OGDH

protein-coding

oxoglutarate dehydrogenase, the group of Oxoglutarate dehydrogenase family

Gene 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]

MANE transcript

NM_002541.4

Inheritance

AR

ClinVar variants

P:5U:112B:85

Top phenotype

Oxoglutarate dehydrogenase deficiency

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr7:44,606,572-44,709,066

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~102.5 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

oxoglutaricaciduriaMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0008759

Submitter: G2P

mitochondrial diseaseDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0044970

Submitter: ClinGen

The relationship between *OGDH* and *OGDH*-related primary mitochondrial disease was evaluated using the ClinGen Clinical Validity Framework as of February 19, 2026. The *OGDH* gene encodes oxoglutarate dehydrogenase, the E1 component of the α-ketoglutarate dehydrogenase (α-KGDH) complex. α-KGDH catalyzes the conversion of α-ketoglutarate to succinyl-coenzyme A (succinyl-CoA) in the tricarboxylic acid (TCA) cycle. The *OGDH* gene was first reported in relation to autosomal recessive *OGDH*-related primary mitochondrial disease in 2021 (PMID: 32383294), however the biochemical etiology was reported in several papers between 1982-2000 (PMIDs: 1640293, 10774994, 8295396, 7075624). *OGDH* has been associated with a single disease entity to date; oxoglutarate dehydrogenase deficiency [OMIM# 203740]. This is one disease entity according to the ClinGen Lumping and Splitting Framework, and has been renamed as *OGDH*-related primary mitochondrial disease. Evidence supporting this gene-disease relationship includes case-level data and experimental data. This curation included four missense variants identified in five unrelated cases from two publications (PMIDs: 32383294, 36520152). The age of onset ranges from the neonatal period to early childhood and the reported outcomes range from death at 12 months old to living at 6 years old. Clinical features in affected individuals include global developmental delay, hypotonia, dystonia, dysmetria, ataxia, seizures, microcephaly, decompensation with illness, and dysmorphic features (bitemporal narrowing, full cheeks, nasal bridge abnormalities (broad, depressed), and micrognathia). Of note, there are reports of sudden deteriorations after events such as head trauma (PMID: 32383294) or anesthesia (reported in a case where only the biochemical phenotype was known, PMID: 8295396). Brain imaging shows ventriculomegaly, brain atrophy, agenesis of the corpus callosum, hypoplasia of the pons, delayed myelination, deep gray matter signal abnormalities (dentate nuclei, globi pallidi, subthalamic nuclei) and MRS showing lactate peak. Elevated lactate, elevated ammonia, and elevated urine α-ketoglutarate are also noted. The mechanism of disease is loss of function. This gene-disease relationship is also supported by a biochemical function shared with other genes associated with primary mitochondrial disease (PMID: 33340416) and *Drosophila melanogaster* model (PMID: 32383294). In summary, there is definitive evidence to support the relationship between *OGDH* and autosomal recessive *OGDH*-related primary mitochondrial disease. This relationship has been repeatedly demonstrated in both the research and clinical diagnostic settings and has been upheld over time. This classification was approved by the NICHD/NINDS U24 ClinGen Mitochondrial Disease Gene Curation Expert Panel on February 19, 2026 (SOP Version 11).

oxoglutaricaciduriaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008759

Submitter: Labcorp Genetics (formerly Invitae)

oxoglutaricaciduriaLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0008759

Submitter: Labcorp Genetics (formerly Invitae)

oxoglutaricaciduriaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0008759

Submitter: PanelApp Australia

oxoglutaricaciduriaLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0008759

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Oxoglutarate dehydrogenase deficiencyAR

Manifestation: Biochemical; Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 32383294Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OGDH variants in ClinVar

4 Conditions Cataloged
OxoglutaricaciduriaTotal: 157
not specifiedTotal: 71
not providedTotal: 30
OGDH-related disorderTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002541.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
4
clinvar
72
clinvar
7
clinvar
83
missense
4
clinvar
1
clinvar
102
clinvar
6
clinvar
113
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
4
clinvar
4
Total41112787202

Highest pathogenic variant AF is 0.000006841162

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 125 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002541.4RefSeqNP_002532.222MANE Select
ENST00000222673.6EnsemblENSP00000222673.522MANE Select
NM_001003941.3RefSeqNP_001003941.18Standard
NM_001165036.2RefSeqNP_001158508.122Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Citrate cycle (TCA cycle) - Homo sapiens (human)
  • Tryptophan metabolism - Homo sapiens (human)
  • Lysine degradation - Homo sapiens (human)
  • Valproic Acid Pathway, Pharmacodynamics
  • Pathway_PA165964473

Biological Process

  • generation of precursor metabolites and energy
  • glycolytic process
  • tricarboxylic acid cycle
  • 2-oxoglutarate metabolic process
  • succinyl-CoA metabolic process

Molecular Function

  • oxoglutarate dehydrogenase (succinyl-transferring) activity
  • thiamine pyrophosphate binding
  • heat shock protein binding
  • oxoglutarate dehydrogenase (NAD+) activity
  • metal ion binding

Cellular Component

  • nucleus
  • mitochondrion
  • mitochondrial matrix
  • mitochondrial membrane
  • oxoglutarate dehydrogenase complex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000222673
Coding exons
22
Length
102495
Individuals with no LoFs
125734
Homozygous LoFs
0
Heterozygous LoFs
14
Defined
125748
p
0.0000557
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense4.763046440.4720.00004106748
Missense (PolyPhen)110333.030.330313419
Synonymous0.04122652660.9970.00001802001
Loss of Function5.70852.60.1520.00000262575

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.000120.00012rare
Ashkenazi Jewish00.0absent
East Asian0.0000540.000054rare
Finnish00.0absent
European (Non-Finnish)0.0000350.000035rare
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: 2-oxoglutarate dehydrogenase (E1) component of the 2- oxoglutarate dehydrogenase complex, which mediates the decarboxylation of alpha-ketoglutarate (PubMed:24495017). The 2- oxoglutarate dehydrogenase complex catalyzes the overall conversion of 2-oxoglutarate to succinyl-CoA and CO(2) (PubMed:24495017). The 2-oxoglutarate dehydrogenase complex is mainly active in the mitochondrion (PubMed:29211711). A fraction of the 2-oxoglutarate dehydrogenase complex also localizes in the nucleus and is required for lysine succinylation of histones: associates with KAT2A on chromatin and provides succinyl-CoA to histone succinyltransferase KAT2A (PubMed:29211711). {ECO:0000269|PubMed:24495017, ECO:0000269|PubMed:29211711}.;

Recessive Scores

pRec
0.636

Intolerance Scores

LoFtool
0.136
RVIS EVS
-0.48
RVIS percentile EVS
22.75

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.981

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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