OGDH
protein-codingoxoglutarate 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
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~102.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0008759
Submitter: G2P
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).
Inheritance Pattern: AR
Disease ID:MONDO:0008759
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: Unknown
Disease ID:MONDO:0008759
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0008759
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0008759
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to OGDH variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 72 | 7 | 83 | ||
| missense | 4 | 1 | 102 | 6 | 113 | |
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 4 | 1 | 112 | 78 | 7 | 202 |
Highest pathogenic variant AF is 0.000006841162
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002532.2 | 22 | MANE Select | |
| Ensembl | ENSP00000222673.5 | 22 | MANE Select | |
| RefSeq | NP_001003941.1 | 8 | Standard | |
| RefSeq | NP_001158508.1 | 22 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 4.76 | 304 | 644 | 0.472 | 0.0000410 | 6748 |
| Missense (PolyPhen) | 110 | 333.03 | 0.33031 | 3419 | ||
| Synonymous | 0.0412 | 265 | 266 | 0.997 | 0.0000180 | 2001 |
| Loss of Function | 5.70 | 8 | 52.6 | 0.152 | 0.00000262 | 575 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |