Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	3081
Gene name Gene Name - the full gene name approved by the HGNC.	Homogentisate 1,2-dioxygenase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	HGD
Synonyms (NCBI Gene) Gene synonyms aliases	AKU, HGO
Chromosome Chromosome number	3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	3q13.33
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes the enzyme homogentisate 1,2 dioxygenase. This enzyme is involved in the catabolism of the amino acids tyrosine and phenylalanine. Mutations in this gene are the cause of the autosomal recessive metabolism disorder alkaptonuria.[provided

Show/Hide all(43)

SNP ID	Visualize variation	Clinical significance	Consequence
rs28941783	C>T	Pathogenic	Missense variant, coding sequence variant
rs28942100	G>A	Pathogenic	Intron variant, missense variant, coding sequence variant, 3 prime UTR variant
rs34214309	C>-,CC	Likely-pathogenic	Genic downstream transcript variant, intron variant, frameshift variant, coding sequence variant
rs120074170	A>C,G	Pathogenic-likely-pathogenic	Missense variant, intron variant, coding sequence variant, genic downstream transcript variant
rs120074171	C>A,G,T	Pathogenic	Synonymous variant, coding sequence variant, genic downstream transcript variant, intron variant, missense variant
rs120074172	T>C	Pathogenic	Missense variant, downstream transcript variant, coding sequence variant, genic downstream transcript variant
rs120074173	T>C	Pathogenic	Missense variant, downstream transcript variant, coding sequence variant, genic downstream transcript variant
rs120074174	C>A,T	Pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant
rs143370662	A>G	Likely-pathogenic	Terminator codon variant, stop lost, genic downstream transcript variant
rs149165166	A>C,G	Pathogenic, likely-benign	5 prime UTR variant, coding sequence variant, synonymous variant, missense variant
rs200808744	C>T	Likely-pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant
rs368717991	C>G	Pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant, downstream transcript variant
rs369517993	G>A,T	Pathogenic	Coding sequence variant, stop gained, missense variant, 5 prime UTR variant
rs397515346	->C	Pathogenic	Coding sequence variant, frameshift variant
rs397515347	C>T	Pathogenic	Splice acceptor variant
rs397515516	->G	Pathogenic	Genic downstream transcript variant, coding sequence variant, downstream transcript variant, frameshift variant
rs397515517	T>-	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant
rs397515518	C>A,T	Likely-pathogenic	Splice donor variant
rs544956641	G>A	Likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant
rs552207335	C>T	Likely-pathogenic	Splice donor variant
rs562853291	C>G,T	Likely-pathogenic	Missense variant, coding sequence variant, intron variant, 3 prime UTR variant
rs760206323	C>A,T	Likely-pathogenic	Downstream transcript variant, splice donor variant, genic downstream transcript variant
rs767159114	C>G	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, missense variant
rs786204422	A>T	Likely-pathogenic	Stop gained, coding sequence variant, 5 prime UTR variant
rs786204662	CC>-,C	Pathogenic, likely-pathogenic	Splice acceptor variant, intron variant, 3 prime UTR variant, coding sequence variant
rs1057516307	A>G	Likely-pathogenic	Intron variant, splice donor variant
rs1057516352	C>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1057516355	C>G	Likely-pathogenic	Initiator codon variant, 5 prime UTR variant, missense variant
rs1057516362	CC>AAT	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1057516467	C>T	Likely-pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant
rs1057516662	CTCACA>-	Likely-pathogenic	Splice donor variant, 5 prime UTR variant, coding sequence variant
rs1057516847	->C	Likely-pathogenic	Genic downstream transcript variant, downstream transcript variant, frameshift variant, coding sequence variant
rs1057516849	G>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1057516911	G>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1057516921	G>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1057516976	TT>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1057517081	CTC>TA	Pathogenic	Genic downstream transcript variant, downstream transcript variant, frameshift variant, coding sequence variant
rs1057517089	G>-	Likely-pathogenic	Genic downstream transcript variant, intron variant, frameshift variant, coding sequence variant
rs1057517370	C>T	Likely-pathogenic	Splice acceptor variant
rs1057517418	->A	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant
rs1390061303	C>A	Pathogenic	Coding sequence variant, 5 prime UTR variant, missense variant
rs1553716979	C>T	Likely-pathogenic	Genic downstream transcript variant, splice donor variant
rs1553721650	TGCTCACATCCATGGTGTTCAAGGGGAATATGAGGGATTCTCTTTAACTCTGGATTTTTGGGGATCCTACTGGAAACCCTACAGTTAATTTCACTAGTTTGGATTGGCTGCTGTGCCACCAATCCAATTTTAATCTTTGTGTTGTCATTGCTCTGTATCTTCATTGCCCCTATGACTTGGGAAACCTCTAGACAGTTCACAGGCTAGATTGGAAGAGCCACGGTGGGTGGAGGCACTTTGGCCTGAAAGCTAGTC	Pathogenic	Splice donor variant, intron variant, splice acceptor variant, 5 prime UTR variant, coding sequence variant

Show/Hide all(2)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018123	hsa-miR-335-5p	Microarray	18185580
MIRT029700	hsa-miR-26b-5p	Microarray	19088304

Show/Hide all(19)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004411	Function	Homogentisate 1,2-dioxygenase activity	IBA
GO:0004411	Function	Homogentisate 1,2-dioxygenase activity	IEA
GO:0004411	Function	Homogentisate 1,2-dioxygenase activity	IMP	8782815
GO:0004411	Function	Homogentisate 1,2-dioxygenase activity	TAS	8782815
GO:0005515	Function	Protein binding	IPI	21044950, 32296183
GO:0005829	Component	Cytosol	TAS
GO:0006520	Process	Amino acid metabolic process	IEA
GO:0006520	Process	Amino acid metabolic process	IEA
GO:0006559	Process	L-phenylalanine catabolic process	IBA
GO:0006559	Process	L-phenylalanine catabolic process	IEA
GO:0006559	Process	L-phenylalanine catabolic process	TAS	8782815
GO:0006570	Process	Tyrosine metabolic process	IEA
GO:0006572	Process	L-tyrosine catabolic process	IEA
GO:0006572	Process	L-tyrosine catabolic process	TAS	8782815
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0042802	Function	Identical protein binding	IPI	25416956, 32296183
GO:0046872	Function	Metal ion binding	IEA
GO:0051213	Function	Dioxygenase activity	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867, 23533145

MIM	HGNC	e!Ensembl
607474	4892	ENSG00000113924

Protein

UniProt ID

Q93099

Protein name

Homogentisate 1,2-dioxygenase (EC 1.13.11.5) (Homogentisate oxygenase) (Homogentisic acid oxidase) (Homogentisicase)

Protein function

Catalyzes the conversion of homogentisate to maleylacetoacetate.

PDB

1EY2 , 1EYB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04209	HgmA	5 → 434	homogentisate 1,2-dioxygenase	Family

Tissue specificity

TISSUE SPECIFICITY: Highest expression in the prostate, small intestine, colon, kidney and liver.

Sequence

MAELKYISGFGNECSSEDPRCPGSLPEGQNNPQVCPYNLYAEQLSGSAFTCPRSTNKRSW
LYRILPSVSHKPFESIDEGQVTHNWDEVDPDPNQLRWKPFEIPKASQKKVDFVSGLHTLC
GAGDIKSNNGLAIHIFLCNTSMENRCFYNSDGDFLIVPQKGNLLIYTEFGKMLVQPNEIC
VIQRGMRFSIDVFEETRGYILEVYGVHFELPDLGPIGANGLANPRDFLIPIAWYEDRQVP
GGYTVINKYQGKLFAAKQDVSPFNVVAWHGNYTPYKYNLKNFMVINSVAFDHADPSIFTV
LTAKSVRPGVAIADFVIFPPRWGVADKTFRPPYYHRNCMSEFMGLIRGHYEAKQGGFLPG
GGSLHSTMTPHGPDADCFEKASKVKLAPERIADGTMAFMFESSLSLAVTKWGLKASRCLD
ENYHKCWEPLKSHFTPNSRNPAEPN

Sequence length

445

Interactions

View interactions

	KEGG		Reactome
	Tyrosine metabolism Metabolic pathways		Tyrosine catabolism

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Alkaptonuria	alkaptonuria	rs120074172, rs1390061303, rs786204422, rs1057516976, rs120074173, rs569846003, rs767159114, rs1057516911, rs120074174, rs1553716979, rs760206323, rs1057516662, rs397515516, rs368717991, rs1057516847 View all (32 more)	N/A

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Alkaptonuria	Associate	10205262, 10340975, 10594001, 12501223, 15529343, 19862842, 20694448, 22105303, 22606059, 24876668, 25233259, 25804398, 28158906, 28643719, 30737480 View all (12 more)
Alkaptonuria	Inhibit	34799606, 39737503, 39842076
Alkaptonuric ochronosis	Associate	10340975
Bone Diseases	Associate	25804398
Carcinoma Hepatocellular	Associate	38200408
Cataract	Associate	19275895, 19382745, 20553008
Ochronosis	Associate	36376482
Osteoarthropathy Primary Hypertrophic	Associate	36376482
Primary hyperoxaluria type 1	Associate	40120493
Spondylitis Ankylosing	Associate	39213249
Thyroid Cancer Papillary	Associate	36465624
Tuberculosis Pulmonary	Associate	36787336

HGD (homogentisate 1,2-dioxygenase)