OGDH oxoglutarate dehydrogenase [Homo sapiens (human)] - Gene

Summary

Official Symbol: OGDHprovided by HGNC
Official Full Name: oxoglutarate dehydrogenaseprovided by HGNC
Primary source: HGNC:HGNC:8124
See related: Ensembl:ENSG00000105953 MIM:613022; AllianceGenome:HGNC:8124
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: E1k; E1o; KGD1; OGDC; AKGDH; OGDH2; OGDHD; OGDH-E1
Summary: This gene encodes one subunit of the 2-oxoglutarate dehydrogenase complex. This complex catalyzes the overall conversion of 2-oxoglutarate (alpha-ketoglutarate) to succinyl-CoA and CO(2) during the Krebs cycle. The protein is located in the mitochondrial matrix and uses thiamine pyrophosphate as a cofactor. A congenital deficiency in 2-oxoglutarate dehydrogenase activity is believed to lead to hypotonia, metabolic acidosis, and hyperlactatemia. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Sep 2009]
Expression: Ubiquitous expression in heart (RPKM 71.3), kidney (RPKM 57.5) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7p13

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (44606627..44709066)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (44766778..44869231)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (44646226..44748665)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Biallelic variants in OGDH encoding oxoglutarate dehydrogenase lead to a neurodevelopmental disorder characterized by global developmental delay, movement disorder, and metabolic abnormalities.
Title: Biallelic variants in OGDH encoding oxoglutarate dehydrogenase lead to a neurodevelopmental disorder characterized by global developmental delay, movement disorder, and metabolic abnormalities.
A biallelic pathogenic variant in the OGDH gene results in a neurological disorder with features of a mitochondrial disease.
Title: A biallelic pathogenic variant in the OGDH gene results in a neurological disorder with features of a mitochondrial disease.
DHTKD1 and OGDH display substrate overlap in cultured cells and form a hybrid 2-oxo acid dehydrogenase complex in vivo.
Title: DHTKD1 and OGDH display substrate overlap in cultured cells and form a hybrid 2-oxo acid dehydrogenase complex in vivo.
Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues.
Title: Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues.
there is the direct interaction between SIRT5 and 2-oxoglutarate dehydrogenase (OGDH), and desuccinylation of OGDH by SIRT5 inhibits the activity of OGDH complex.
Title: OGDH mediates the inhibition of SIRT5 on cell proliferation and migration of gastric cancer.
The data indicate that amino acid/nucleotide metabolism-related genes OGDH, PPAT and PCCA acquire somatic mutations in microsatellite instability-high gastric cancers and colorectal cancers and that mutational intratumoral heterogeneity may occur in at least some of these tumors.
Title: Frameshift mutations of OGDH, PPAT and PCCA genes in gastric and colorectal cancers.
PIK3CA mutant cancer cells require PIK3CA but also require the expression of the TCA cycle enzyme 2-oxoglutarate dehydrogenase (OGDH).
Title: PIK3CA mutant tumors depend on oxoglutarate dehydrogenase.
oxoglutarate dehydrogenase (OGDH) and lipoic acid synthase (LIAS), which when mutated stabilize HIF1alpha in a non-hydroxylated form.
Title: Mitochondrial Protein Lipoylation and the 2-Oxoglutarate Dehydrogenase Complex Controls HIF1α Stability in Aerobic Conditions.
Tissue-specific expression of OGDH splice variants may thus provide a mechanism that tunes the control of the enzyme to the specialized metabolic and signalling needs of individual cell types
Title: Calcium-insensitive splice variants of mammalian E1 subunit of 2-oxoglutarate dehydrogenase complex with tissue-specific patterns of expression.
ATP consumption is demonstrated in respiration-impaired isolated mice and in situ neuronal mitochondria from transgenic mice with dihydrolipoyl succinyltransferase deficiency.
Title: The negative impact of α-ketoglutarate dehydrogenase complex deficiency on matrix substrate-level phosphorylation.

Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Oxoglutaricaciduria MedGen: C2752074 OMIM: 203740 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies upregulation of oxoglutarate (alpha-ketoglutarate) dehydrogenase (OGDH) expression by HIV-1 Vpr in Vpr transduced macrophages	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GDB:4585311 (e-PCR)
- UniSTS:19205

GDB:1318360 (e-PCR)
- UniSTS:65798

SHGC-171927 (e-PCR)
- UniSTS:184584

D7S2068E (e-PCR)
- UniSTS:34848

STS-T70286 (e-PCR)
- UniSTS:52771

D7S2643 (e-PCR)
- UniSTS:77092

D11S2560 (e-PCR)
- UniSTS:37928

MARC_4335-4336:996679558:1 (e-PCR)
- UniSTS:269358

D8S2279 (e-PCR)
- UniSTS:473907

RH11783 (e-PCR)
- UniSTS:32061

D15S1477 (e-PCR)
- UniSTS:474482

RH70029 (e-PCR)
- UniSTS:70526

STS-AA005110 (e-PCR)
- UniSTS:64900

D7S2436 (e-PCR), detects polymorphism
- UniSTS:38022

D7S2436 (e-PCR), detects polymorphism
- UniSTS:73367

GDB:1317390 (e-PCR)
- UniSTS:3065

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables oxoglutarate dehydrogenase (NAD+) activity	IEA Inferred from Electronic Annotation more info
enables oxoglutarate dehydrogenase (succinyl-transferring) activity	IBA Inferred from Biological aspect of Ancestor more info
enables oxoglutarate dehydrogenase (succinyl-transferring) activity	IDA Inferred from Direct Assay more info	PubMed
enables oxoglutarate dehydrogenase (succinyl-transferring) activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables thiamine pyrophosphate binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in 2-oxoglutarate metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in cerebellar cortex development	IEA Inferred from Electronic Annotation more info
involved_in generation of precursor metabolites and energy	ISS Inferred from Sequence or Structural Similarity more info
involved_in glycolytic process	IEA Inferred from Electronic Annotation more info
involved_in hippocampus development	IEA Inferred from Electronic Annotation more info
involved_in olfactory bulb mitral cell layer development	IEA Inferred from Electronic Annotation more info
involved_in pyramidal neuron development	IEA Inferred from Electronic Annotation more info
involved_in striatum development	IEA Inferred from Electronic Annotation more info
involved_in succinyl-CoA metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in tangential migration from the subventricular zone to the olfactory bulb	IEA Inferred from Electronic Annotation more info
involved_in thalamus development	IEA Inferred from Electronic Annotation more info
involved_in tricarboxylic acid cycle	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in mitochondrial matrix	TAS Traceable Author Statement more info
located_in mitochondrial membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of oxoglutarate dehydrogenase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of oxoglutarate dehydrogenase complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: 2-oxoglutarate dehydrogenase complex component E1

Names: 2-oxoglutarate dehydrogenase, mitochondrial; OGDC-E1; alpha-KGDH-E1; oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide); oxoglutarate decarboxylase; oxoglutarate dehydrogenase (succinyl-transferring); testicular tissue protein Li 131; thiamine diphosphate (ThDP)-dependent 2-oxoglutarate dehydrogenase

NP_001003941.1

EC 1.2.4.2

NP_001158508.1

EC 1.2.4.2

NP_001350452.1

EC 1.2.4.2

NP_002532.2

EC 1.2.4.2

XP_005249816.1

EC 1.2.4.2

XP_011513710.1

EC 1.2.4.2

XP_047276382.1

EC 1.2.4.2

XP_047276383.1

EC 1.2.4.2

XP_047276384.1

EC 1.2.4.2

XP_047276385.1

EC 1.2.4.2

XP_054214282.1

EC 1.2.4.2

XP_054214283.1

EC 1.2.4.2

XP_054214284.1

EC 1.2.4.2

XP_054214285.1

EC 1.2.4.2

XP_054214286.1

EC 1.2.4.2

XP_054214287.1

EC 1.2.4.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_023260.1 RefSeqGene

Range

5106..107545

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001003941.3 → NP_001003941.1 2-oxoglutarate dehydrogenase complex component E1 isoform 2 precursor

See identical proteins and their annotated locations for NP_001003941.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 3' end of coding region, compared to variant 1. Variant 2 encodes isoform 2 which has a shorter and distinct C-terminus, compared to isoform 1. Variant 2 is supported by transcriptional evidence although the protein product is predicted.

Source sequence(s)

BC009580

Consensus CDS

CCDS47580.1

UniProtKB/TrEMBL

A0A140VJQ5

Related

ENSP00000388084.2, ENST00000443864.6

Conserved Domains (1) summary

cl25580
Location:49 → 405

OxoGdeHyase_C; 2-oxoglutarate dehydrogenase C-terminal
NM_001165036.2 → NP_001158508.1 2-oxoglutarate dehydrogenase complex component E1 isoform 3 precursor

See identical proteins and their annotated locations for NP_001158508.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) has multiple differences in the presence and absence of exons in the 5' coding region, compared to variant 1. These differences result in a shorter protein (isoform 3), compared to isoform 1.

Source sequence(s)

AC004859, AK304439, AK304690, BU682361

Consensus CDS

CCDS55107.1

UniProtKB/TrEMBL

B4DF00

Related

ENSP00000392878.1, ENST00000449767.5

Conserved Domains (1) summary

PRK09404
Location:49 → 1011

sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed
NM_001363523.2 → NP_001350452.1 2-oxoglutarate dehydrogenase complex component E1 isoform 4 precursor

Status: REVIEWED

Source sequence(s)

AC004859, AC011894

Consensus CDS

CCDS87498.1

UniProtKB/TrEMBL

B4DF00, E9PDF2

Related

ENSP00000388183.1, ENST00000447398.6

Conserved Domains (1) summary

PRK09404
Location:49 → 1026

sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed
NM_002541.4 → NP_002532.2 2-oxoglutarate dehydrogenase complex component E1 isoform 1 precursor

See identical proteins and their annotated locations for NP_002532.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC004859, AK304690, AK314179, BU682361

Consensus CDS

CCDS34627.1

UniProtKB/Swiss-Prot

B4E2U9, D3DVL0, E9PBM1, Q02218, Q96DD3, Q9UDX0

UniProtKB/TrEMBL

B4DF00

Related

ENSP00000222673.5, ENST00000222673.6

Conserved Domains (1) summary

PRK09404
Location:49 → 1015

sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

44606627..44709066

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047420428.1 → XP_047276384.1 2-oxoglutarate dehydrogenase complex component E1 isoform X3
XM_011515408.3 → XP_011513710.1 2-oxoglutarate dehydrogenase complex component E1 isoform X1

See identical proteins and their annotated locations for XP_011513710.1

UniProtKB/TrEMBL

B4DF00, E9PCR7

Conserved Domains (1) summary

PRK09404
Location:49 → 1030

sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed
XM_047420427.1 → XP_047276383.1 2-oxoglutarate dehydrogenase complex component E1 isoform X2

UniProtKB/Swiss-Prot

B4E2U9, D3DVL0, E9PBM1, Q02218, Q96DD3, Q9UDX0
XM_005249759.6 → XP_005249816.1 2-oxoglutarate dehydrogenase complex component E1 isoform X1

See identical proteins and their annotated locations for XP_005249816.1

UniProtKB/TrEMBL

B4DF00, E9PCR7

Related

ENSP00000414662.1, ENST00000444676.5

Conserved Domains (1) summary

PRK09404
Location:49 → 1030

sucA; 2-oxoglutarate dehydrogenase E1 component; Reviewed
XM_047420426.1 → XP_047276382.1 2-oxoglutarate dehydrogenase complex component E1 isoform X1

UniProtKB/TrEMBL

E9PCR7
XM_047420429.1 → XP_047276385.1 2-oxoglutarate dehydrogenase complex component E1 isoform X4

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

44766778..44869231

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054358311.1 → XP_054214286.1 2-oxoglutarate dehydrogenase complex component E1 isoform X3
XM_054358308.1 → XP_054214283.1 2-oxoglutarate dehydrogenase complex component E1 isoform X1
XM_054358310.1 → XP_054214285.1 2-oxoglutarate dehydrogenase complex component E1 isoform X2
XM_054358307.1 → XP_054214282.1 2-oxoglutarate dehydrogenase complex component E1 isoform X1
XM_054358309.1 → XP_054214284.1 2-oxoglutarate dehydrogenase complex component E1 isoform X1
XM_054358312.1 → XP_054214287.1 2-oxoglutarate dehydrogenase complex component E1 isoform X4

UniProtKB/TrEMBL

B4DH65