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    GPD2 glycerol-3-phosphate dehydrogenase 2 [ Homo sapiens (human) ]

    Gene ID: 2820, updated on 2-Nov-2024

    Summary

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    Official Symbol
    GPD2provided by HGNC
    Official Full Name
    glycerol-3-phosphate dehydrogenase 2provided by HGNC
    Primary source
    HGNC:HGNC:4456
    See related
    Ensembl:ENSG00000115159 MIM:138430; AllianceGenome:HGNC:4456
    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
    GDH2; GPDM; mGDH; mGPDH
    Summary
    The protein encoded by this gene localizes to the inner mitochondrial membrane and catalyzes the conversion of glycerol-3-phosphate to dihydroxyacetone phosphate, using FAD as a cofactor. Along with GDP1, the encoded protein constitutes the glycerol phosphate shuttle, which reoxidizes NADH formed during glycolysis. Two transcript variants encoding the same protein have been found for this gene.[provided by RefSeq, Jan 2010]
    Expression
    Ubiquitous expression in colon (RPKM 11.8), brain (RPKM 10.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GPD2 in Genome Data Viewer
    Location:
    2q24.1
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (156400281..156586403)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (156852575..157039187)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (157292064..157442915)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:157197537-157198092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:157198093-157198646 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12018 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16661 Neighboring gene uncharacterized LOC124906082 Neighboring gene uncharacterized LOC440918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16662 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16663 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12019 Neighboring gene small nucleolar RNA U13 Neighboring gene tRNA-Ala (anticodon CGC) 3-1 Neighboring gene tRNA-Gly (anticodon GCC) 2-2 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12021 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16664 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12022 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16666 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16668 Neighboring gene uncharacterized LOC105373707 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:157486818-157487485 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:157487486-157488152 Neighboring gene long intergenic non-protein coding RNA 1958

    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. Mutation in the calcium-binding domain of the mitochondrial glycerophosphate dehydrogenase gene in a family of diabetic subjects. Novials A, et al. Biochem Biophys Res Commun, 1997 Feb 24. PMID 9070847
    2. mGPDH Deficiency leads to melanoma metastasis via induced NRF2. Li X, et al. J Cell Mol Med, 2021 Jun. PMID 33939274, Free PMC Article
    3. Haploinsufficiency of the GPD2 gene in a patient with nonsyndromic mental retardation. Daoud H, et al. Hum Genet, 2009 Jan. PMID 19011903
    4. A ferroptosis defense mechanism mediated by glycerol-3-phosphate dehydrogenase 2 in mitochondria. Wu S, et al. Proc Natl Acad Sci U S A, 2022 Jun 28. PMID 35749365, Free PMC Article
    5. High activity of mitochondrial glycerophosphate dehydrogenase and glycerophosphate-dependent ROS production in prostate cancer cell lines. Chowdhury SK, et al. Biochem Biophys Res Commun, 2005 Aug 12. PMID 15967408

    See all (82) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Glycerol 3-phosphate dehydrogenases (1 and 2) in cancer and other diseases.
      Title: Glycerol 3-phosphate dehydrogenases (1 and 2) in cancer and other diseases.
    2. GPD2: The relationship with cancer and neural stemness.
      Title: GPD2: The relationship with cancer and neural stemness.
    3. A ferroptosis defense mechanism mediated by glycerol-3-phosphate dehydrogenase 2 in mitochondria.
      Title: A ferroptosis defense mechanism mediated by glycerol-3-phosphate dehydrogenase 2 in mitochondria.
    4. mGPDH Deficiency leads to melanoma metastasis via induced NRF2.
      Title: mGPDH Deficiency leads to melanoma metastasis via induced NRF2.
    5. Deficiency of Mitochondrial Glycerol 3-Phosphate Dehydrogenase Exacerbates Podocyte Injury and the Progression of Diabetic Kidney Disease.
      Title: Deficiency of Mitochondrial Glycerol 3-Phosphate Dehydrogenase Exacerbates Podocyte Injury and the Progression of Diabetic Kidney Disease.
    6. mRNA and protein levels reduced in livers of patients with nonalcoholic fatty liver disease
      Title: Deficiency of Mitochondrial Glycerol 3-Phosphate Dehydrogenase Contributes to Hepatic Steatosis.
    7. We report 3 additional patients with a de novo deletion encompassing NR4A2: 2 patients have deletions encompassing only NR4A2 gene and 1 patient has a deletion including NR4A2 and the first exon of GPD2
      Title: NR4A2 haploinsufficiency is associated with intellectual disability and autism spectrum disorder.
    8. Here, the authors identify mGPDH as a critical regulator of skeletal muscle regeneration. Specifically, it regulates myogenic markers and myoblast differentiation by controlling mitochondrial biogenesis via CaMKKbeta/AMPK.
      Title: Mitochondrial glycerol 3-phosphate dehydrogenase promotes skeletal muscle regeneration.
    9. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    10. the up-regulation of mGPDH, due to a highly glycolytic environment, contributes to the overall increase in ROS generation and may result in the progression of prostate cancer
      Title: Increased expression of mitochondrial glycerophosphate dehydrogenase and antioxidant enzymes in prostate cancer cell lines/cancer.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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
    Type 2 diabetes mellitus
    MedGen: C0011860 OMIM: 125853 GeneReviews: WFS1 Spectrum Disorder
    		Compare labs

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis.
    EBI GWAS Catalog
    Genome-wide association of lipid-lowering response to statins in combined study populations.
    EBI GWAS Catalog

    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 glycerol-3-phosphate dehydrogenase 2 (GPD2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 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 calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables glycerol-3-phosphate dehydrogenase (quinone) activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables glycerol-3-phosphate dehydrogenase (quinone) activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in glycerol catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glycerol-3-phosphate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glycerophosphate shuttle TAS
    Traceable Author Statement
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane 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
    		  

    General protein information

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    Preferred Names
    glycerol-3-phosphate dehydrogenase, mitochondrial
    Names
    GPD-M
    GPDH-M
    glycerol-3-phosphate dehydrogenase 2 (mitochondrial)
    mitochondrial glycerophosphate dehydrogenase
    mitohondrial glycerophosphate dehydrogenase
    mtGPD
    testicular tissue protein Li 76
    NP_000399.3
    NP_001076581.2
    XP_005246526.1
    XP_011509279.1
    XP_016859319.1
    XP_024308566.1
    XP_047299919.1
    XP_047299920.1
    XP_047299921.1
    XP_047299922.1
    XP_054197387.1
    XP_054197388.1
    XP_054197389.1
    XP_054197390.1
    XP_054197391.1
    XP_054197392.1
    XP_054197393.1
    XP_054197394.1

    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.

    Genomic

    1. NG_016606.3 RefSeqGene

      Range
      41100..191124
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_000408.5 → NP_000399.3  glycerol-3-phosphate dehydrogenase, mitochondrial precursor

      See identical proteins and their annotated locations for NP_000399.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC011308, AC092686
      Consensus CDS
      CCDS2202.1
      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9
      UniProtKB/TrEMBL
      A0A140VJK2
      Related
      ENSP00000409708.2, ENST00000438166.7
      Conserved Domains (2) summary
      PLN02464
      Location:1 → 599
      PLN02464; glycerol-3-phosphate dehydrogenase
      cd00051
      Location:627 → 689
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    2. NM_001083112.3 → NP_001076581.2  glycerol-3-phosphate dehydrogenase, mitochondrial precursor

      See identical proteins and their annotated locations for NP_001076581.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC011308, AC092686
      Consensus CDS
      CCDS2202.1
      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9
      UniProtKB/TrEMBL
      A0A140VJK2
      Related
      ENSP00000308610.5, ENST00000310454.10
      Conserved Domains (2) summary
      PLN02464
      Location:1 → 599
      PLN02464; glycerol-3-phosphate dehydrogenase
      cd00051
      Location:627 → 689
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      156400281..156586403
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047443963.1 → XP_047299919.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9

    2. XM_011510977.3 → XP_011509279.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_011509279.1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9
      UniProtKB/TrEMBL
      A0A140VJK2
      Conserved Domains (2) summary
      PLN02464
      Location:1 → 599
      PLN02464; glycerol-3-phosphate dehydrogenase
      cd00051
      Location:627 → 689
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    3. XM_017003830.2 → XP_016859319.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9
      UniProtKB/TrEMBL
      A0A140VJK2
      Conserved Domains (2) summary
      PLN02464
      Location:1 → 599
      PLN02464; glycerol-3-phosphate dehydrogenase
      cd00051
      Location:627 → 689
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    4. XM_047443964.1 → XP_047299920.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9

    5. XM_024452798.2 → XP_024308566.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9
      UniProtKB/TrEMBL
      A0A140VJK2
      Conserved Domains (2) summary
      PLN02464
      Location:1 → 599
      PLN02464; glycerol-3-phosphate dehydrogenase
      cd00051
      Location:627 → 689
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    6. XM_005246469.3 → XP_005246526.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_005246526.1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9
      UniProtKB/TrEMBL
      A0A140VJK2
      Related
      ENSP00000386425.1, ENST00000409674.5
      Conserved Domains (2) summary
      PLN02464
      Location:1 → 599
      PLN02464; glycerol-3-phosphate dehydrogenase
      cd00051
      Location:627 → 689
      EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

    7. XM_047443965.1 → XP_047299921.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X2

      UniProtKB/TrEMBL
      Q53T76

    8. XM_047443966.1 → XP_047299922.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      156852575..157039187
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054341414.1 → XP_054197389.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9

    2. XM_054341413.1 → XP_054197388.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9

    3. XM_054341412.1 → XP_054197387.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9

    4. XM_054341415.1 → XP_054197390.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9

    5. XM_054341417.1 → XP_054197392.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9

    6. XM_054341416.1 → XP_054197391.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A8K4V0, B3KSA9, P43304, Q59FR1, Q9HAP9

    7. XM_054341418.1 → XP_054197393.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X2

      UniProtKB/TrEMBL
      Q53T76

    8. XM_054341419.1 → XP_054197394.1  glycerol-3-phosphate dehydrogenase, mitochondrial isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P43304.3 GenPept UniProtKB/Swiss-Prot:P43304

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