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 fou... See more...

Aliases for GPD2 Gene

Aliases for GPD2 Gene

  • Glycerol-3-Phosphate Dehydrogenase 2 2 3 5
  • Glycerol-3-Phosphate Dehydrogenase 2 (Mitochondrial) 2 3
  • Glycerol-3-Phosphate Dehydrogenase, Mitochondrial 3 4
  • EC 1.1.5.3 4 52
  • GPDH-M 3 4
  • GPD-M 3 4
  • MtGPD 3 4
  • Mitochondrial Glycerophosphate Dehydrogenase 3
  • Testicular Tissue Protein Li 76 3
  • MGPDH 3
  • GDH2 3
  • GPDM 3

External Ids for GPD2 Gene

Previous GeneCards Identifiers for GPD2 Gene

  • GC02P155224
  • GC02P155821
  • GC02P157255
  • GC02P157495
  • GC02P157481
  • GC02P157118
  • GC02P156988
  • GC02P157291
  • GC02P149177

Summaries for GPD2 Gene

Entrez Gene Summary for GPD2 Gene

  • 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]

GeneCards Summary for GPD2 Gene

GPD2 (Glycerol-3-Phosphate Dehydrogenase 2) is a Protein Coding gene. Diseases associated with GPD2 include Diabetes Mellitus, Noninsulin-Dependent and Rare Diabetes Mellitus Type 2. Among its related pathways are Mitochondrial LC-Fatty Acid Beta-Oxidation and Metabolism. Gene Ontology (GO) annotations related to this gene include calcium ion binding and glycerol-3-phosphate dehydrogenase (quinone) activity.

Additional gene information for GPD2 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GPD2 Gene

Genomics for GPD2 Gene

GeneHancer (GH) Regulatory Elements for GPD2 Gene

Promoters and enhancers for GPD2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J156338 Promoter/Enhancer 2.7 UCNEbase EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 500.2 -94.0 -94023 6.3 HNRNPK ZBTB40 EP300 SIN3A TCF12 NRF1 GTF2E2 PHF8 ZIC2 POLR2A FLJ46875-001 NR4A2 piR-35707 GPD2 lnc-GPD2-1
GH02J156434 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 517.8 +1.8 1797 4.9 ZNF217 NRF1 TCF12 PHF8 ZFX ZIC2 REST POLR2A CLOCK ZNF263 GPD2 NR4A2 piR-43098
GH02J156473 Promoter 0.8 EPDnew 511.5 +38.3 38263 0.1 NCOR1 FOSL1 TAL1 TCF12 GATA2 JUN CREM TEAD4 GATA1 ARID1B GPD2 HSALNG0019800 piR-43098
GH02J156331 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 19.9 -101.9 -101941 5.9 HNRNPK ZNF217 CTCF ZSCAN5C SIN3A NRF1 TCF12 POLR2G SP1 PHF8 NR4A2 GPD2 LINC01876 lnc-GPD2-1 ENSG00000282440
GH02J156430 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 22.6 -4.2 -4159 1.5 TCF12 GTF2E2 JUND FOS ZBTB5 ZBTB11 AFF1 TRIM28 HINFP ATF2 GPD2 NR4A2 RF01210-218
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GPD2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GPD2

Top Transcription factor binding sites by QIAGEN in the GPD2 gene promoter:
  • Brachyury
  • Lmo2
  • Nkx2-5
  • Pax-2
  • SRY

Genomic Locations for GPD2 Gene

Genomic Locations for GPD2 Gene
chr2:156,435,290-156,613,735
(GRCh38/hg38)
Size:
178,446 bases
Orientation:
Plus strand
chr2:157,291,802-157,470,247
(GRCh37/hg19)
Size:
178,446 bases
Orientation:
Plus strand

Genomic View for GPD2 Gene

Genes around GPD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GPD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GPD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GPD2 Gene

Proteins for GPD2 Gene

  • Protein details for GPD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P43304-GPDM_HUMAN
    Recommended name:
    Glycerol-3-phosphate dehydrogenase, mitochondrial
    Protein Accession:
    P43304
    Secondary Accessions:
    • A8K4V0
    • B3KSA9
    • Q59FR1
    • Q9HAP9

    Protein attributes for GPD2 Gene

    Size:
    727 amino acids
    Molecular mass:
    80853 Da
    Cofactor:
    Name=FAD; Xref=ChEBI:CHEBI:57692;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAD92636.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for GPD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GPD2 Gene

Selected DME Specific Peptides for GPD2 Gene

P43304:
  • MTIAGTTD
  • ICQPSAGVHIVMPGYYSPE
  • YYDGQHNDARMNLAI
  • DIDRYKKRFH
  • GGKWTTYR
  • YKWWQLPYYWVGIK
  • TLQNTSEFDILVIGGGATG
  • TRGLKTALVE
  • SGTSSRS
  • DFSSGTSS
  • EQYRMVKEAL
  • RTVGLFLQGGKDWSPTLYIRLVQDYGLESEVAQHLA

Post-translational modifications for GPD2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Abcam antibodies for GPD2

Domains & Families for GPD2 Gene

Gene Families for GPD2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for GPD2 Gene

Blocks:
  • FAD-dependent glycerol-3-phosphate dehydrogenase family signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GPD2 Gene

GenScript: Design optimal peptide antigens:
  • mtGPD (GPDM_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P43304

UniProtKB/Swiss-Prot:

GPDM_HUMAN :
  • Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family.
Family:
  • Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family.
genes like me logo Genes that share domains with GPD2: view

Function for GPD2 Gene

Molecular function for GPD2 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=a quinone + sn-glycerol 3-phosphate = a quinol + dihydroxyacetone phosphate; Xref=Rhea:RHEA:18977, ChEBI:CHEBI:24646, ChEBI:CHEBI:57597, ChEBI:CHEBI:57642, ChEBI:CHEBI:132124; EC=1.1.5.3;.
UniProtKB/Swiss-Prot EnzymeRegulation:
Calcium-binding enhance the activity of the enzyme.
GENATLAS Biochemistry:
glycerol-3-phosphate dehydrogenase,tightly linked to D2S141,FAD dependent,mitochondrial,intermembrane space predominantly expressed in islet cell

Enzyme Numbers (IUBMB) for GPD2 Gene

Phenotypes From GWAS Catalog for GPD2 Gene

Gene Ontology (GO) - Molecular Function for GPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004368 glycerol-3-phosphate dehydrogenase (quinone) activity TAS --
GO:0005509 calcium ion binding IEA,TAS --
GO:0016491 oxidoreductase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0052590 sn-glycerol-3-phosphate:ubiquinone oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with GPD2: view
genes like me logo Genes that share phenotypes with GPD2: view

Human Phenotype Ontology for GPD2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for GPD2 Gene

MGI Knock Outs for GPD2:

Clone Products

No data available for Transcription Factor Targets and HOMER Transcription for GPD2 Gene

Localization for GPD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GPD2 Gene

Mitochondrion.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for GPD2 gene
Compartment Confidence
mitochondrion 5
extracellular 2
peroxisome 2
cytosol 2
plasma membrane 1
cytoskeleton 1
nucleus 1
endoplasmic reticulum 1
lysosome 1

Gene Ontology (GO) - Cellular Components for GPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IBA 21873635
GO:0005743 mitochondrial inner membrane TAS --
GO:0009331 glycerol-3-phosphate dehydrogenase complex IEA --
genes like me logo Genes that share ontologies with GPD2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GPD2 Gene

Pathways & Interactions for GPD2 Gene

genes like me logo Genes that share pathways with GPD2: view

Pathways by source for GPD2 Gene

UniProtKB/Swiss-Prot P43304-GPDM_HUMAN

  • Pathway: Polyol metabolism; glycerol degradation via glycerol kinase pathway; glycerone phosphate from sn-glycerol 3-phosphate (anaerobic route): step 1/1.

Gene Ontology (GO) - Biological Process for GPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006072 glycerol-3-phosphate metabolic process IEA --
GO:0006094 gluconeogenesis IEA --
GO:0006127 glycerophosphate shuttle TAS --
GO:0019563 glycerol catabolic process IEA --
GO:0035264 multicellular organism growth IEA --
genes like me logo Genes that share ontologies with GPD2: view

No data available for SIGNOR curated interactions for GPD2 Gene

Drugs & Compounds for GPD2 Gene

(6) Drugs for GPD2 Gene - From: HMDB and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Calcium Approved Nutra 7884
FAD Approved Pharma 0
Dihydroxyacetone phosphate Investigational Pharma 0

(9) Additional Compounds for GPD2 Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
glycerol 3-phosphate
  • (R)-Glycerol 1-phosphate
  • D-(Glycerol 1-phosphate)
  • D-Glycerol 1-phosphate
  • Glycerol-3-phosphate
  • Glycerophosphoric acid
57-03-4
FADH
  • 1,5-dihydro-FAD
  • DIHYDROFLAVINE-adenine dinucleotide
  • Flavin adenine dinucleotide (reduced)
  • 1,5-dihydro-P-5-Ester with adenosine
  • 1,5-dihydro-Riboflavin 5'-(trihydrogen diphosphate) p'->5'-ester with adenosine
1910-41-4
genes like me logo Genes that share compounds with GPD2: view

Transcripts for GPD2 Gene

mRNA/cDNA for GPD2 Gene

2 REFSEQ mRNAs :
21 NCBI additional mRNA sequence :
13 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GPD2 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20
SP1:
SP2: - - -
SP3: - -
SP4: - - - - - - -

Relevant External Links for GPD2 Gene

GeneLoc Exon Structure for
GPD2

Expression for GPD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GPD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for GPD2 Gene

This gene is overexpressed in Nasal epithelium (35.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GPD2 Gene



Protein tissue co-expression partners for GPD2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GPD2

SOURCE GeneReport for Unigene cluster for GPD2 Gene:

Hs.512382

Evidence on tissue expression from TISSUES for GPD2 Gene

  • Nervous system(4.8)
  • Blood(4.4)
  • Pancreas(2.7)
  • Thyroid gland(2.5)
  • Liver(2.2)
  • Heart(2.1)
  • Intestine(2.1)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with GPD2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for GPD2 Gene

Orthologs for GPD2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GPD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GPD2 31 30
  • 99.72 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GPD2 31 30
  • 92.16 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GPD2 31 30
  • 91.18 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GPD2 31
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gpd2 17 31 30
  • 86.2 (n)
oppossum
(Monodelphis domestica)
Mammalia GPD2 31
  • 86 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gpd2 30
  • 85.14 (n)
chicken
(Gallus gallus)
Aves GPD2 31 30
  • 77.99 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GPD2 31
  • 79 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gpd2 30
  • 75.26 (n)
Str.20311 30
zebrafish
(Danio rerio)
Actinopterygii gpd2 31 30
  • 71.47 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta Gpo-1 31 30
  • 59.5 (n)
OneToMany
CG2137 31 32
  • 43 (a)
OneToMany
BG:DS08249.2 32
  • 37 (a)
CG7311 31
  • 35 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004437 30
  • 59.17 (n)
worm
(Caenorhabditis elegans)
Secernentea T25G3.4 31 30
  • 58.31 (n)
OneToMany
Y50E8A.6 31 32
  • 44 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GUT2 33 31
  • 40 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons SDP6 30
  • 53.38 (n)
rice
(Oryza sativa)
Liliopsida Os04g0224900 30
  • 55.52 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 70 (a)
OneToMany
-- 31
  • 63 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU05454 30
  • 56.96 (n)
Species where no ortholog for GPD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GPD2 Gene

ENSEMBL:
Gene Tree for GPD2 (if available)
TreeFam:
Gene Tree for GPD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GPD2: view image

Paralogs for GPD2 Gene

(2) SIMAP similar genes for GPD2 Gene using alignment to 7 proteins:

  • GPDM_HUMAN
  • E7EM56_HUMAN
  • E9PDK4_HUMAN
  • F5GYK7_HUMAN
  • F8W6E4_HUMAN
  • Q53RD0_HUMAN
  • Q53T76_HUMAN

Pseudogenes.org Pseudogenes for GPD2 Gene

genes like me logo Genes that share paralogs with GPD2: view

No data available for Paralogs for GPD2 Gene

Variants for GPD2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GPD2 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
713776 Likely Benign: not provided 156,550,697(+) A/G MISSENSE_VARIANT
725226 Likely Benign: not provided 156,569,514(+) G/A SYNONYMOUS_VARIANT
736230 Likely Benign: not provided 156,510,884(+) T/C SYNONYMOUS_VARIANT
rs1057521483 Uncertain Significance: not provided 156,496,174(+) G/A MISSENSE_VARIANT
rs1057522190 Likely Benign: not specified 156,550,627(+) A/G SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for GPD2 Gene

Structural Variations from Database of Genomic Variants (DGV) for GPD2 Gene

Variant ID Type Subtype PubMed ID
esv1213858 CNV deletion 17803354
esv2622933 CNV deletion 19546169
esv2664126 CNV deletion 23128226
esv2721009 CNV deletion 23290073
esv2721010 CNV deletion 23290073
esv2721011 CNV deletion 23290073
esv2721012 CNV deletion 23290073
esv3593037 CNV loss 21293372
esv3593038 CNV loss 21293372
nsv214820 CNV deletion 16902084
nsv2987 CNV deletion 18451855
nsv834431 CNV loss 17160897

Variation tolerance for GPD2 Gene

Residual Variation Intolerance Score: 37% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.67; 57.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GPD2 Gene

Human Gene Mutation Database (HGMD)
GPD2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPD2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPD2 Gene

Disorders for GPD2 Gene

MalaCards: The human disease database

(6) MalaCards diseases for GPD2 Gene - From: OMIM, ClinVar, GTR, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
diabetes mellitus, noninsulin-dependent
  • niddm
rare diabetes mellitus type 2
  • rare insulin-independent diabetes mellitus
bacterial gastritis
diabetes mellitus
  • diabetes
methylmalonic acidemia
  • methylmalonic aciduria
- elite association - COSMIC cancer census association via MalaCards
Search GPD2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for GPD2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GPD2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GPD2 Gene

Publications for GPD2 Gene

  1. Mitochondrial glycerol-3-phosphate dehydrogenase. Cloning of an alternatively spliced human islet-cell cDNA, tissue distribution, physical mapping, and identification of a polymorphic genetic marker. (PMID: 8549872) Ferrer J … Permutt MA (Diabetes 1996) 3 4 23 54
  2. Structural organization and mapping of the human mitochondrial glycerol phosphate dehydrogenase-encoding gene and pseudogene. (PMID: 8682323) Brown LJ … MacDonald MJ (Gene 1996) 3 4 23 54
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 41 54
  4. Haploinsufficiency of the GPD2 gene in a patient with nonsyndromic mental retardation. (PMID: 19011903) Daoud H … Briault S (Human genetics 2009) 3 23 54
  5. High activity of mitochondrial glycerophosphate dehydrogenase and glycerophosphate-dependent ROS production in prostate cancer cell lines. (PMID: 15967408) Chowdhury SK … Singh G (Biochemical and biophysical research communications 2005) 3 23 54

Products for GPD2 Gene

Sources for GPD2 Gene