Aliases for GPCPD1 Gene

Aliases for GPCPD1 Gene

  • Glycerophosphocholine Phosphodiesterase 1 2 3 5
  • GDE5 2 3 4
  • Glycerophosphocholine Phosphodiesterase GPCPD1 3 4
  • Glycerophosphodiester Phosphodiesterase 5 3 4
  • KIAA1434 2 4
  • GDPD6 2 3
  • Glycerophosphocholine Phosphodiesterase GDE1 Homolog (S. Cerevisiae) 2
  • Putative Glycerophosphocholine Phosphodiesterase GPCPD1 3
  • Glycerophosphocholine Phosphodiesterase GDE1 Homolog 3
  • Putative Glycerophosphodiester Phosphodiesterase 5 3
  • Endometrial Differential 3 3
  • Preimplantation Protein 4 3
  • EC 3.1.4.2 4
  • GPCPD1 5
  • PREI4 3
  • EDI3 3

External Ids for GPCPD1 Gene

Previous GeneCards Identifiers for GPCPD1 Gene

  • GC20M005525
  • GC20M005481
  • GC20M005582
  • GC20M005800
  • GC20M006310
  • GC20M006366
  • GC20M006395
  • GC20M006506
  • GC20M005860
  • GC20M005923
  • GC20M005980
  • GC20M006042
  • GC20M006101
  • GC20M006153
  • GC20M006212
  • GC20M006267

Summaries for GPCPD1 Gene

GeneCards Summary for GPCPD1 Gene

GPCPD1 (Glycerophosphocholine Phosphodiesterase 1) is a Protein Coding gene. Diseases associated with GPCPD1 include Dental Anomalies And Short Stature and Avoidant Personality Disorder. Among its related pathways are Phospholipase D signaling pathway and Metabolism. Gene Ontology (GO) annotations related to this gene include carbohydrate binding and starch binding.

UniProtKB/Swiss-Prot Summary for GPCPD1 Gene

  • May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity.

Additional gene information for GPCPD1 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GPCPD1 Gene

Genomics for GPCPD1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for GPCPD1 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
GH20J005607 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 638 +0.5 493 6.7 SP1 CREB1 GATAD2A HNRNPL ATF7 PRDM10 ZNF629 TFE3 SOX13 CTCF GPCPD1 TRMT6 ENSG00000230563 CDS2 LINC00654 SHLD1 HE856208 PROKR2
GH20J005641 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 36.5 -34.2 -34193 7 SP1 BACH1 STAT3 SMAD5 RAD21 TCF12 IKZF2 TRIM22 PKNOX1 CEBPA GPCPD1 TRMT6 piR-50308-370 piR-41306-159 SHLD1
GH20J005648 Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 25.3 -43.8 -43760 11.7 CREB1 ZNF629 TFE3 RFX1 ZNF692 BACH1 JUND PKNOX1 POLR2A REST GPCPD1 TRMT6 SHLD1 PROKR2 piR-41306-159 piR-50308-370
GH20J005688 Enhancer 0.9 FANTOM5 dbSUPER 26 -77.8 -77843 0.4 RXRB GABPA EGR1 SAP130 GABPB1 GATAD1 SMAD4 HOMEZ VEZF1 RARA GPCPD1 TRMT6 MCM8 CHGB lnc-GPCPD1-5 HSALNG0128422 SHLD1
GH20J005687 Enhancer 0.6 FANTOM5 dbSUPER 37.9 -77.0 -77040 0.3 SPI1 HLF GPCPD1 TRMT6 MCM8 CHGB HSALNG0128422 lnc-GPCPD1-5 SHLD1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GPCPD1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GPCPD1

Genomic Locations for GPCPD1 Gene

Genomic Locations for GPCPD1 Gene
chr20:5,544,439-5,611,046
(GRCh38/hg38)
Size:
66,608 bases
Orientation:
Minus strand
chr20:5,525,080-5,591,672
(GRCh37/hg19)
Size:
66,593 bases
Orientation:
Minus strand

Genomic View for GPCPD1 Gene

Genes around GPCPD1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GPCPD1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GPCPD1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GPCPD1 Gene

Proteins for GPCPD1 Gene

  • Protein details for GPCPD1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NPB8-GPCP1_HUMAN
    Recommended name:
    Glycerophosphocholine phosphodiesterase GPCPD1
    Protein Accession:
    Q9NPB8
    Secondary Accessions:
    • D3DW06
    • Q9BQL8
    • Q9NUX0

    Protein attributes for GPCPD1 Gene

    Size:
    672 amino acids
    Molecular mass:
    76035 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA91994.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA92672.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for GPCPD1 Gene

neXtProt entry for GPCPD1 Gene

Post-translational modifications for GPCPD1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for GPCPD1 Gene

Domains & Families for GPCPD1 Gene

Gene Families for GPCPD1 Gene

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

Protein Domains for GPCPD1 Gene

InterPro:
Blocks:
  • Glycerophosphoryl diester phosphodiesterase
ProtoNet:

Suggested Antigen Peptide Sequences for GPCPD1 Gene

GenScript: Design optimal peptide antigens:
  • Glycerophosphodiester phosphodiesterase 5 (GPCP1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NPB8

UniProtKB/Swiss-Prot:

GPCP1_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 GPCPD1: view

Function for GPCPD1 Gene

Molecular function for GPCPD1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + sn-glycerol 3-phosphocholine = choline + H(+) + sn-glycerol 3-phosphate; Xref=Rhea:RHEA:16061, ChEBI:CHEBI:15354, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:16870, ChEBI:CHEBI:57597; EC=3.1.4.2;.

Enzyme Numbers (IUBMB) for GPCPD1 Gene

Phenotypes From GWAS Catalog for GPCPD1 Gene

Gene Ontology (GO) - Molecular Function for GPCPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0030246 carbohydrate binding IEA --
GO:0047389 glycerophosphocholine phosphodiesterase activity IEA,IBA 21873635
GO:2001070 starch binding IEA --
genes like me logo Genes that share ontologies with GPCPD1: view
genes like me logo Genes that share phenotypes with GPCPD1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GPCPD1

Clone Products

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for GPCPD1 Gene

Localization for GPCPD1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GPCPD1 Gene

Cytoplasm, cytosol.

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 GPCPD1 gene
Compartment Confidence
cytosol 4
nucleus 3
plasma membrane 2
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for GPCPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IEA --
genes like me logo Genes that share ontologies with GPCPD1: view

Pathways & Interactions for GPCPD1 Gene

genes like me logo Genes that share pathways with GPCPD1: view

Gene Ontology (GO) - Biological Process for GPCPD1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0007519 skeletal muscle tissue development IEA --
GO:0046475 glycerophospholipid catabolic process IEA,IBA 21873635
genes like me logo Genes that share ontologies with GPCPD1: view

No data available for SIGNOR curated interactions for GPCPD1 Gene

Drugs & Compounds for GPCPD1 Gene

(3) Drugs for GPCPD1 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Choline Approved Nutra 223
Choline alfoscerate Experimental, Investigational Pharma 0

(1) Additional Compounds for GPCPD1 Gene - From: 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
genes like me logo Genes that share compounds with GPCPD1: view

Transcripts for GPCPD1 Gene

mRNA/cDNA for GPCPD1 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GPCPD1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GPCPD1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b · 9c ^ 10 ^ 11a · 11b ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^
SP1: - - - - -
SP2: - -
SP3: - -
SP4: - - -
SP5: - - - -
SP6: - - - -
SP7:
SP8:
SP9:
SP10:
SP11:

ExUns: 18 ^ 19a · 19b ^ 20a · 20b ^ 21 ^ 22 ^ 23a · 23b · 23c
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7: - - -
SP8:
SP9:
SP10:
SP11:

Relevant External Links for GPCPD1 Gene

GeneLoc Exon Structure for
GPCPD1

Expression for GPCPD1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GPCPD1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GPCPD1 Gene

This gene is overexpressed in Whole Blood (x5.2).

Protein differential expression in normal tissues from HIPED for GPCPD1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (12.6), Monocytes (7.7), Fetal heart (7.3), Frontal cortex (6.8), and Testis (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for GPCPD1 Gene



Protein tissue co-expression partners for GPCPD1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GPCPD1

SOURCE GeneReport for Unigene cluster for GPCPD1 Gene:

Hs.636359

mRNA Expression by UniProt/SwissProt for GPCPD1 Gene:

Q9NPB8-GPCP1_HUMAN
Tissue specificity: Widely expressed, with highest expression in spinal chord.

Evidence on tissue expression from TISSUES for GPCPD1 Gene

  • Nervous system(4.7)
  • Skin(2.5)
genes like me logo Genes that share expression patterns with GPCPD1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for GPCPD1 Gene

Orthologs for GPCPD1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for GPCPD1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia GPCPD1 30 31
  • 99.45 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia GPCPD1 30 31
  • 94.35 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia GPCPD1 30 31
  • 93.9 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Gpcpd1 30 17 31
  • 89.24 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Gpcpd1 30
  • 88.71 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 88 (a)
OneToMany
-- 31
  • 86 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia GPCPD1 31
  • 78 (a)
OneToOne
Chicken
(Gallus gallus)
Aves -- 31
  • 77 (a)
OneToMany
GPCPD1 30
  • 75.85 (n)
-- 31
  • 60 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia GPCPD1 31
  • 72 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia gpcpd1 30
  • 72.73 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.15092 30
Zebrafish
(Danio rerio)
Actinopterygii gpcpd1 30 31
  • 64.57 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG2818 30 31
  • 48.54 (n)
OneToMany
CG3942 31
  • 24 (a)
OneToMany
CG18135 31
  • 24 (a)
OneToMany
CG9394 31
  • 23 (a)
OneToMany
CG11619 31
  • 23 (a)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009843 30
Worm
(Caenorhabditis elegans)
Secernentea K10B3.6 31
  • 28 (a)
OneToMany
T05H10.7 31
  • 27 (a)
OneToMany
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GDE1 31 33
  • 14 (a)
OneToOne
Rice
(Oryza sativa)
Liliopsida Os08g0535700 30
  • 44.78 (n)
Species where no ortholog for GPCPD1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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 Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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 GPCPD1 Gene

ENSEMBL:
Gene Tree for GPCPD1 (if available)
TreeFam:
Gene Tree for GPCPD1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GPCPD1: view image

Paralogs for GPCPD1 Gene

(1) SIMAP similar genes for GPCPD1 Gene using alignment to 2 proteins:

  • GPCP1_HUMAN
  • H0Y565_HUMAN

Pseudogenes.org Pseudogenes for GPCPD1 Gene

genes like me logo Genes that share paralogs with GPCPD1: view

No data available for Paralogs for GPCPD1 Gene

Variants for GPCPD1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GPCPD1 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
780073 Benign: not provided 5,578,575(-) G/A SYNONYMOUS_VARIANT
rs2273373 - p.Thr273Ile

Additional dbSNP identifiers (rs#s) for GPCPD1 Gene

Structural Variations from Database of Genomic Variants (DGV) for GPCPD1 Gene

Variant ID Type Subtype PubMed ID
dgv4241n100 CNV gain 25217958
dgv4242n100 CNV gain 25217958
esv2678474 CNV deletion 23128226
esv2722141 CNV deletion 23290073
esv2762059 CNV gain 21179565
esv3077124 CNV deletion 24192839
esv3556775 CNV deletion 23714750
esv5676 CNV loss 19470904
nsv1066860 CNV gain 25217958
nsv1071345 CNV deletion 25765185
nsv1138915 CNV deletion 24896259
nsv585328 CNV loss 21841781
nsv585329 CNV loss 21841781
nsv585330 CNV gain 21841781

Variation tolerance for GPCPD1 Gene

Residual Variation Intolerance Score: 35.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.55; 77.86% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GPCPD1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GPCPD1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GPCPD1 Gene

Disorders for GPCPD1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for GPCPD1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
dental anomalies and short stature
  • dass
avoidant personality disorder
  • anxious personality disorder
specific developmental disorder
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for GPCPD1

genes like me logo Genes that share disorders with GPCPD1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GPCPD1 Gene

Publications for GPCPD1 Gene

  1. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4
  2. Association of common genetic variants in GPCPD1 with scaling of visual cortical surface area in humans. (PMID: 22343285) Bakken TE … Carlson H (Proceedings of the National Academy of Sciences of the United States of America 2012) 3 41
  3. A novel glycerophosphodiester phosphodiesterase, GDE5, controls skeletal muscle development via a non-enzymatic mechanism. (PMID: 20576599) Okazaki Y … Yanaka N (The Journal of biological chemistry 2010) 2 3
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  5. 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

Products for GPCPD1 Gene

  • Signalway Proteins for GPCPD1

Sources for GPCPD1 Gene