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Aliases for GPD2 Gene

Aliases for GPD2 Gene

  • Glycerol-3-Phosphate Dehydrogenase 2 2 3 5
  • Glycerol-3-Phosphate Dehydrogenase 2 (Mitochondrial) 2 3
  • EC 1.1.5.3 4 56
  • GPDH-M 3 4
  • GPD-M 3 4
  • MtGPD 3 4
  • Glycerol-3-Phosphate Dehydrogenase, Mitochondrial 3
  • 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 Griscelli Syndrome, Type 3. Among its related pathways are Metabolism and Glycerophospholipid biosynthesis. Gene Ontology (GO) annotations related to this gene include calcium ion binding and glycerol-3-phosphate dehydrogenase activity.

Additional gene information for GPD2 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies 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
GH02I156434 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 567.9 +1.8 1797 4.9 HDGF PKNOX1 SIN3A YY1 POLR2B GLIS2 GATA2 E2F8 FOS ZNF263 GPD2 NR4A2 PIR36097
GH02I156331 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 19.9 -101.5 -101516 5 FEZF1 IRF4 YY1 ZNF213 ZNF143 SP3 NFYC MEF2D ZNF610 GLIS1 NR4A2 GPD2 LINC01876 ENSG00000282440
GH02I156430 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 22.7 -4.2 -4159 1.5 PKNOX1 ATF1 ARNT ZNF766 FOS ATF7 RUNX3 JUNB NCOA1 REST GPD2 NR4A2 PIR56645
GH02I156454 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 18.9 +21.2 21175 3.9 CTCF CLOCK PAX8 EBF1 BMI1 BATF ZFHX2 CTBP1 EGR1 ATF7 GPD2 NR4A2 PIR36097 LOC105373707
GH02I156463 Enhancer 0.9 Ensembl ENCODE dbSUPER 28.4 +29.7 29710 2.4 JUN ZNF133 HMBOX1 CBFA2T3 GABPA GPD2 NR4A2 PIR36097 LOC105373707
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GPD2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GPD2 gene promoter:

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)

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

Domains & Families for GPD2 Gene

Gene Families for GPD2 Gene

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

Suggested Antigen Peptide Sequences for GPD2 Gene

GenScript: Design optimal peptide antigens:

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

GENATLAS Biochemistry:
glycerol-3-phosphate dehydrogenase,tightly linked to D2S141,FAD dependent,mitochondrial,intermembrane space predominantly expressed in islet cell
UniProtKB/Swiss-Prot CatalyticActivity:
sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol.
UniProtKB/Swiss-Prot EnzymeRegulation:
Calcium-binding enhance the activity of the enzyme.

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 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

Animal Models for GPD2 Gene

MGI Knock Outs for GPD2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Human Phenotype Ontology , 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 1
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for GPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
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

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

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

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
glycerol 3-phosphate
  • 1-(Dihydrogen phosphate) Glycerol
  • 1-Glycerophosphate
  • 1-Glycerophosphorate
  • 1-Glycerophosphoric acid
  • 3-Glycerophosphate
57-03-4
FADH
  • 1,5-Dihydro-FAD
  • 1,5-Dihydro-P-5-ester with adenosine
  • 1,5-Dihydro-Riboflavin 5'-(trihydrogen diphosphate) P'->5'-ester with adenosine
  • Adenosine 5'-(trihydrogen pyrophosphate), 5'-5'-ester with 5,10-dihydro-7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)alloxazine
  • Adenosine 5'-(trihydrogen pyrophosphate), 5'->5'-ester with 5,10-dihydro-7,8-dimethyl-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)alloxazine
1910-41-4
genes like me logo Genes that share compounds with GPD2: view

Transcripts for GPD2 Gene

Unigene Clusters for GPD2 Gene

Glycerol-3-phosphate dehydrogenase 2 (mitochondrial):
Representative Sequences:

CRISPR Products

Inhibitory RNA 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
ECgene alternative splicing isoforms for
GPD2

Expression for GPD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for GPD2 Gene



Protein tissue co-expression partners for GPD2 Gene

NURSA nuclear receptor signaling pathways regulating expression of GPD2 Gene:

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(2.4)
  • Heart(2.1)
  • Intestine(2.1)
  • Liver(2.1)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with GPD2: view

Primer Products

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 33 34
  • 99.72 (n)
cow
(Bos Taurus)
Mammalia GPD2 33 34
  • 92.16 (n)
dog
(Canis familiaris)
Mammalia GPD2 33 34
  • 91.18 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia GPD2 34
  • 90 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Gpd2 33 16 34
  • 86.2 (n)
oppossum
(Monodelphis domestica)
Mammalia GPD2 34
  • 86 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Gpd2 33
  • 85.14 (n)
chicken
(Gallus gallus)
Aves GPD2 33 34
  • 77.99 (n)
lizard
(Anolis carolinensis)
Reptilia GPD2 34
  • 79 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gpd2 33
  • 75.26 (n)
Str.20311 33
zebrafish
(Danio rerio)
Actinopterygii gpd2 33 34
  • 71.47 (n)
fruit fly
(Drosophila melanogaster)
Insecta Gpo-1 33 34
  • 59.5 (n)
CG2137 35 34
  • 42 (a)
BG:DS08249.2 35
  • 37 (a)
CG7311 34
  • 35 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004437 33
  • 59.17 (n)
worm
(Caenorhabditis elegans)
Secernentea T25G3.4 33 34
  • 58.31 (n)
Y50E8A.6 35 34
  • 42 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GUT2 34 36
  • 40 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons SDP6 33
  • 53.38 (n)
rice
(Oryza sativa)
Liliopsida Os04g0224900 33
  • 55.52 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 70 (a)
OneToMany
-- 34
  • 63 (a)
OneToMany
bread mold
(Neurospora crassa)
Ascomycetes NCU05454 33
  • 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)

Paralogs for GPD2 Gene

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

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 from dbSNP and Humsavar for GPD2 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs121918407 pathogenic, Diabetes mellitus type 2 156,579,109(+) T/C coding_sequence_variant, missense_variant
rs1057522190 likely-benign, not specified 156,550,627(+) A/G coding_sequence_variant, synonymous_variant
rs1057521483 uncertain-significance, not specified 156,496,174(+) G/A coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs142821701 uncertain-significance, not specified 156,513,449(+) C/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs1000011054 -- 156,534,366(+) A/G genic_upstream_transcript_variant, intron_variant

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

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

- 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 22 58
  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 22 58
  3. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  4. Haploinsufficiency of the GPD2 gene in a patient with nonsyndromic mental retardation. (PMID: 19011903) Daoud H … Briault S (Human genetics 2009) 3 22 58
  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 22 58

Products for GPD2 Gene

Sources for GPD2 Gene

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