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    GPD1 glycerol-3-phosphate dehydrogenase 1 [ Homo sapiens (human) ]

    Gene ID: 2819, updated on 2-May-2024

    Summary

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    Official Symbol
    GPD1provided by HGNC
    Official Full Name
    glycerol-3-phosphate dehydrogenase 1provided by HGNC
    Primary source
    HGNC:HGNC:4455
    See related
    Ensembl:ENSG00000167588 MIM:138420; AllianceGenome:HGNC:4455
    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
    GPD-C; HTGTI; GPDH-C
    Summary
    This gene encodes a member of the NAD-dependent glycerol-3-phosphate dehydrogenase family. The encoded protein plays a critical role in carbohydrate and lipid metabolism by catalyzing the reversible conversion of dihydroxyacetone phosphate (DHAP) and reduced nicotine adenine dinucleotide (NADH) to glycerol-3-phosphate (G3P) and NAD+. The encoded cytosolic protein and mitochondrial glycerol-3-phosphate dehydrogenase also form a glycerol phosphate shuttle that facilitates the transfer of reducing equivalents from the cytosol to mitochondria. Mutations in this gene are a cause of transient infantile hypertriglyceridemia. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Mar 2012]
    Expression
    Biased expression in fat (RPKM 448.5), kidney (RPKM 83.8) and 3 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    12q13.12
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (50104008..50111313)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (50067090..50074395)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (50497791..50505096)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4445 Neighboring gene acid sensing ion channel subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6340 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6341 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:50474871-50475040 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:50477618-50478350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6342 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4446 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:50479817-50480548 Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6343 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6344 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6345 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6346 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6347 Neighboring gene cytochrome c oxidase assembly factor COX14 Neighboring gene ceramide synthase 5 Neighboring gene uncharacterized LOC124902931

    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
    • 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. [Transient infantile hypertriglyceridemia caused by GPD1 deficiency: report of two cases and literature review]. Xie XB, et al. Zhonghua Er Ke Za Zhi, 2020 Nov 2. PMID 33120465
    2. The Organization of Active Site Side Chains of Glycerol-3-phosphate Dehydrogenase Promotes Efficient Enzyme Catalysis and Rescue of Variant Enzymes. Cristobal JR, et al. Biochemistry, 2020 Apr 28. PMID 32250105, Free PMC Article
    3. Comparative Proteome Analysis of Breast Cancer Tissues Highlights the Importance of Glycerol-3-phosphate Dehydrogenase 1 and Monoacylglycerol Lipase in Breast Cancer Metabolism. Yoneten KK, et al. Cancer Genomics Proteomics, 2019 Sep-Oct. PMID 31467232, Free PMC Article
    4. Primary Deuterium Kinetic Isotope Effects: A Probe for the Origin of the Rate Acceleration for Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase. Reyes AC, et al. Biochemistry, 2018 Jul 24. PMID 29927590, Free PMC Article
    5. Glycerol-3-phosphate dehydrogenase 1 deficiency induces compensatory amino acid metabolism during fasting in mice. Sato T, et al. Metabolism, 2016 Nov. PMID 27733253

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Non-bioenergetic roles of mitochondrial GPD2 promote tumor progression.
      Title: Non-bioenergetic roles of mitochondrial GPD2 promote tumor progression.
    2. Decreased serum levels of glycerol-3- phosphate dehydrogenase 1 and monoacylglycerol lipase act as diagnostic biomarkers for breast cancer.
      Title: Decreased serum levels of glycerol-3- phosphate dehydrogenase 1 and monoacylglycerol lipase act as diagnostic biomarkers for breast cancer.
    3. A HIF1alpha-GPD1 feedforward loop inhibits the progression of renal clear cell carcinoma via mitochondrial function and lipid metabolism.
      Title: A HIF1α-GPD1 feedforward loop inhibits the progression of renal clear cell carcinoma via mitochondrial function and lipid metabolism.
    4. The Organization of Active Site Side Chains of Glycerol-3-phosphate Dehydrogenase Promotes Efficient Enzyme Catalysis and Rescue of Variant Enzymes.
      Title: The Organization of Active Site Side Chains of Glycerol-3-phosphate Dehydrogenase Promotes Efficient Enzyme Catalysis and Rescue of Variant Enzymes.
    5. [Transient infantile hypertriglyceridemia caused by GPD1 deficiency: report of two cases and literature review].
      Title: [Transient infantile hypertriglyceridemia caused by GPD1 deficiency: report of two cases and literature review].
    6. Bioinformatics analyses performed with differentially regulated proteins highlighted the changes occurring in triacylglyceride (TAG) metabolism, and directed our attention to TAG metabolism-associated proteins, namely glycerol-3-phosphate dehydrogenase 1 (GPD1) and monoacylglycerol lipase (MAGL).
      Title: Comparative Proteome Analysis of Breast Cancer Tissues Highlights the Importance of Glycerol-3-phosphate Dehydrogenase 1 and Monoacylglycerol Lipase in Breast Cancer Metabolism.
    7. These results support the conclusion that the rate acceleration for Glycerol-3-Phosphate Dehydrogenase-catalyzed reactions is due to the stabilization of the transition state for hydride transfer by interactions with the protein catalyst.
      Title: Primary Deuterium Kinetic Isotope Effects: A Probe for the Origin of the Rate Acceleration for Hydride Transfer Catalyzed by Glycerol-3-Phosphate Dehydrogenase.
    8. To recognize this entity by considering GPD1 mutations in appropriate clinical settings.
      Title: Expanding the molecular diversity and phenotypic spectrum of glycerol 3-phosphate dehydrogenase 1 deficiency.
    9. Although these data indicate that a lack of GPD1 inhibits gluconeogenesis from glycerol, chronic GPD1 deficiency may induce an adaptation that enhances gluconeogenesis from glycogenic amino acids
      Title: Glycerol-3-phosphate dehydrogenase 1 deficiency induces compensatory amino acid metabolism during fasting in mice.
    10. The R269A mutation of GPDH1 results in a 110-fold increase in K(m) (2.8 kcal/mol effect) and a 41,000-fold decrease in k(cat) (6.3 kcal/mol effect), which corresponds to a 9.1 kcal/mol destabilization of the transition state.
      Title: Enzyme architecture: optimization of transition state stabilization from a cation-phosphodianion pair.
    Submit: New GeneRIF Correction See all GeneRIFs (19)

    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
    Transient infantile hypertriglyceridemia and hepatosteatosis
    MedGen: C3280953 OMIM: 614480 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

    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

    Clone Names

    • FLJ26652

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables NAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables glycerol-3-phosphate dehydrogenase (NAD+) activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables glycerol-3-phosphate dehydrogenase (quinone) activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in NADH oxidation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to cAMP IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to tumor necrosis factor IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gluconeogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glycerol-3-phosphate catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glycerol-3-phosphate metabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in glycerolipid metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glycerophosphate shuttle IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of glycolytic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular exosome HDA PubMed 

    General protein information

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    Preferred Names
    glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
    Names
    epididymis secretory sperm binding protein
    glycerol-3-phosphate dehydrogenase 1 (soluble)
    glycerol-3-phosphate dehydrogenase [NAD+], cytoplasmic
    glycerophosphate dehydrogenase
    NP_001244128.1
    NP_005267.2

    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_032168.1 RefSeqGene

      Range
      5190..12495
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001257199.2 → NP_001244128.1  glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AI245302, AK130162, CA307120, CD244782
      Consensus CDS
      CCDS58229.1
      UniProtKB/TrEMBL
      B2R6C0
      Related
      ENSP00000446768.1, ENST00000548814.1
      Conserved Domains (3) summary
      TIGR03376
      Location:5 → 319
      glycerol3P_DH; glycerol-3-phosphate dehydrogenase (NAD(+))
      pfam01210
      Location:5 → 149
      NAD_Gly3P_dh_N; NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
      pfam07479
      Location:171 → 312
      NAD_Gly3P_dh_C; NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus

    2. NM_005276.4 → NP_005267.2  glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic isoform 1

      See identical proteins and their annotated locations for NP_005267.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AI245302, AK130162, BC032234, CA307120, CD244782, DC305085
      Consensus CDS
      CCDS8799.1
      UniProtKB/Swiss-Prot
      F8W1L5, P21695, Q8N1B0
      UniProtKB/TrEMBL
      A0A024R138, B2R6C0
      Related
      ENSP00000301149.3, ENST00000301149.8
      Conserved Domains (1) summary
      TIGR03376
      Location:5 → 342
      glycerol3P_DH; glycerol-3-phosphate dehydrogenase (NAD(+))

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      50104008..50111313
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      50067090..50074395
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P21695.4 GenPept UniProtKB/Swiss-Prot:P21695

    Gene LinkOut

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

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