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Aliases for GDE1 Gene

Aliases for GDE1 Gene

  • Glycerophosphodiester Phosphodiesterase 1 2 3 5
  • Membrane Interacting Protein Of RGS16 2 3
  • RGS16-Interacting Membrane Protein 3 4
  • EC 3.1.4.44 4 58
  • MIR16 3 4
  • Membrane-Interacting Protein Of RGS16 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 Amyotrophic Lateral Sclerosis 1. Among its related pathways are Metabolism and Glycerophospholipid biosynthesis. GO annotations related to this gene include phosphoric diester hydrolase activity and glycerophosphoinositol glycerophosphodiesterase activity.

UniProtKB/Swiss-Prot for GDE1 Gene

  • Has glycerophosphoinositol phosphodiesterase activity. 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 , fRNAdb sequence ontologies and piRNA Summary for GDE1 Gene

Genomics for GDE1 Gene

Regulatory Elements for GDE1 Gene

Enhancers for GDE1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH16H019487 1.2 Ensembl ENCODE 4.6 +33.8 33834 2 HDGF PKNOX1 ARNT ZFP64 TCF12 ZNF766 GATA2 ATF7 ZNF202 ZC3H11A COQ7 RPS15A SYT17 KNOP1 CCP110 TMC5 GDE1 ENSG00000260592 GC16P019498
GH16H019554 1.1 ENCODE 5 -33.5 -33481 2 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF302 RPS15A CCP110 ENSG00000263253 ENSG00000260017 ENSG00000263237 C16orf62 COQ7 TMC5 KNOP1 GDE1
GH16H019381 0.8 ENCODE 5.1 +139.5 139527 1 SOX13 FOXA2 MAX CEBPG FEZF1 ZIC2 GLIS2 PATZ1 PRDM10 GATAD2A TMC5 SYT17 GDE1 GC16P019387 GC16P019371
GH16H019515 0.8 ENCODE 4.7 +5.6 5556 2 FOXA2 KLF17 NFXL1 BATF ZNF121 ZNF366 FOS ZNF362 JUNB ZEB2 C16orf62 COQ7 CCP110 KNOP1 GDE1 GC16P019512
GH16H019580 0.6 dbSUPER 5.5 -59.5 -59517 2 MAFF ZNF316 FOXA2 MAFG EMSY MAFK CCP110 KNOP1 GDE1 C16orf62 GC16M019688 GC16M019687
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around GDE1 on UCSC Golden Path with GeneCards custom track

Promoters for GDE1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000084178 645 1401 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF766

Genomic Location for GDE1 Gene

Chromosome:
16
Start:
19,501,689 bp from pter
End:
19,522,145 bp from pter
Size:
20,457 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 RGS16 (By similarity). Interacts with PRAF2.
    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

Suggested Antigen Peptide Sequences for GDE1 Gene

GenScript: Design optimal peptide antigens:

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 CatalyticActivity:
1-(sn-glycero-3-phospho)-1D-myo-inositol + H(2)O = myo-inositol + sn-glycerol 3-phosphate.
UniProtKB/Swiss-Prot Function:
Has glycerophosphoinositol phosphodiesterase activity. Has little or no activity towards glycerophosphocholine. GDE1 activity can be modulated by G-protein signaling pathways (By similarity).

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 IEA,TAS 10760272
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with GDE1: view

Phenotypes for GDE1 Gene

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

Animal Models for GDE1 Gene

MGI Knock Outs for GDE1:

Animal Model Products

  • Taconic Biosciences Mouse Models for GDE1

CRISPR Products

miRNA for GDE1 Gene

miRTarBase miRNAs that target GDE1

miRNA Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GDE1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 5
endoplasmic reticulum 2
extracellular 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (2)
  • Nucleus (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 IEA,TAS 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
Water Approved Pharma 0
Choline Approved Nutra 166
Choline alfoscerate Experimental Pharma 0
Ethanolamine Experimental Pharma 0
Inositol Investigational Nutra 90

(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
  • 1-(Sn-glycero-3-Phospho)-1D-myo-inositol
  • 3-Phosphoglyceroinositol
  • Glyerophosphoinositol
  • GroPIns
  • Sn-glycero-3-Phospho-1-inositol
glycerol 3-phosphate
  • 1-(Dihydrogen phosphate) Glycerol
  • 1-Glycerophosphate
  • 1-Glycerophosphorate
  • 1-Glycerophosphoric acid
  • 3-Glycerophosphate
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

Unigene Clusters for GDE1 Gene

Glycerophosphodiester phosphodiesterase 1:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for GDE1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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
ECgene alternative splicing isoforms for
GDE1

Expression for GDE1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for GDE1 Gene



NURSA nuclear receptor signaling pathways regulating expression of GDE1 Gene:

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

Primer Products

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 33 34
  • 99.7 (n)
dog
(Canis familiaris)
Mammalia GDE1 33
  • 91.84 (n)
-- 34
  • 91 (a)
OneToMany
-- 34
  • 80 (a)
OneToMany
cow
(Bos Taurus)
Mammalia GDE1 33 34
  • 89.33 (n)
mouse
(Mus musculus)
Mammalia Gde1 33 16 34
  • 86.4 (n)
rat
(Rattus norvegicus)
Mammalia Gde1 33
  • 86.1 (n)
oppossum
(Monodelphis domestica)
Mammalia GDE1 34
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia GDE1 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDE1 33 34
  • 72.98 (n)
lizard
(Anolis carolinensis)
Reptilia GDE1 34
  • 62 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gde1 33
  • 65.05 (n)
Str.15048 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.14702 33
zebrafish
(Danio rerio)
Actinopterygii gde1 33 34
  • 61.32 (n)
zgc56068 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001253 33
  • 41.06 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG14883 33 34
  • 39.86 (n)
worm
(Caenorhabditis elegans)
Secernentea T12B3.3 33 34
  • 47.33 (n)
T22G5.1 34
  • 22 (a)
OneToMany
ZC155.4 34
  • 21 (a)
OneToMany
T09B9.3 34
  • 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)

Paralogs for GDE1 Gene

No data available for Paralogs for GDE1 Gene

Variants for GDE1 Gene

Sequence variations from dbSNP and Humsavar for GDE1 Gene

SNP ID Clin Chr 16 pos Sequence Context AA Info Type
rs1000258770 -- 19,520,813(+) GCAAA(A/T)GTGCC intron-variant
rs1000339648 -- 19,501,461(+) GTGCC(A/C)CCATG downstream-variant-500B
rs1000391769 -- 19,513,568(+) ATCTG(A/C)CTTCC intron-variant
rs1000417210 -- 19,505,686(+) AAGGA(C/T)TCTGT intron-variant
rs1000520740 -- 19,522,057(+) GCACC(C/G)GCAGC nc-transcript-variant, upstream-variant-2KB, utr-variant-5-prime

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)

Relevant External Links for GDE1 Gene

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

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

Disorders for GDE1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
amyotrophic lateral sclerosis 1
  • amyotrophic lateral sclerosis
- elite association - COSMIC cancer census association via MalaCards
Search GDE1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for GDE1

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 60
  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 22 60
  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 60
  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 60
  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 60

Products for GDE1 Gene

Sources for GDE1 Gene

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