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

Gene ID: 2820, updated on 13-Apr-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (156400281..156586403)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (156852575..157039187)
105.20220307 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
  • 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. GPD2: The relationship with cancer and neural stemness. Mikeli M, et al. Cells Dev, 2023 Mar. PMID 36592694
  2. 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
  3. mGPDH Deficiency leads to melanoma metastasis via induced NRF2. Li X, et al. J Cell Mol Med, 2021 Jun. PMID 33939274, Free PMC Article
  4. Mitochondrial glycerol 3-phosphate dehydrogenase promotes skeletal muscle regeneration. Liu X, et al. EMBO Mol Med, 2018 Dec. PMID 30389681, Free PMC Article
  5. Haploinsufficiency of the GPD2 gene in a patient with nonsyndromic mental retardation. Daoud H, et al. Hum Genet, 2009 Jan. PMID 19011903

See all (71) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. GPD2: The relationship with cancer and neural stemness.
    Title: GPD2: The relationship with cancer and neural stemness.
  2. 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.
  3. mGPDH Deficiency leads to melanoma metastasis via induced NRF2.
    Title: mGPDH Deficiency leads to melanoma metastasis via induced NRF2.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  9. 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.
  10. testis-specific promoter of mitochondrial GPDH
    Title: Germ cell nuclear factor relieves cAMP-response element modulator tau-mediated activation of the testis-specific promoter of human mitochondrial glycerol-3-phosphate dehydrogenase.
Submit: New GeneRIF Correction See all GeneRIFs (11)

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 II 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
part_of glycerol-3-phosphate dehydrogenase (FAD) complex IEA
Inferred from Electronic Annotation
more info
  
located_in mitochondrial inner membrane TAS
Traceable Author Statement
more info
  
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_2023_10

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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