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	728294
Gene name	D-2-hydroxyglutarate dehydrogenase
Gene symbol	D2HGDH
Synonyms (NCBI Gene)	D2HGD
Chromosome	2
Chromosome location	2q37.3
Summary	This gene encodes D-2hydroxyglutarate dehydrogenase, a mitochondrial enzyme belonging to the FAD-binding oxidoreductase/transferase type 4 family. This enzyme, which is most active in liver and kidney but also active in heart and brain, converts D-2-hydro

Show/Hide all (18)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121434360	T>C	Pathogenic	Non coding transcript variant, stop lost, 3 prime UTR variant, coding sequence variant, missense variant, genic downstream transcript variant, terminator codon variant
rs121434361	T>G	Pathogenic	Non coding transcript variant, 5 prime UTR variant, coding sequence variant, missense variant
rs121434362	A>G	Pathogenic	Non coding transcript variant, 3 prime UTR variant, missense variant, coding sequence variant, genic downstream transcript variant, synonymous variant
rs145731647	A>G,T	Likely-benign, pathogenic	Intron variant
rs146408017	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs146578303	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity, benign	Non coding transcript variant, missense variant, coding sequence variant, genic downstream transcript variant, intron variant
rs147210645	C>A,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs149504235	G>A,C	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Non coding transcript variant, missense variant, coding sequence variant, genic downstream transcript variant, intron variant
rs149628174	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Non coding transcript variant, missense variant, coding sequence variant, genic downstream transcript variant, intron variant
rs267606759	G>A,T	Pathogenic	Non coding transcript variant, intron variant, downstream transcript variant, missense variant, coding sequence variant, 3 prime UTR variant, genic downstream transcript variant
rs369135156	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Downstream transcript variant, genic downstream transcript variant, intron variant
rs587783517	C>T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs749330477	->TC	Pathogenic	Non coding transcript variant, frameshift variant, 5 prime UTR variant, coding sequence variant
rs753528947	A>G	Pathogenic	Splice acceptor variant
rs797045506	T>-	Pathogenic	Coding sequence variant, intron variant, frameshift variant, non coding transcript variant, 3 prime UTR variant, genic downstream transcript variant
rs797045507	T>C	Likely-pathogenic	Genic downstream transcript variant, splice donor variant, intron variant
rs1559361049	T>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1559364994	T>C	Likely-pathogenic	Splice donor variant

Show/Hide all (60)

miRTarBase ID	miRNA	Experiments	Reference
MIRT047376	hsa-miR-34a-5p	CLASH	23622248
MIRT922388	hsa-miR-1243	CLIP-seq
MIRT922389	hsa-miR-1273f	CLIP-seq
MIRT922390	hsa-miR-143	CLIP-seq
MIRT922391	hsa-miR-181a	CLIP-seq
MIRT922392	hsa-miR-181b	CLIP-seq
MIRT922393	hsa-miR-181c	CLIP-seq
MIRT922394	hsa-miR-181d	CLIP-seq
MIRT922395	hsa-miR-3654	CLIP-seq
MIRT922396	hsa-miR-3942-3p	CLIP-seq
MIRT922397	hsa-miR-4262	CLIP-seq
MIRT922398	hsa-miR-4313	CLIP-seq
MIRT922399	hsa-miR-433	CLIP-seq
MIRT922400	hsa-miR-4638-3p	CLIP-seq
MIRT922401	hsa-miR-4684-3p	CLIP-seq
MIRT922402	hsa-miR-4708-5p	CLIP-seq
MIRT922403	hsa-miR-4770	CLIP-seq
MIRT922404	hsa-miR-576-3p	CLIP-seq
MIRT1973204	hsa-miR-1234	CLIP-seq
MIRT1973205	hsa-miR-1307	CLIP-seq
MIRT1973206	hsa-miR-136	CLIP-seq
MIRT1973207	hsa-miR-15a	CLIP-seq
MIRT1973208	hsa-miR-15b	CLIP-seq
MIRT1973209	hsa-miR-16	CLIP-seq
MIRT1973210	hsa-miR-195	CLIP-seq
MIRT1973211	hsa-miR-214	CLIP-seq
MIRT1973212	hsa-miR-3173-3p	CLIP-seq
MIRT1973213	hsa-miR-3183	CLIP-seq
MIRT1973214	hsa-miR-361-3p	CLIP-seq
MIRT1973215	hsa-miR-3615	CLIP-seq
MIRT1973216	hsa-miR-3619-5p	CLIP-seq
MIRT1973217	hsa-miR-3677-5p	CLIP-seq
MIRT1973218	hsa-miR-3909	CLIP-seq
MIRT1973219	hsa-miR-424	CLIP-seq
MIRT1973220	hsa-miR-4291	CLIP-seq
MIRT1973221	hsa-miR-4433	CLIP-seq
MIRT1973222	hsa-miR-4638-5p	CLIP-seq
MIRT1973223	hsa-miR-4722-3p	CLIP-seq
MIRT1973224	hsa-miR-4722-5p	CLIP-seq
MIRT1973225	hsa-miR-4723-3p	CLIP-seq
MIRT1973226	hsa-miR-4763-5p	CLIP-seq
MIRT1973227	hsa-miR-4779	CLIP-seq
MIRT1973228	hsa-miR-497	CLIP-seq
MIRT1973229	hsa-miR-550a	CLIP-seq
MIRT1973230	hsa-miR-761	CLIP-seq
MIRT1973231	hsa-miR-885-3p	CLIP-seq
MIRT1973232	hsa-miR-922	CLIP-seq
MIRT1973204	hsa-miR-1234	CLIP-seq
MIRT1973206	hsa-miR-136	CLIP-seq
MIRT2208890	hsa-miR-198	CLIP-seq
MIRT1973211	hsa-miR-214	CLIP-seq
MIRT2208891	hsa-miR-3126-5p	CLIP-seq
MIRT1973216	hsa-miR-3619-5p	CLIP-seq
MIRT2208892	hsa-miR-4419a	CLIP-seq
MIRT2208893	hsa-miR-4510	CLIP-seq
MIRT2208894	hsa-miR-4740-3p	CLIP-seq
MIRT2208895	hsa-miR-544b	CLIP-seq
MIRT1973230	hsa-miR-761	CLIP-seq
MIRT2208896	hsa-miR-941	CLIP-seq
MIRT922404	hsa-miR-576-3p	CLIP-seq

Show/Hide all (25)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003824	Function	Catalytic activity	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA
GO:0005739	Component	Mitochondrion	IEA
GO:0005739	Component	Mitochondrion	ISS	15070399
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006089	Process	Lactate metabolic process	ISS	15070399
GO:0006103	Process	2-oxoglutarate metabolic process	TAS
GO:0006108	Process	Malate metabolic process	IDA	33431826
GO:0008270	Function	Zinc ion binding	IDA	33431826
GO:0010042	Process	Response to manganese ion	ISS	15070399
GO:0010043	Process	Response to zinc ion	ISS	15070399
GO:0016491	Function	Oxidoreductase activity	IEA
GO:0032025	Process	Response to cobalt ion	ISS	15070399
GO:0032026	Process	Response to magnesium ion	ISS	15070399
GO:0046872	Function	Metal ion binding	IEA
GO:0050660	Function	Flavin adenine dinucleotide binding	IEA
GO:0051592	Process	Response to calcium ion	ISS	15070399
GO:0051990	Function	(R)-2-hydroxyglutarate dehydrogenase activity	EXP	15070399
GO:0051990	Function	(R)-2-hydroxyglutarate dehydrogenase activity	IDA	15070399
GO:0051990	Function	(R)-2-hydroxyglutarate dehydrogenase activity	IEA
GO:0051990	Function	(R)-2-hydroxyglutarate dehydrogenase activity	IMP	20020533, 33431826
GO:0071949	Function	FAD binding	IEA
GO:1901275	Process	Tartrate metabolic process	ISS	15070399

MIM	HGNC	e!Ensembl
609186	28358	ENSG00000180902

Q8N465

Protein name

D-2-hydroxyglutarate dehydrogenase, mitochondrial (EC 1.1.99.39)

Protein function

Catalyzes the oxidation of D-2-hydroxyglutarate (D-2-HG) to alpha-ketoglutarate (PubMed:15070399, PubMed:15609246, PubMed:16037974, PubMed:20020533, PubMed:33431826). Also catalyzes the oxidation of other D-2-hydroxyacids, such as D-malate (D-MA

PDB

6LPN , 6LPP , 6LPQ , 6LPT , 6LPU , 6LPX

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01565	FAD_binding_4	100 → 239	FAD binding domain	Domain
PF02913	FAD-oxidase_C	275 → 516	FAD linked oxidases, C-terminal domain	Domain

Sequence

MLPRRPLAWPAWLLRGAPGAAGSWGRPVGPLARRGCCSAPGTPEVPLTRERYPVRRLPFS
TVSKQDLAAFERIVPGGVVTDPEALQAPNVDWLRTLRGCSKVLLRPRTSEEVSHILRHCH
ERNLAVNPQGGNTGMVGGSVPVFDEIILSTARMNRVLSFHSVSGILVCQAGCVLEELSRY
VEERDFIMPLDLGAKGSCHIGGNVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLT
SLRKDNTGYDLKQLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCK
GMLGEILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNAGHDAEKLGHFLEH
ALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKYDLSLPVERLYDIVTDLRA
RLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPSLLAALEPHVYEWTAGQQGSVSAEHGVGF
RKRDVLGYSKPPGALQLMQQLKALLDPKGILNPYKTLPSQA

Sequence length

521

Interactions

View interactions

	Reactome
			Interconversion of 2-oxoglutarate and 2-hydroxyglutarate

368

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
D-2-hydroxyglutaric aciduria	Pathogenic; Likely pathogenic	rs797045506, rs797045507	RCV000192342 RCV000192863
D-2-hydroxyglutaric aciduria 1	Pathogenic; Likely pathogenic	rs1699275754, rs2125158367, rs121434360, rs121434361, rs145731647, rs753528947, rs121434362, rs749330477, rs142050154, rs1692452859, rs1158737546, rs2549948325, rs1692428076, rs1559364994, rs1559361049, rs1559404382 View all (1 more)	RCV001322380 RCV001988194 RCV000001926 RCV000001927 RCV000001928 RCV000001929 RCV000001930 RCV000001931 RCV005095992 RCV002471951 RCV002715131 RCV002829837 RCV003990934 RCV000691213 RCV000694373 RCV000703265

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
D2HGDH-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	rs138467167, rs145731647, rs149504235, rs146578303, rs111670322, rs145300657, rs778541885, rs750097168, rs375565047, rs140447217, rs145839736, rs375162898, rs547293002, rs768485205, rs748635429 View all (11 more)	RCV004757450 RCV003905263 RCV003945167 RCV003917442 RCV003905262 RCV003926657 RCV003906537 RCV004757567 RCV003907681 RCV003957729 RCV004757207 RCV003957730 RCV004757608 RCV003899828 RCV003967251 RCV003983096 RCV004757239 RCV003925457 RCV004757240 RCV003915370 RCV004757279 RCV003968075 RCV003968352 RCV003898020 RCV003973103 RCV003963077
Gastric cancer	Likely benign	rs781581192	RCV005913534

Show/Hide Text Mining Associations (9)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
2 Hydroxyglutaricaciduria	Associate	15609246, 30908763, 31349060
Carcinoma Ovarian Epithelial	Associate	33173439
Glioma	Associate	32386320, 36541697
Leukemia Myeloid Acute	Associate	33284559
Lymphoma Large B Cell Diffuse	Associate	26178471
Neoplasms	Associate	21625441, 26178471, 27322736
Osteoporosis	Associate	38169377
Prostatic Neoplasms	Associate	27322736
Squamous Cell Carcinoma of Head and Neck	Associate	31927533

D2HGDH (D-2-hydroxyglutarate dehydrogenase)