Aliases for GDE1 Gene

Aliases for GDE1 Gene

  • Glycerophosphodiester Phosphodiesterase 1 2 3 4 5
  • Membrane Interacting Protein Of RGS16 2 3
  • RGS16-Interacting Membrane Protein 3 4
  • EC 3.1.4.44 4 52
  • MIR16 3 4
  • Membrane-Interacting Protein Of RGS16 4
  • EC 3.1.4.- 4
  • 363E6.2 3

External Ids for GDE1 Gene

Previous GeneCards Identifiers for GDE1 Gene

  • GC16M019422
  • GC16M018049

Summaries for GDE1 Gene

GeneCards Summary for GDE1 Gene

GDE1 (Glycerophosphodiester Phosphodiesterase 1) is a Protein Coding gene. Diseases associated with GDE1 include Serine Deficiency and Cone-Rod Dystrophy 2. Among its related pathways are PI Metabolism and Metabolism. Gene Ontology (GO) annotations related to this gene include phosphoric diester hydrolase activity and glycerophosphoinositol glycerophosphodiesterase activity. An important paralog of this gene is GDPD2.

UniProtKB/Swiss-Prot Summary for GDE1 Gene

  • Has glycerophosphoinositol phosphodiesterase activity. Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Has little or no activity towards glycerophosphocholine. GDE1 activity can be modulated by G-protein signaling pathways (By similarity).

Additional gene information for GDE1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GDE1 Gene

Genomics for GDE1 Gene

GeneHancer (GH) Regulatory Elements for GDE1 Gene

Promoters and enhancers for GDE1 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
GH16J019520 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 505 -0.8 -792 6.2 ZBTB40 ZNF217 EP300 CTCF ZSCAN5C SIN3A NRF1 POLR2G SP1 GTF2E2 CCP110 GDE1 lnc-TMC5-3 RPS15A KNOP1 ENSG00000259871 SYT17
GH16J019554 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 5 -33.4 -33429 2.7 ZBTB40 ZNF217 CTCF TCF12 SIN3A MYC NRF1 USF1 POLR2G JUND VPS35L CCP110 RPS15A COQ7 TMC5 KNOP1 GDE1 HSALNG0110010
GH16J019485 Enhancer 1.1 Ensembl ENCODE 4.6 +34.1 34127 4.4 NRF1 TEAD4 PHB2 ZNF623 ZNF510 TOE1 CTBP1 MYC TAF9B HDAC3 ENSG00000260592 COQ7 RPS15A SYT17 KNOP1 CCP110 TMC5 ENSG00000261195 GDE1 L13714-171
GH16J019381 Enhancer 0.9 Ensembl ENCODE 5.1 +138.4 138429 3.8 ZIC2 TEAD1 CTBP1 OSR2 FOXA2 ZBTB17 CEBPB ELF1 GATA3 SMAD4 TMC5 SYT17 KNOP1 GDE1 piR-31199-125 piR-42694-059 LOC105371114 ENSG00000259925
GH16J019515 Enhancer 0.8 ENCODE 4.8 +5.5 5538 3 CUX1 OSR2 ZNF316 FOXA2 NFIC MAFF FOS FOSL2 MAFK FOSL1 VPS35L COQ7 CCP110 KNOP1 GDE1 lnc-KNOP1-4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GDE1 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GDE1

Top Transcription factor binding sites by QIAGEN in the GDE1 gene promoter:
  • FOXI1
  • HFH-3
  • MEF-2A
  • Pax-2
  • Pax-2a
  • Pax-4a
  • POU2F1
  • POU2F1a
  • POU3F2

Genomic Locations for GDE1 Gene

Genomic Locations for GDE1 Gene
chr16:19,501,693-19,522,128
(GRCh38/hg38)
Size:
20,436 bases
Orientation:
Minus strand
chr16:19,513,015-19,533,467
(GRCh37/hg19)
Size:
20,453 bases
Orientation:
Minus strand

Genomic View for GDE1 Gene

Genes around GDE1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GDE1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GDE1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GDE1 Gene

Proteins for GDE1 Gene

  • Protein details for GDE1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZC3-GDE1_HUMAN
    Recommended name:
    Glycerophosphodiester phosphodiesterase 1
    Protein Accession:
    Q9NZC3
    Secondary Accessions:
    • O43334
    • Q6PKF7
    • Q7KYR4

    Protein attributes for GDE1 Gene

    Size:
    331 amino acids
    Molecular mass:
    37718 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Interacts with PRAF2 (PubMed:16472945). Interacts with RGS16 (By similarity).
    SequenceCaution:
    • Sequence=AAC05440.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=AAC05803.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

neXtProt entry for GDE1 Gene

Selected DME Specific Peptides for GDE1 Gene

Q9NZC3:
  • VCSFLPEVIYKMRQTD
  • HRPWSLSHTGDGKPR
  • KKWSAKGIQVV
  • FSFEPVPS

Post-translational modifications for GDE1 Gene

Other Protein References for GDE1 Gene

Domains & Families for GDE1 Gene

Gene Families for GDE1 Gene

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

Protein Domains for GDE1 Gene

Blocks:
  • Glycerophosphoryl diester phosphodiesterase
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GDE1 Gene

GenScript: Design optimal peptide antigens:
  • RGS16-interacting membrane protein (GDE1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NZC3

UniProtKB/Swiss-Prot:

GDE1_HUMAN :
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
Family:
  • Belongs to the glycerophosphoryl diester phosphodiesterase family.
genes like me logo Genes that share domains with GDE1: view

Function for GDE1 Gene

Molecular function for GDE1 Gene

UniProtKB/Swiss-Prot Function:
Has glycerophosphoinositol phosphodiesterase activity. Hydrolyzes lysoglycerophospholipids to produce lysophosphatidic acid (LPA) and the corresponding amines. Has little or no activity towards glycerophosphocholine. GDE1 activity can be modulated by G-protein signaling pathways (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + sn-glycero-3-phospho-1D-myo-inositol = H(+) + myo-inositol + sn-glycerol 3-phosphate; Xref=Rhea:RHEA:16501, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17268, ChEBI:CHEBI:57597, ChEBI:CHEBI:58444; EC=3.1.4.44; Evidence=. ;.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + N-acyl-sn-glycero-3-phosphoethanolamine = H(+) + N-acylethanolamine + sn-glycerol 3-phosphate; Xref=Rhea:RHEA:53160, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:52640, ChEBI:CHEBI:57597, ChEBI:CHEBI:85225; Evidence=. ;.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + N-acyl-1-O-(1Z-alkenyl)-sn-glycero-3-phosphoethanolamine = 1-O-(1Z-alkenyl)-sn-glycero-3-phosphate + H(+) + N-acylethanolamine; Xref=Rhea:RHEA:53176, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:52640, ChEBI:CHEBI:77283, ChEBI:CHEBI:140403; Evidence=. ;.

Enzyme Numbers (IUBMB) for GDE1 Gene

Gene Ontology (GO) - Molecular Function for GDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004622 lysophospholipase activity ISS --
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0008889 glycerophosphodiester phosphodiesterase activity TAS 10760272
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with GDE1: view
genes like me logo Genes that share phenotypes with GDE1: view

Animal Models for GDE1 Gene

MGI Knock Outs for GDE1:
  • Gde1 Gde1<tm1b(EUCOMM)Hmgu>
  • Gde1 Gde1<tm1Crv>

Animal Model Products

  • Taconic Biosciences Mouse Models for GDE1

CRISPR Products

miRNA for GDE1 Gene

miRTarBase miRNAs that target GDE1

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for GDE1 Gene

Localization for GDE1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GDE1 Gene

Cell membrane; Multi-pass membrane protein. Cytoplasmic vesicle membrane; Multi-pass membrane protein. Note=Perinuclear vesicles and cell membrane. {ECO:0000250 UniProtKB:Q9JL55}.

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 GDE1 gene
Compartment Confidence
plasma membrane 4
extracellular 2
endoplasmic reticulum 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
nucleus 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleoplasm (2)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for GDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane TAS 10760272
GO:0030659 cytoplasmic vesicle membrane IEA --
GO:0031410 cytoplasmic vesicle IEA --
genes like me logo Genes that share ontologies with GDE1: view

Pathways & Interactions for GDE1 Gene

genes like me logo Genes that share pathways with GDE1: view

Gene Ontology (GO) - Biological Process for GDE1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process TAS,IEA 10760272
GO:0006644 phospholipid metabolic process ISS,IEA --
GO:0046475 glycerophospholipid catabolic process TAS --
GO:0070291 N-acylethanolamine metabolic process IEA,ISS --
genes like me logo Genes that share ontologies with GDE1: view

No data available for SIGNOR curated interactions for GDE1 Gene

Drugs & Compounds for GDE1 Gene

(6) Drugs for GDE1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Inositol Approved, Investigational, Withdrawn Pharma 111
Magnesium Approved, Experimental, Investigational Pharma 0
Water Approved Pharma 0
Choline Approved Nutra 222
Choline alfoscerate Experimental, Investigational Pharma 0

(3) Additional Compounds for GDE1 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
1-(sn-Glycero-3-phospho)-1D-myo-inositol
  • 3-Phosphoglyceroinositol
  • Glyerophosphoinositol
  • GroPIns
  • sn-glycero-3-phospho-1-Inositol
  • 1-(sn-glycero-3-phospho)-1D-myo-Inositol
glycerol 3-phosphate
  • (R)-Glycerol 1-phosphate
  • D-(Glycerol 1-phosphate)
  • D-Glycerol 1-phosphate
  • Glycerol-3-phosphate
  • Glycerophosphoric acid
57-03-4
Glycerylphosphorylethanolamine
  • 2-Aminoethyl ester 1-glycerophosphoric acid
  • a-Glycerophosphorylethanolamine
  • alpha-Glycerophosphorylethanolamine
  • Glycerol 3-phosphoethanolamine
  • Glycerol 3-phosphorylethanolamine
1190-00-7
genes like me logo Genes that share compounds with GDE1: view

Transcripts for GDE1 Gene

mRNA/cDNA for GDE1 Gene

3 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GDE1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b
SP1: - -
SP2: - -
SP3: - - -
SP4:
SP5:

Relevant External Links for GDE1 Gene

GeneLoc Exon Structure for
GDE1

Expression for GDE1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GDE1 Gene

Protein differential expression in normal tissues from HIPED for GDE1 Gene

This gene is overexpressed in Nasal epithelium (55.1) and Pancreas (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GDE1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GDE1

SOURCE GeneReport for Unigene cluster for GDE1 Gene:

Hs.512607

mRNA Expression by UniProt/SwissProt for GDE1 Gene:

Q9NZC3-GDE1_HUMAN
Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for GDE1 Gene

  • Nervous system(4.9)
  • Intestine(4.5)
  • Kidney(4.5)
  • Pancreas(2.5)
  • Lung(2.2)
  • Eye(2.1)
genes like me logo Genes that share expression patterns with GDE1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for GDE1 Gene

Orthologs for GDE1 Gene

This gene was present in the common ancestor of animals.

Orthologs for GDE1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GDE1 31 30
  • 99.7 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GDE1 30
  • 91.84 (n)
-- 31
  • 91 (a)
OneToMany
-- 31
  • 80 (a)
OneToMany
cow
(Bos Taurus)
Mammalia GDE1 31 30
  • 89.33 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gde1 17 31 30
  • 86.4 (n)
rat
(Rattus norvegicus)
Mammalia Gde1 30
  • 86.1 (n)
oppossum
(Monodelphis domestica)
Mammalia GDE1 31
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GDE1 31
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDE1 31 30
  • 72.98 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GDE1 31
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gde1 30
  • 65.05 (n)
Str.15048 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.14702 30
zebrafish
(Danio rerio)
Actinopterygii gde1 31 30
  • 61.32 (n)
OneToOne
zgc56068 30
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001253 30
  • 41.06 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG14883 31 30
  • 39.86 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea T12B3.3 31 30
  • 47.33 (n)
OneToMany
T22G5.1 31
  • 22 (a)
OneToMany
ZC155.4 31
  • 21 (a)
OneToMany
T09B9.3 31
  • 18 (a)
OneToMany
Species where no ortholog for GDE1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • 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 (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 GDE1 Gene

ENSEMBL:
Gene Tree for GDE1 (if available)
TreeFam:
Gene Tree for GDE1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GDE1: view image

Paralogs for GDE1 Gene

Paralogs for GDE1 Gene

genes like me logo Genes that share paralogs with GDE1: view

Variants for GDE1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GDE1 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs2072086 - p.Arg218Gln
rs34137361 - p.Glu328Lys

Additional dbSNP identifiers (rs#s) for GDE1 Gene

Structural Variations from Database of Genomic Variants (DGV) for GDE1 Gene

Variant ID Type Subtype PubMed ID
esv3407263 CNV insertion 20981092
nsv436835 CNV insertion 17901297
nsv571582 CNV gain 21841781
nsv833163 CNV gain 17160897

Variation tolerance for GDE1 Gene

Residual Variation Intolerance Score: 53.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.38; 27.17% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GDE1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GDE1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GDE1 Gene

Disorders for GDE1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for GDE1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
serine deficiency
cone-rod dystrophy 2
  • cord2
- elite association - COSMIC cancer census association via MalaCards
Search GDE1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for GDE1

genes like me logo Genes that share disorders with GDE1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GDE1 Gene

Publications for GDE1 Gene

  1. Genomic organization, characterization, and molecular 3D model of GDE1, a novel mammalian glycerophosphoinositol phosphodiesterase. (PMID: 16472945) Bachmann AS … Mocz G (Gene 2006) 2 3 4 54
  2. GDE1/MIR16 is a glycerophosphoinositol phosphodiesterase regulated by stimulation of G protein-coupled receptors. (PMID: 12576545) Zheng B … Farquhar MG (Proceedings of the National Academy of Sciences of the United States of America 2003) 2 3 23 54
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 54
  4. MIR16, a putative membrane glycerophosphodiester phosphodiesterase, interacts with RGS16. (PMID: 10760272) Zheng B … Farquhar MG (Proceedings of the National Academy of Sciences of the United States of America 2000) 3 4 54
  5. Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q. (PMID: 10493829) Loftus BJ … Adams MD (Genomics 1999) 3 4 54

Products for GDE1 Gene

Sources for GDE1 Gene