00000117305 | ||
Pathway | NCI Pathway Interaction Database: HMGCL | |
KEGG: HMGCL | ||
REACTOME: HMGCL | ||
ConsensusPathDB | ||
Pathway Commons: HMGCL | ||
Metabolism | MetaCyc: HMGCL | |
HUMANCyc: HMGCL | ||
Regulation | Ensembl's Regulation: ENSG00000117305 | |
miRBase: chr1 :24,128,366-24,151,949 | ||
TargetScan: NM_000191 | ||
cisRED: ENSG00000117305 | ||
Context | iHOP: HMGCL | |
cancer metabolism search in PubMed: HMGCL | ||
UCL Cancer Institute: HMGCL | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for HMGCL(metabolism pathway, cancer, disease, phenome) |
![]() | |
Cancer | CGAP: HMGCL |
Familial Cancer Database: HMGCL |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
![]() | |
KEGG_BUTANOATE_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
![]() | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: HMGCL |
MedGen: HMGCL (Human Medical Genetics with Condition) | |
ClinVar: HMGCL | |
Phenotype | MGI: HMGCL (International Mouse Phenotyping Consortium) |
PhenomicDB: HMGCL |
Mutations for HMGCL |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
![]() |
There's no structural variation information in COSMIC data for this gene. |
![]() |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HMGCL related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
AB209902 | POLE | 1 | 3576 | 12 | 133225513 | 133254307 | HMGCL | 3572 | 5067 | 1 | 24128377 | 24147086 | |
BF749404 | HMGCL | 30 | 335 | 1 | 24128813 | 24130950 | HMGCL | 333 | 640 | 1 | 24128619 | 24128927 | |
AI202943 | HMGCL | 10 | 347 | 1 | 24128367 | 24128704 | VPS37B | 345 | 423 | 12 | 123379777 | 123379856 |
![]() |
Top |
![]() |
There's no copy number variation information in COSMIC data for this gene. |
Top |
![]() |
|
![]() |
Top |
![]() |
Stat. for Non-Synonymous SNVs (# total SNVs=13) | (# total SNVs=9) |
![]() | ![]() |
(# total SNVs=1) | (# total SNVs=0) |
![]() |
Top |
![]() |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr1:24137288-24137288 | p.Y167H | 2 |
chr1:24140706-24140706 | p.A157A | 2 |
chr1:24143254-24143254 | p.D87Y | 1 |
chr1:24130916-24130923 | p.V282fs*31 | 1 |
chr1:24151878-24151878 | p.R10W | 1 |
chr1:24137263-24137263 | p.P175L | 1 |
chr1:24144012-24144012 | p.S69C | 1 |
chr1:24130925-24130925 | p.L281L | 1 |
chr1:24144014-24144014 | p.L68L | 1 |
chr1:24130960-24130960 | p.A269V | 1 |
Top |
![]() |
|
![]() |
Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   |   |   | 4 |   |   |   |   |   | 1 |   |   | 3 | 1 |   |   | 8 | 1 |   | 4 |
# mutation |   |   |   | 4 |   |   |   |   |   | 1 |   |   | 3 | 1 |   |   | 8 | 1 |   | 4 |
nonsynonymous SNV |   |   |   | 1 |   |   |   |   |   | 1 |   |   | 1 |   |   |   | 4 |   |   | 2 |
synonymous SNV |   |   |   | 3 |   |   |   |   |   |   |   |   | 2 | 1 |   |   | 4 | 1 |   | 2 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
Top |
![]() |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr1:24130925 | p.T221T,HMGCL | 1 |
chr1:24143192 | p.L59L,HMGCL | 1 |
chr1:24130960 | p.L210L,HMGCL | 1 |
chr1:24143197 | p.I50I,HMGCL | 1 |
chr1:24130962 | p.A198V,HMGCL | 1 |
chr1:24143201 | p.R41Q,HMGCL | 1 |
chr1:24130967 | p.Y197Y,HMGCL | 1 |
chr1:24144014 | p.P40T,HMGCL | 1 |
chr1:24130998 | p.P196S,HMGCL | 1 |
chr1:24144041 | p.I35M,HMGCL | 1 |
![]() |
![]() |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
![]() |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, 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] |
Top |
Gene Expression for HMGCL |
![]() |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
![]() |
![]() |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
![]() |
Top |
![]() |
* This plots show the correlation between CNV and gene expression. |
![]() | |
![]() |
Top |
Gene-Gene Network Information |
![]() |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
![]() | |
ACBD4,AKR7A2,CCDC24,CHCHD5,COQ4,GAMT,GHDC, HEXIM2,HMGCL,JMJD8,MYL5,NPRL2,NSMCE1,PARK7, RAB17,STK16,TEX264,TMEM115,TMEM219,TMEM222,ZNF688 | ATP5I,COX14,APOPT1,C21orf33,COPS7A,COX6B1,ECH1, HAX1,HMGCL,MAF1,MRPL16,MRPL40,MRPL41,MRPS11, NDUFA8,NDUFB8,PARK7,PRDX2,PSMD4,TACO1,WBSCR16 |
![]() | |
AKR7A2,ATPIF1,MINOS1,KDF1,STPG1,CPT2,FUCA1, GALE,GPN2,HMGCL,LYPLA2,PAFAH2,PEF1,PIGV, PQLC2,RPS6KA1,TMCO4,TMEM125,TMEM50A,TMEM54,TSPO | ABCC6P2,ACADS,AIFM3,AUH,C11orf71,PPP1R36,KDF1, C21orf33,COX5B,DUSP23,GJB1,HMGCL,MAN1B1,PCTP, PGLS,PXMP2,TEX264,THAP4,TMEM134,TST,TSTD1 |
![]() |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
Top |
![]() |
Top |
Pharmacological Information for HMGCL |
There's no related Drug. |
Top |
Cross referenced IDs for HMGCL |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |