mutated Ligand Binding Site gene DataBase





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Gene Summary

Ligand Binding Site Mutation Information

Protein Structure Related Information

Gene Expression and Gene-Gene Network

Phenotype Information

Pharmacological Information

Conservation Information for LBS

Gene summary for HGD
Gene summary
Basic gene Info.Gene symbolHGD
Gene namehomogentisate 1,2-dioxygenase
CytomapUCSC genome browser: 3q13.33
Type of geneprotein-coding
Descriptionhomogentisate oxidasehomogentisate oxygenasehomogentisic acid oxidasehomogentisicase
Modification date20141222
dbXrefs MIM : 607474
Ensembl : ENSG00000113924
HPRD : 06315
Vega : OTTHUMG00000159441
ProteinUniProt: Q93099
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HGD
BioGPS: 3081
PathwayNCI Pathway Interaction Database: HGD
Pathway Commons: HGD
ContextiHOP: HGD
ligand binding site mutation search in PubMed: HGD
UCL Cancer Institute: HGD
Assigned class in mutLBSgeneDBC: This gene just belongs to mutLBSgenes.

Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez

Ligand binding site mutations for HGD
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.

Cancer type specific mutLBS sorted by frequency
LBSAAchange of nsSNVCancer type# samples
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.

Protein structure related information for HGD
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.
LBSAAchange of nsSNVRelative stability change
(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 HGD from PDB

Differential gene expression and gene-gene network for HGD
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)
* Left PPI network was created from samples with mutations in the LBS of HGD and the right PPI network was created from samples without mutations in the LBS of HGD. Only genes with p-value < 0.05 are shown.
Red circle: input gene. Orange circle: LBSgene. Blue circle: other gene.


Phenotype information for HGD
Gene level disease information (DisGeNet)
Disease IDDisease name# PubMedAssociation type
umls:C0002066Alkaptonuria34Biomarker, GeneticVariation

Mutation level pathogenic information (ClinVar annotation)
Allele IDAA changeClinical significanceOriginPhenotype IDs

Pharmacological information for HGD
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.
Drug information targeting mutLBSgene (Approved drugs only)
Drug statusDrugBank IDNameTypeDrug structure

Gene-centered ligand-gene interaction network

Ligands binding to mutated ligand binding site of HGD go to BioLip
Ligand IDLigand short nameLigand long namePDB IDPDB namemutLBS
FE2IRON(2+)1ey2AH335 E341 H371

Conservation information for LBS of HGD
Multiple alignments for Q93099 in multiple species
LBSAA sequence# speciesSpecies
E341RNCMSEFMGLI5Homo sapiens, Arabidopsis thaliana, Oryza sativa subsp. japonica, Mus musculus, Drosophila melanogaster
E341RNCMSEYMGLI1Caenorhabditis elegans
H335RPPYYHRNCMS6Homo sapiens, Arabidopsis thaliana, Oryza sativa subsp. japonica, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans
H371STMTPHGPDAD1Homo sapiens
H371SCMTPHGPDTT1Arabidopsis thaliana
H371SCMTPHGPDTK1Oryza sativa subsp. japonica
H371SAMTPHGPDAD1Mus musculus
H371SMMTPHGPDVK1Drosophila melanogaster
H371SMMTPHGPDFN1Caenorhabditis elegans

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