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    IDH3G isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gamma [ Homo sapiens (human) ]

    Gene ID: 3421, updated on 28-Oct-2024

    Summary

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    Official Symbol
    IDH3Gprovided by HGNC
    Official Full Name
    isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit gammaprovided by HGNC
    Primary source
    HGNC:HGNC:5386
    See related
    Ensembl:ENSG00000067829 MIM:300089; AllianceGenome:HGNC:5386
    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
    H-IDHG
    Summary
    Isocitrate dehydrogenases catalyze the oxidative decarboxylation of isocitrate to 2-oxoglutarate. These enzymes belong to two distinct subclasses, one of which utilizes NAD(+) as the electron acceptor and the other NADP(+). Five isocitrate dehydrogenases have been reported: three NAD(+)-dependent isocitrate dehydrogenases, which localize to the mitochondrial matrix, and two NADP(+)-dependent isocitrate dehydrogenases, one of which is mitochondrial and the other predominantly cytosolic. NAD(+)-dependent isocitrate dehydrogenases catalyze the allosterically regulated rate-limiting step of the tricarboxylic acid cycle. Each isozyme is a heterotetramer that is composed of two alpha subunits, one beta subunit, and one gamma subunit. The protein encoded by this gene is the gamma subunit of one isozyme of NAD(+)-dependent isocitrate dehydrogenase. This gene is a candidate gene for periventricular heterotopia. Several alternatively spliced transcript variants of this gene have been described, but only some of their full length natures have been determined. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in kidney (RPKM 22.6), heart (RPKM 18.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IDH3G in Genome Data Viewer
    Location:
    Xq28
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (153785768..153794375, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (152059431..152068038, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (153051223..153059830, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene PLXNB3 antisense RNA 1 Neighboring gene plexin B3 Neighboring gene uncharacterized LOC124905227 Neighboring gene SRSF protein kinase 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:153059193-153059920 Neighboring gene CRISPRi-validated cis-regulatory element chrX.2654 Neighboring gene signal sequence receptor subunit 4 Neighboring gene PDZ domain containing 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 21072 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:153092379-153092957 Neighboring gene ReSE screen-validated silencer GRCh37_chrX:153099642-153099888 Neighboring gene CYCS pseudogene 45

    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. Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase. Bzymek KP, et al. Biochemistry, 2007 May 8. PMID 17432878
    2. Identification and functional characterization of a novel, tissue-specific NAD(+)-dependent isocitrate dehydrogenase beta subunit isoform. Kim YO, et al. J Biol Chem, 1999 Dec 24. PMID 10601238
    3. Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase. Soundar S, et al. J Biol Chem, 2006 Jul 28. PMID 16737955
    4. Molecular mechanism of the allosteric regulation of the αγ heterodimer of human NAD-dependent isocitrate dehydrogenase. Ma T, et al. Sci Rep, 2017 Jan 18. PMID 28098230, Free PMC Article
    5. The genomic organization of a human creatine transporter (CRTR) gene located in Xq28. Sandoval N, et al. Genomics, 1996 Jul 15. PMID 8661155

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. active sites of the human NAD-IDH are shared between alpha and gamma subunits and between alpha and beta subunits
      Title: Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase.
    2. Aspartate-190 is a determinant of IDH gamma subunit affinity for the manganese (MnII) ion, as well as for nicotinamide-adenine dinucleotide (NAD), but is not directly required for the catalytic reaction.
      Title: Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    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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    Replication interactions

    Interaction Pubs
    Knockdown of IDH3G by shRNA significantly inhibits HIV-1 replication in CD4+ T-cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef Genome-wide shRNA screening identifies IDH3G, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells 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 ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables NAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables isocitrate dehydrogenase (NAD+) activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables magnesium ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in carbohydrate metabolic process NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in isocitrate metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in isocitrate metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in tricarboxylic acid cycle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tricarboxylic acid cycle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of isocitrate dehydrogenase complex (NAD+) IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of isocitrate dehydrogenase complex (NAD+) IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    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
    		  
    located_in mitochondrion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in mitochondrion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
    Names
    IDH-gamma
    NAD (H)-specific isocitrate dehydrogenase gamma subunit
    NAD(+)-specific ICDH subunit gamma
    NAD+-specific ICDH
    isocitrate dehydrogenase (NAD(+)) 3 gamma
    isocitrate dehydrogenase 3 (NAD(+)) gamma
    isocitrate dehydrogenase 3 (NAD+) gamma
    isocitrate dehydrogenase 3 gamma
    isocitrate dehydrogenase, NAD(+)-specific, mitochondrial, gamma subunit
    isocitric dehydrogenase subunit gamma
    NP_004126.1
    NP_777358.1

    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.

    mRNA and Protein(s)

    1. NM_004135.4 → NP_004126.1  isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial isoform a precursor

      See identical proteins and their annotated locations for NP_004126.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      BC000933, BI831096
      Consensus CDS
      CCDS14730.1
      UniProtKB/Swiss-Prot
      E9PDD5, P51553, Q9BUU5
      UniProtKB/TrEMBL
      E7EQB8
      Related
      ENSP00000217901.5, ENST00000217901.10
      Conserved Domains (1) summary
      TIGR00175
      Location:52 → 383
      mito_nad_idh; isocitrate dehydrogenase, NAD-dependent, mitochondrial type

    2. NM_174869.3 → NP_777358.1  isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial isoform b precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding region resulting in a frameshift, compared to variant 1. Variant 2 encodes a shorter isoform (b) with a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      BC000933, BI831096, U69268
      Consensus CDS
      CCDS44019.1
      UniProtKB/TrEMBL
      E7EQB8
      Related
      ENSP00000359110.3, ENST00000370092.7
      Conserved Domains (1) summary
      TIGR00175
      Location:52 → 364
      mito_nad_idh; isocitrate dehydrogenase, NAD-dependent, mitochondrial type

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      153785768..153794375 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      152059431..152068038 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P51553.1 GenPept UniProtKB/Swiss-Prot:P51553

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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