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    OGDH oxoglutarate dehydrogenase [ Homo sapiens (human) ]

    Gene ID: 4967, updated on 3-Nov-2024

    Summary

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    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; HsOGDH; 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

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    See OGDH in Genome Data Viewer
    Location:
    7p13
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44606627..44709066)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44766778..44869231)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (44646226..44748665)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44605263-44605762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25943 Neighboring gene DEAD-box helicase 56 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25944 Neighboring gene transmembrane p24 trafficking protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44646637-44647200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18148 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25949 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44674956-44675111 Neighboring gene OGDH intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25951 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:44679045-44679572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44685039-44685539 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44717745-44717958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44740093-44740593 Neighboring gene uncharacterized LOC124901622 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25952 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25953 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18150 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18151 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44794273-44794954 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44807583-44808109 Neighboring gene zinc finger MIZ-type containing 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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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    Related articles in PubMed

    1. Cloning and nucleotide sequence of the cDNA encoding human 2-oxoglutarate dehydrogenase (lipoamide). Koike K, et al. Proc Natl Acad Sci U S A, 1992 Mar 1. PMID 1542694, Free PMC Article
    2. Hypoxic regulation of glutamine metabolism through HIF1 and SIAH2 supports lipid synthesis that is necessary for tumor growth. Sun RC, et al. Cell Metab, 2014 Feb 4. PMID 24506869, Free PMC Article
    3. The gene encoding human 2-oxoglutarate dehydrogenase: structural organization and mapping to chromosome 7p13-p14. Koike K. Gene, 1995 Jul 4. PMID 7622061
    4. Localization of the gene (OGDH) coding for the E1k component of the alpha-ketoglutarate dehydrogenase complex to chromosome 7p13-p11.2. Szabo P, et al. Genomics, 1994 Mar 15. PMID 8020988
    5. Exercise training induces similar elevations in the activity of oxoglutarate dehydrogenase and peak oxygen uptake in the human quadriceps muscle. Blomstrand E, et al. Pflugers Arch, 2011 Aug. PMID 21611730

    See all (115) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. OGDH and Bcl-xL loss causes synthetic lethality in glioblastoma.
      Title: OGDH and Bcl-xL loss causes synthetic lethality in glioblastoma.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (17)

    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)

    Genotypes

    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

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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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

    Homology

    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
    		  
    located_in mitochondrion HTP PubMed 
    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
    NP_001158508.1
    NP_001350452.1
    NP_002532.2
    XP_005249816.1
    XP_011513710.1
    XP_047276382.1
    XP_047276383.1
    XP_047276384.1
    XP_047276385.1
    XP_054214282.1
    XP_054214283.1
    XP_054214284.1
    XP_054214285.1
    XP_054214286.1
    XP_054214287.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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

    1. NG_023260.1 RefSeqGene

      Range
      5106..107545
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    2. 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

    3. 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

    4. 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_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      44606627..44709066
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420428.1 → XP_047276384.1  2-oxoglutarate dehydrogenase complex component E1 isoform X3

    2. 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

    3. XM_047420427.1 → XP_047276383.1  2-oxoglutarate dehydrogenase complex component E1 isoform X2

      UniProtKB/Swiss-Prot
      B4E2U9, D3DVL0, E9PBM1, Q02218, Q96DD3, Q9UDX0

    4. 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

    5. XM_047420426.1 → XP_047276382.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

      UniProtKB/TrEMBL
      E9PCR7

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      44766778..44869231
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358311.1 → XP_054214286.1  2-oxoglutarate dehydrogenase complex component E1 isoform X3

    2. XM_054358308.1 → XP_054214283.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

    3. XM_054358310.1 → XP_054214285.1  2-oxoglutarate dehydrogenase complex component E1 isoform X2

    4. XM_054358307.1 → XP_054214282.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

    5. XM_054358309.1 → XP_054214284.1  2-oxoglutarate dehydrogenase complex component E1 isoform X1

    6. XM_054358312.1 → XP_054214287.1  2-oxoglutarate dehydrogenase complex component E1 isoform X4

      UniProtKB/TrEMBL
      B4DH65
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q02218.3 GenPept UniProtKB/Swiss-Prot:Q02218

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