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GPD1 Gene(Protein Coding)

Glycerol-3-Phosphate Dehydrogenase 1

GCID:
GC12P050105
GIFtS:
55
Genes Participants
UDN Logo

Aliases for GPD1 Gene

Aliases for GPD1 Gene

  • Glycerol-3-Phosphate Dehydrogenase 1 2 3 5
  • Glycerol-3-Phosphate Dehydrogenase 1 (Soluble) 2 3
  • EC 1.1.1.8 4 56
  • GPDH-C 3 4
  • GPD-C 3 4
  • Glycerol-3-Phosphate Dehydrogenase [NAD(+)], Cytoplasmic 3
  • Glycerol-3-Phosphate Dehydrogenase [NAD+], Cytoplasmic 3
  • Glycerophosphate Dehydrogenase 3
  • EC 1.1.1 56
  • HTGTI 3

External Ids for GPD1 Gene

Previous GeneCards Identifiers for GPD1 Gene

  • GC12P050792
  • GC12P050553
  • GC12P050214
  • GC12P048784
  • GC12P050497
  • GC12P047531

Summaries for GPD1 Gene

Entrez Gene Summary for GPD1 Gene

  • 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]

GeneCards Summary for GPD1 Gene

GPD1 (Glycerol-3-Phosphate Dehydrogenase 1) is a Protein Coding gene. Diseases associated with GPD1 include Hypertriglyceridemia, Transient Infantile and Brugada Syndrome. Among its related pathways are Metabolism and Acyl chain remodelling of PE. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor. An important paralog of this gene is GPD1L.

Additional gene information for GPD1 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 GPD1 Gene

Genomics for GPD1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for GPD1 Gene

Promoters and enhancers for GPD1 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
GH12I050102 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.6 649 4.4 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF48 ETS1 YY1 GLIS2 SP3 GPD1 CERS5 LIMA1 COX14 GC12M050105
GH12I050101 Enhancer 0.9 ENCODE dbSUPER 550.8 -2.0 -1954 0 CTCF SAP130 MAX CEBPG RAD21 RFX5 HNF4G SMC3 ZNF600 RXRA GPD1 SMARCD1
GH12I050106 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 0.4 +6.3 6259 6.6 CLOCK MLX DMAP1 YY1 E2F8 ZNF143 SP3 NFYC MEF2D ZNF610 COX14 GC12M050105 CERS5 FAM186B LMBR1L ATF1 LIMA1 ENSG00000272368 GPD1
GH12I050084 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 0.4 -18.5 -18455 2.2 PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF143 SMARCD1 LMBR1L LOC100422296 CERS5 BCDIN3D ENSG00000257298 ENSG00000257964 DHH PRPH PRPF40B
GH12I050103 Enhancer 0.9 ENCODE dbSUPER 0.8 -2.1 -2076 0.2 CTCF SAP130 MAX CEBPG RAD21 RFX5 HNF4G SMC3 ZNF600 RXRA GPD1 SMARCD1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around GPD1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the GPD1 gene promoter:

Genomic Locations for GPD1 Gene

Genomic Locations for GPD1 Gene
chr12:50,103,819-50,111,320
(GRCh38/hg38)
Size:
7,502 bases
Orientation:
Plus strand
chr12:50,497,602-50,505,102
(GRCh37/hg19)

Genomic View for GPD1 Gene

Genes around GPD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GPD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GPD1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for GPD1 Gene

Proteins for GPD1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for GPD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P21695-GPDA_HUMAN
    Recommended name:
    Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
    Protein Accession:
    P21695
    Secondary Accessions:
    • F8W1L5
    • Q8N1B0

    Protein attributes for GPD1 Gene

    Size:
    349 amino acids
    Molecular mass:
    37568 Da
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for GPD1 Gene

    Alternative splice isoforms for GPD1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GPD1 Gene

Protein Expression for GPD1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for GPD1 Gene

P21695:
  • EKELLNGQ
  • ENVKYLPGHKLPPNVVAVPDVV
  • WGSAIAKIVG
  • KLTEIIN
  • GDNTKAAVIRLGLME
  • QPVGEFI
  • ADLITTC
  • ENVKYLPG
  • FCETTIG
  • QTPNFRI
  • FVVPHQF
  • VAEAFARTGK
  • VCIVGSGNWGSA
  • HENVKYL
  • GLKLISEVIGE
  • GDNTKAA
  • SVLMGANIA
  • SLIKGVDEGP
  • GALKNVVA
  • ESCGVAD
  • CLQNHPEH

Post-translational modifications for GPD1 Gene

No Post-translational modifications

Other Protein References for GPD1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for GPD1 Gene

Gene Families for GPD1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for GPD1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for GPD1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P21695

UniProtKB/Swiss-Prot:

GPDA_HUMAN :
  • Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family.
Family:
  • Belongs to the NAD-dependent glycerol-3-phosphate dehydrogenase family.
genes like me logo Genes that share domains with GPD1: view

Function for GPD1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for GPD1 Gene

GENATLAS Biochemistry:
glycerol-3-phosphate dehydrogenase,NAD dependent,cytoplasmic
UniProtKB/Swiss-Prot CatalyticActivity:
sn-glycerol 3-phosphate + NAD(+) = glycerone phosphate + NADH.
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by zinc ions and sulfate.

Enzyme Numbers (IUBMB) for GPD1 Gene

Phenotypes From GWAS Catalog for GPD1 Gene

Gene Ontology (GO) - Molecular Function for GPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004367 glycerol-3-phosphate dehydrogenase [NAD+] activity TAS --
GO:0004368 glycerol-3-phosphate dehydrogenase activity IEA --
GO:0016491 oxidoreductase activity IEA --
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor IEA --
GO:0042803 protein homodimerization activity IEA --
genes like me logo Genes that share ontologies with GPD1: view
genes like me logo Genes that share phenotypes with GPD1: view

Human Phenotype Ontology for GPD1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for GPD1

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for GPD1 Gene

Localization for GPD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GPD1 Gene

Cytoplasm.

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 GPD1 gene
Compartment Confidence
extracellular 5
cytosol 5
mitochondrion 3
peroxisome 2
nucleus 2
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for GPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005739 mitochondrion IEA --
GO:0005829 cytosol TAS --
GO:0009331 glycerol-3-phosphate dehydrogenase complex IEA --
GO:0070062 extracellular exosome HDA,IDA 19056867
genes like me logo Genes that share ontologies with GPD1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GPD1 Gene

Pathways & Interactions for GPD1 Gene

genes like me logo Genes that share pathways with GPD1: view

Gene Ontology (GO) - Biological Process for GPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process IEA --
GO:0006072 glycerol-3-phosphate metabolic process IEA --
GO:0006094 gluconeogenesis IEA --
GO:0006116 NADH oxidation IEA --
GO:0006127 glycerophosphate shuttle IEA --
genes like me logo Genes that share ontologies with GPD1: view

No data available for SIGNOR curated interactions for GPD1 Gene

Drugs & Compounds for GPD1 Gene

Products:

  1. Drug

(19) Drugs for GPD1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
NADH Approved Nutra Target 0
Dihydroxyacetone phosphate Investigational Pharma 0
NAD Pharma Full agonist, Agonist 0

(25) Additional Compounds for GPD1 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
Hydrogen Ion
  • Hydrogen cation
  • Hydron
  • Proton
genes like me logo Genes that share compounds with GPD1: view

Transcripts for GPD1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for GPD1 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(207) Selected AceView cDNA sequences:
(7) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for GPD1 Gene

Glycerol-3-phosphate dehydrogenase 1 (soluble):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for GPD1

Alternative Splicing Database (ASD) splice patterns (SP) for GPD1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14
SP1: - - - - -
SP2: - - - -
SP3: - - - - - -
SP4: - -
SP5: - - -
SP6:
SP7:

Relevant External Links for GPD1 Gene

GeneLoc Exon Structure for
GPD1
ECgene alternative splicing isoforms for
GPD1

Expression for GPD1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for GPD1 Gene

mRNA expression in normal human tissues for GPD1 Gene
mRNA expression by BioGPS for GPD1 GenemRNA expression by GTEx for GPD1 Gene

mRNA differential expression in normal tissues according to GTEx for GPD1 Gene

This gene is overexpressed in Adipose - Subcutaneous (x12.5), Adipose - Visceral (Omentum) (x10.5), Muscle - Skeletal (x7.0), and Breast - Mammary Tissue (x6.1).

Protein differential expression in normal tissues from HIPED for GPD1 Gene

This gene is overexpressed in Nasopharynx (41.8) and Adipocyte (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for GPD1 Gene



NURSA nuclear receptor signaling pathways regulating expression of GPD1 Gene:

GPD1

SOURCE GeneReport for Unigene cluster for GPD1 Gene:

Hs.524418

Evidence on tissue expression from TISSUES for GPD1 Gene

  • Liver(4.5)
  • Nervous system(4.3)
  • Pancreas(4.2)
  • Muscle(2.7)
  • Kidney(2.5)

Phenotype-based relationships between genes and organs from Gene ORGANizer for GPD1 Gene

Germ Layers:
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
Organs:
Head and neck:
  • ear
Thorax:
  • heart
Abdomen:
  • duodenum
  • intestine
  • liver
  • pancreas
  • small intestine
General:
  • blood vessel
genes like me logo Genes that share expression patterns with GPD1: view

Primer Products

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for GPD1 Gene

Orthologs for GPD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GPD1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia GPD1 33 34
  • 99.71 (n)
cow
(Bos Taurus)
 Mammalia GPD1 33 34
  • 91.6 (n)
dog
(Canis familiaris)
 Mammalia GPD1 33 34
  • 90.07 (n)
mouse
(Mus musculus)
 Mammalia Gpd1 33 16 34
  • 89.59 (n)
rat
(Rattus norvegicus)
 Mammalia Gpd1 33
  • 89.3 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia GPD1 34
  • 82 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves GPD1 34
  • 77 (a)
 OneToOne
LOC426881 33
  • 75.26 (n)
lizard
(Anolis carolinensis)
 Reptilia GPD1 34
  • 84 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia gpd1 33
  • 74.4 (n)
Str.11109 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.2478 33
zebrafish
(Danio rerio)
 Actinopterygii gpd1a 33 34
  • 71.69 (n)
gpd1b 34
  • 71 (a)
 OneToMany
wufc30a07 33
fruit fly
(Drosophila melanogaster)
 Insecta Gpdh 35 33 34
  • 67.91 (n)
CG3215 35 34
  • 45 (a)
CG43343 34
  • 11 (a)
 ManyToMany
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP007593 33
  • 66.57 (n)
worm
(Caenorhabditis elegans)
 Secernentea gpdh-2 33 34
  • 59.58 (n)
F47G4.3 35
  • 50 (a)
gpdh-1 34
  • 45 (a)
 ManyToMany
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_ADR311C 33
  • 56.67 (n)
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0C04004g 33
  • 54.81 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes GPD1 33 34 36
  • 53.47 (n)
GPD2 34
  • 35 (a)
 ManyToMany
rice
(Oryza sativa)
 Liliopsida Os.24891 33
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes gpd1 33
  • 57.29 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea CSA.1608 34
  • 57 (a)
 OneToMany
bread mold
(Neurospora crassa)
 Ascomycetes NCU00742 33
  • 55.45 (n)
Species where no ortholog for GPD1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • 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)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for GPD1 Gene

ENSEMBL:
Gene Tree for GPD1 (if available)
TreeFam:
Gene Tree for GPD1 (if available)

Paralogs for GPD1 Gene

Paralogs for GPD1 Gene

(1) SIMAP similar genes for GPD1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with GPD1: view

Variants for GPD1 Gene

Sequence variations from dbSNP and Humsavar for GPD1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
rs199673455 pathogenic, Hypertriglyceridemia, transient infantile, Hypertriglyceridemia, transient infantile (HTGTI) [MIM:614480] 50,107,640(+) G/A/C coding_sequence_variant, missense_variant
rs200327418 pathogenic, Hypertriglyceridemia, transient infantile 50,106,287(+) G/C splice_acceptor_variant
rs1001021106 -- 50,111,290(+) A/G 3_prime_UTR_variant
rs1001091099 -- 50,110,927(+) G/A 3_prime_UTR_variant
rs1001479399 -- 50,104,044(+) C/T 5_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for GPD1 Gene

Variant ID Type Subtype PubMed ID
nsv558840 CNV loss 21841781

Variation tolerance for GPD1 Gene

Residual Variation Intolerance Score: 75.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.71; 46.41% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GPD1 Gene

Human Gene Mutation Database (HGMD)
GPD1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPD1 Gene

Disorders for GPD1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for GPD1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search GPD1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

GPDA_HUMAN
  • Hypertriglyceridemia, transient infantile (HTGTI) [MIM:614480]: An autosomal recessive disorder characterized by onset of moderate to severe transient hypertriglyceridemia in infancy that normalizes with age. The hypertriglyceridemia is associated with hepatomegaly, moderately elevated transaminases, persistent fatty liver, and the development of hepatic fibrosis. {ECO:0000269 PubMed:22226083, ECO:0000269 PubMed:24549054}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for GPD1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with GPD1: view

No data available for Genatlas for GPD1 Gene

Publications for GPD1 Gene

  1. Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1). (PMID: 16460752) Ou X … Rao Z (Journal of molecular biology 2006) 3 4 22 58
  2. Sequence conservation and structural organization of the glycerol-3-phosphate dehydrogenase promoter in mice and humans. (PMID: 2398890) Gwynn B … Birkenmeier EH (Molecular and cellular biology 1990) 3 4 22 58
  3. A compound heterozygous mutation in GPD1 causes hepatomegaly, steatohepatitis, and hypertriglyceridemia. (PMID: 24549054) Joshi M … Agrawal PB (European journal of human genetics : EJHG 2014) 3 4 58
  4. Transient infantile hypertriglyceridemia, fatty liver, and hepatic fibrosis caused by mutated GPD1, encoding glycerol-3-phosphate dehydrogenase 1. (PMID: 22226083) Basel-Vanagaite L … Shamir R (American journal of human genetics 2012) 3 4 58
  5. The influence of obstructive sleep apnea on the expression of glycerol-3-phosphate dehydrogenase 1 gene. (PMID: 20404019) Guindalini C … Tufik S (Experimental biology and medicine (Maywood, N.J.) 2010) 3 22 58

Products for GPD1 Gene

  • Addgene plasmids for GPD1

Sources for GPD1 Gene

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