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

569

Show/Hide Causal Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
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 RCV001381505 RCV001389681 RCV001389370 RCV001384280 RCV001542260 RCV001799114 RCV001799115 RCV001799116 RCV002021839 RCV001999116 RCV001867438 RCV001941999 RCV001946825 RCV002003374 RCV001956399 RCV001949356 RCV001884025 RCV002010401 RCV000144263 RCV003989139 RCV002306462 RCV002306482 RCV002309567 RCV002309692 RCV002309792 RCV002309975 RCV002306963 RCV002310175 RCV002310475 RCV000003315 RCV000003316 RCV000003318 RCV000003319 RCV000003320 RCV000003321 RCV000003322 RCV000003323 RCV000003325 RCV000169601 RCV000169458 RCV000169217 RCV000169542 RCV000169012 RCV003068918 RCV002602808 RCV002643585 RCV002654663 RCV002651719 RCV002666755 RCV002770588 RCV002825176 RCV002816201 RCV002876271 RCV002858383 RCV002953408 RCV002958845 RCV003016938 RCV003011893 RCV003028652 RCV003045772 RCV003026967 RCV003146013 RCV003336654 RCV003336655 RCV003336659 RCV003336660 RCV003336662 RCV003336663 RCV003336664 RCV003336665 RCV003336666 RCV003336667 RCV003336668 RCV003336669 RCV003336670 RCV003336671 RCV003336672 RCV003336673 RCV003336674 RCV003336675 RCV003336676 RCV003336677 RCV003336678 RCV003336679 RCV003336680 RCV003336681 RCV003336682 RCV003336683 RCV003336684 RCV003337701 RCV003337702 RCV003337703 RCV003337704 RCV003337705 RCV003337706 RCV003337707 RCV003337708 RCV003337709 RCV003387456 RCV003387457 RCV003387458 RCV003387459 RCV003387460 RCV003387461 RCV003387462 RCV003387463 RCV003387464 RCV003387465 RCV003387466 RCV003387467 RCV003387468 RCV003387469 RCV003387470 RCV003387471 RCV003387472 RCV003387473 RCV003387474 RCV003387475 RCV003387476 RCV003387477 RCV003387478 RCV003387479 RCV003387480 RCV003387481 RCV003387482 RCV003387483 RCV003387484 RCV003387485 RCV003387486 RCV003387487 RCV003387488 RCV003387489 RCV003387490 RCV003388974 RCV003388975 RCV003388976 RCV003388978 RCV003388980 RCV003388981 RCV003388982 RCV003388983 RCV003388984 RCV003388985 RCV003388986 RCV003388987 RCV003388988 RCV003388989 RCV003388990 RCV003388991 RCV003388992 RCV003388993 RCV003388994 RCV003388996 RCV003388997 RCV003388998 RCV003388999 RCV003389000 RCV003389001 RCV003389002 RCV003389003 RCV003389004 RCV003389005 RCV003389006 RCV003389007 RCV003389008 RCV003389009 RCV003389010 RCV003389011 RCV003389012 RCV003389013 RCV003389014 RCV003389015 RCV003389016 RCV003389017 RCV003389018 RCV003389019 RCV003389020 RCV003389021 RCV003389022 RCV003389025 RCV003482188 RCV003501954 RCV003500089 RCV003500112 RCV003607764 RCV003607803 RCV003608275 RCV003607042 RCV003860527 RCV003990601 RCV003990870 RCV003990954 RCV000409498 RCV000409868 RCV000411251 RCV000410483 RCV000409682 RCV000410964 RCV000411140 RCV000411569 RCV000411150 RCV000409303 RCV000411862 RCV000411315 RCV000412288 RCV000409762 RCV000411822 RCV000412076 RCV000411427 RCV000410442 RCV000410834 RCV000412049 RCV000503877 RCV000668985 RCV000670576 RCV000665152 RCV000672087 RCV000793180 RCV000797747 RCV000055777 RCV003387491 RCV000055781 RCV000055782 RCV001067792 RCV001054603 RCV001037383 RCV001061073 RCV001075890 RCV001194660 RCV001194659 RCV001194658 RCV001194657 RCV001194656 RCV001194655 RCV001215109 RCV001242145 RCV001232918 RCV001242049
Clear cell carcinoma of kidney	Likely pathogenic; Pathogenic	rs755734596, rs397515347	RCV005914900 RCV005887239
Colon adenocarcinoma	Likely pathogenic	rs370920635	RCV005932733
Familial cancer of breast	Pathogenic	rs397515347	RCV005887237
Familial prostate cancer	Likely pathogenic; Pathogenic	rs1057516307	RCV005900628
Gastric cancer	Pathogenic	rs1469714335	RCV005932732
HGD-related disorder	Pathogenic; Likely pathogenic	rs1559781702, rs1941184654, rs397515347, rs1057517081, rs397515516	RCV003401973 RCV003943328 RCV004751195 RCV003401391 RCV004751249
Nonpapillary renal cell carcinoma	Pathogenic	rs397515347	RCV005887238
See cases	Pathogenic; Likely pathogenic	rs120074173, rs1390061303	RCV004584308 RCV004584392

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Familial pancreatic carcinoma	Uncertain significance	rs752157530	RCV005930465
Hepatocellular carcinoma	Benign; Likely benign	rs2293734	RCV005897579

Show/Hide Text Mining Associations (12)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)