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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	3081
Gene name	Homogentisate 1,2-dioxygenase
Gene symbol	HGD
Synonyms (NCBI Gene)	AKUHGO
Chromosome	3
Chromosome location	3q13.33
Summary	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

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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Alkaptonuria	Likely pathogenic; Pathogenic	rs564979861, rs2107510544, rs2107483632, rs760206323, rs2107489196, rs1320184173, rs1184695718, rs2107548853, rs373921680, rs755734596, rs1295089623, rs1168687230, rs2107489383, rs375283568, rs1397264922 View all (207 more)	RCV001376082 RCV001376105 RCV001384371 RCV001386852 RCV001389892 View all (238 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Clear cell carcinoma of kidney	Likely pathogenic; Pathogenic	rs755734596, rs397515347	RCV005914900 RCV005887239	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Colon adenocarcinoma	Likely pathogenic	rs370920635	RCV005932733	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Familial cancer of breast	Pathogenic	rs397515347	RCV005887237	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Familial prostate cancer	Likely pathogenic; Pathogenic	rs1057516307	RCV005900628	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Gastric cancer	Pathogenic	rs1469714335	RCV005932732	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
HGD-related disorder	Pathogenic; Likely pathogenic	rs1559781702, rs1941184654, rs397515347, rs1057517081, rs397515516	RCV003401973 RCV003943328 RCV004751195 RCV003401391 RCV004751249	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nonpapillary renal cell carcinoma	Pathogenic	rs397515347	RCV005887238	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Familial pancreatic carcinoma	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (52)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Adenocarcinoma	Adenocarcinoma	BEFREE	22541897, 27855466, 31464710		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenocarcinoma Of Esophagus	Esophageal Cancer	BEFREE	22541897		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenoma	Adenoma	BEFREE	29573208		★★★★★ ★☆☆☆☆ Found in Text Mining only
Adenoma of large intestine	Colorectal adenoma	BEFREE	30918959		★★★★★ ★☆☆☆☆ Found in Text Mining only
Alkaptonuria	Alkaptonuria	BEFREE	10205262, 10340975, 10594001, 11017803, 12501223, 12630963, 12872836, 18945288, 19096913, 19306858, 19765774, 19862842, 21437689, 21720873, 22105303 View all (24 more)		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alkaptonuria	Alkaptonuria	UNIPROT_DG	10205262, 10340975, 10482952, 10594001, 19862842, 21437689, 23353776, 23430897, 25681086, 8782815, 9154114, 9529363, 9630082		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alkaptonuria	Alkaptonuria	CLINVAR_DG	10205262, 10340975, 10465119, 10482952, 10594001, 10970188, 11001939, 12051967, 12114497, 12501223, 12872836, 16085442, 19096913, 19862842, 20462779 View all (12 more)		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alkaptonuria	Alkaptonuria	Pubtator	10205262, 10340975, 10594001, 12501223, 15529343, 19862842, 20694448, 22105303, 22606059, 24876668, 25233259, 25804398, 28158906, 28643719, 30737480 View all (12 more)	Associate	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alkaptonuria	Alkaptonuria	CLINGEN_DG	13271328, 8188247, 8782815, 9154114, 9529363, 9674916		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alkaptonuria	Alkaptonuria	LHGDN	16085442, 18945288		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alkaptonuria	Alkaptonuria	Orphanet			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alkaptonuria	Alkaptonuria	GENOMICS_ENGLAND_DG	27604308		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alkaptonuria	Alkaptonuria	Pubtator	34799606, 39737503, 39842076	Inhibit	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Alkaptonuria	Alkaptonuria	CTD_human_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
ANOPHTHALMIA AND PULMONARY HYPOPLASIA	Syndromic microphthalmia	BEFREE	30385653		★★★★★ ★☆☆☆☆ Found in Text Mining only
Aortic Aneurysm	Aortic Aneurysm	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Aortic valve calcification	Aortic valve calcification	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	BEFREE	9529363		★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthropathy	Arthropathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Atherosclerosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Barrett Esophagus	Barrett esophagus	BEFREE	22541897, 27855466, 28315927, 30479169		★★★★★ ★☆☆☆☆ Found in Text Mining only
Bone Diseases	Bone Disease	BEFREE	25804398		★★★★★ ★☆☆☆☆ Found in Text Mining only
Bone Diseases	Bone disease	Pubtator	25804398	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	38200408	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	Pubtator	19275895, 19382745, 20553008	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	BEFREE	19382745		★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic colitis	Colitis	BEFREE	9744312		★★★★★ ★☆☆☆☆ Found in Text Mining only
Chronic Periodontitis	Periodontitis	BEFREE	25056994		★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	30423034, 31175827		★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital anomaly of nose	Congenital Anomaly Of Nose	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital contractural arachnodactyly	Congenital Contractural Arachnodactyly	BEFREE	26320466		★★★★★ ★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Familial multiple trichoepitheliomata	Multiple Trichoepithelioma	BEFREE	28315927, 31274147		★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Inborn Errors of Metabolism	Inborn Errors Of Metabolism	BEFREE	19096913, 25153563, 28869836		★★★★★ ★☆☆☆☆ Found in Text Mining only
Inflammatory Bowel Diseases	Inflammatory Bowel Disease	BEFREE	31175827		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intervertebral Disc Degeneration	Intervertebral Disc Degeneration	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Intrahepatic Cholangiocarcinoma	Intrahepatic Cholangiocarcinoma	BEFREE	31561245		★★★★★ ★☆☆☆☆ Found in Text Mining only
Irritable Bowel Syndrome	Irritable Bowel Syndrome	BEFREE	31175827		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	29468422, 31127170, 31464710		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myocardial Infarction	Myocardial Infarction	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	29660322, 30085111, 30308535, 31175827		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nephrolithiasis	Nephrolithiasis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ochronosis, hereditary	Alkaptonuria	CLINGEN_DG	13271328, 8188247, 8782815, 9154114, 9529363, 9674916		★★★★★ ★☆☆☆☆ Found in Text Mining only
Osteoarthropathy Primary Hypertrophic	Primary hypertrophic osteoarthropathy	Pubtator	36376482	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Papilloma	Papilloma	BEFREE	17277618		★★★★★ ★☆☆☆☆ Found in Text Mining only
Primary hyperoxaluria type 1	Hyperoxaluria	Pubtator	40120493	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
prostatitis	Prostatitis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spondylitis Ankylosing	Ankylosing spondylitis	Pubtator	39213249	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	17277618		★★★★★ ★☆☆☆☆ Found in Text Mining only
Thyroid Cancer Papillary	Papillary thyroid cancer	Pubtator	36465624	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

HGD (homogentisate 1,2-dioxygenase)