This gene encodes a member of the glycerophosphodiester phosphodiesterase enzyme family. The encoded protein hydrolyzes glycerophosphoinositol to produce inositol 1-phosphate and glycerol. This protein may have a role in osteoblast differentiation and growth. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2010] See more...

Aliases for GDPD2 Gene

Aliases for GDPD2 Gene

  • Glycerophosphodiester Phosphodiesterase Domain Containing 2 2 3 5
  • Osteoblast Differentiation Promoting Factor 2 3 4
  • Glycerophosphodiester Phosphodiesterase Domain-Containing Protein 2 3 4
  • Glycerophosphoinositol Inositolphosphodiesterase GDPD2 3 4
  • Glycerophosphodiester Phosphodiesterase 3 3 4
  • OBDPF 3 4
  • GDE3 3 4
  • EC 3.1.4.43 4

External Ids for GDPD2 Gene

Previous GeneCards Identifiers for GDPD2 Gene

  • GC0XP068510
  • GC0XP069426
  • GC0XP069559
  • GC0XP069642
  • GC0XP063464

Summaries for GDPD2 Gene

Entrez Gene Summary for GDPD2 Gene

  • This gene encodes a member of the glycerophosphodiester phosphodiesterase enzyme family. The encoded protein hydrolyzes glycerophosphoinositol to produce inositol 1-phosphate and glycerol. This protein may have a role in osteoblast differentiation and growth. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jan 2010]

GeneCards Summary for GDPD2 Gene

GDPD2 (Glycerophosphodiester Phosphodiesterase Domain Containing 2) is a Protein Coding gene. Diseases associated with GDPD2 include Epidermolysis Bullosa, Junctional, Non-Herlitz Type. Gene Ontology (GO) annotations related to this gene include phosphoric diester hydrolase activity and glycerophosphoinositol inositolphosphodiesterase activity. An important paralog of this gene is GDPD5.

UniProtKB/Swiss-Prot Summary for GDPD2 Gene

  • Has glycerophosphoinositol inositolphosphodiesterase activity and specifically hydrolyzes glycerophosphoinositol, with no activity for other substrates such as glycerophosphoinositol 4-phosphate, glycerophosphocholine, glycerophosphoethanolamine, and glycerophosphoserine. Accelerates the program of osteoblast differentiation and growth. May play a role in remodeling of the actin cytoskeleton (By similarity).

Additional gene information for GDPD2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for GDPD2 Gene

Genomics for GDPD2 Gene

GeneHancer (GH) Regulatory Elements for GDPD2 Gene

Promoters and enhancers for GDPD2 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
GH0XJ070422 Promoter/Enhancer 1.3 EPDnew Ensembl ENCODE 500.7 +0.5 483 2.6 CTCF TEAD4 RFX1 SMC3 ZBTB17 ZNF263 RAD21 POLR2G ZFHX2 SCRT1 GDPD2 ARR3 LOC105373244 RF00017-8495
GH0XJ070421 Enhancer 0.4 ENCODE 500.7 -1.2 -1185 0.3 NFIC YY1 SP1 GDPD2 RF00017-8494
GH0XJ070475 Promoter/Enhancer 1.2 Ensembl ENCODE 12.5 +56.3 56264 6.8 ZSCAN5C USF1 JUND FOS ZNF639 ZIC2 ZNF423 TRIM28 SAP30 ZNF341 DLG3 DLG3-AS1 RNU4-81P GDPD2 piR-55194-439 RF00017-8495
GH0XJ070398 Enhancer 1 FANTOM5 Ensembl ENCODE 13.2 -24.1 -24130 1.4 SKI FOXA2 CEBPB SMAD4 FOXA1 RARA ETV4 NFIL3 MIXL1 ELF3 piR-61532-356 GDPD2 ARR3 IGBP1 RNY4P23 RF00019-108 KIF4A
GH0XJ070046 Enhancer 0.5 Ensembl 5.1 -375.8 -375830 2 ZNF316 MAFF FOS MAFK MAFG JUN EMSY STAT3 GDPD2 AWAT2 ENSG00000286077
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around GDPD2 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for GDPD2

Top Transcription factor binding sites by QIAGEN in the GDPD2 gene promoter:
  • AREB6
  • CP2
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • MAZR
  • MEF-2A

Genomic Locations for GDPD2 Gene

Genomic Locations for GDPD2 Gene
chrX:70,423,031-70,433,391
(GRCh38/hg38)
Size:
10,361 bases
Orientation:
Plus strand
chrX:69,642,881-69,653,241
(GRCh37/hg19)
Size:
10,361 bases
Orientation:
Plus strand

Genomic View for GDPD2 Gene

Genes around GDPD2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
GDPD2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for GDPD2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for GDPD2 Gene

Proteins for GDPD2 Gene

  • Protein details for GDPD2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9HCC8-GDPD2_HUMAN
    Recommended name:
    Glycerophosphoinositol inositolphosphodiesterase GDPD2
    Protein Accession:
    Q9HCC8
    Secondary Accessions:
    • B4DRH4
    • B4DVC9
    • Q9NXJ6

    Protein attributes for GDPD2 Gene

    Size:
    539 amino acids
    Molecular mass:
    61729 Da
    Cofactor:
    Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAA91014.1; Type=Frameshift; Evidence={ECO:0000305};

    Alternative splice isoforms for GDPD2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for GDPD2 Gene

Post-translational modifications for GDPD2 Gene

  • Glycosylation at Asn442
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for GDPD2 Gene

Domains & Families for GDPD2 Gene

Gene Families for GDPD2 Gene

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

Protein Domains for GDPD2 Gene

Blocks:
  • Glycerophosphoryl diester phosphodiesterase
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for GDPD2 Gene

GenScript: Design optimal peptide antigens:
  • cDNA, FLJ78934, highly similar to Homo sapiens glycerophosphodiester phosphodiesterase domain containing 2 (GDPD2), mRNA (B4DRH4_HUMAN)
  • cDNA FLJ58331, highly similar to Homo sapiens glycerophosphodiester phosphodiesterase domain containing 2 (GDPD2), mRNA (B4DVC9_HUMAN)
  • Osteoblast differentiation promoting factor (GDPD2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9HCC8

UniProtKB/Swiss-Prot:

GDPD2_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 GDPD2: view

Function for GDPD2 Gene

Molecular function for GDPD2 Gene

UniProtKB/Swiss-Prot Function:
Has glycerophosphoinositol inositolphosphodiesterase activity and specifically hydrolyzes glycerophosphoinositol, with no activity for other substrates such as glycerophosphoinositol 4-phosphate, glycerophosphocholine, glycerophosphoethanolamine, and glycerophosphoserine. Accelerates the program of osteoblast differentiation and growth. May play a role in remodeling of the actin cytoskeleton (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + sn-glycero-3-phospho-1D-myo-inositol = 1D-myo-inositol 1-phosphate + glycerol + H(+); Xref=Rhea:RHEA:14033, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:17754, ChEBI:CHEBI:58433, ChEBI:CHEBI:58444; EC=3.1.4.43;.

Enzyme Numbers (IUBMB) for GDPD2 Gene

Gene Ontology (GO) - Molecular Function for GDPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0047394 glycerophosphoinositol inositolphosphodiesterase activity IEA --
genes like me logo Genes that share ontologies with GDPD2: view
genes like me logo Genes that share phenotypes with GDPD2: view

Animal Models for GDPD2 Gene

MGI Knock Outs for GDPD2:
  • Gdpd2 Gdpd2<tm1a(KOMP)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for GDPD2

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for GDPD2

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for GDPD2 Gene

Localization for GDPD2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for GDPD2 Gene

Cell membrane; Multi-pass membrane protein. Cytoplasm. Cytoplasm, cytoskeleton. Note=Colocalizes with the actin cytoskeleton. {ECO:0000250}.

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 GDPD2 gene
Compartment Confidence
plasma membrane 4
cytoskeleton 2
extracellular 1
nucleus 1
cytosol 1

Gene Ontology (GO) - Cellular Components for GDPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0005884 actin filament IEA --
GO:0005886 plasma membrane IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with GDPD2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for GDPD2 Gene

Pathways & Interactions for GDPD2 Gene

PathCards logo

SuperPathways for GDPD2 Gene

No Data Available

Gene Ontology (GO) - Biological Process for GDPD2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006629 lipid metabolic process IEA --
GO:0045669 positive regulation of osteoblast differentiation IEA --
GO:0090527 actin filament reorganization IEA --
genes like me logo Genes that share ontologies with GDPD2: view

No data available for Pathways by source and SIGNOR curated interactions for GDPD2 Gene

Drugs & Compounds for GDPD2 Gene

(2) Drugs for GDPD2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Glycerol Approved, Investigational Pharma 208
Water Approved Pharma 0

(2) Additional Compounds for GDPD2 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
Inositol phosphate
  • D-myo-Inositol (6)-monophosphate
  • D-myo-Inositol (6)-phosphate
  • I6P
  • Ins(6)P
  • Ins6p
15421-51-9
genes like me logo Genes that share compounds with GDPD2: view

Transcripts for GDPD2 Gene

mRNA/cDNA for GDPD2 Gene

4 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
5 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 GDPD2

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for GDPD2 Gene

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

Relevant External Links for GDPD2 Gene

GeneLoc Exon Structure for
GDPD2

Expression for GDPD2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for GDPD2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for GDPD2 Gene

This gene is overexpressed in Spleen (x22.2) and Skin - Not Sun Exposed (Suprapubic) (x4.9).

Protein differential expression in normal tissues from HIPED for GDPD2 Gene

This gene is overexpressed in Spleen (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for GDPD2 Gene



Protein tissue co-expression partners for GDPD2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for GDPD2

SOURCE GeneReport for Unigene cluster for GDPD2 Gene:

Hs.438712

Evidence on tissue expression from TISSUES for GDPD2 Gene

  • Spleen(4.6)
  • Skin(4.3)
  • Nervous system(4.3)
  • Intestine(4.1)
genes like me logo Genes that share expression patterns with GDPD2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for GDPD2 Gene

Orthologs for GDPD2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for GDPD2 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia GDPD2 31 30
  • 99.66 (n)
OneToOne
dog
(Canis familiaris)
Mammalia GDPD2 31 30
  • 90.23 (n)
OneToOne
cow
(Bos Taurus)
Mammalia GDPD2 31 30
  • 87.26 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Gdpd2 17 31 30
  • 86.18 (n)
rat
(Rattus norvegicus)
Mammalia Gdpd2 30
  • 85.69 (n)
oppossum
(Monodelphis domestica)
Mammalia GDPD2 31
  • 66 (a)
OneToOne
chicken
(Gallus gallus)
Aves GDPD2 31 30
  • 62.29 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia GDPD2 31
  • 44 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia gdpd2 30
  • 54.74 (n)
zebrafish
(Danio rerio)
Actinopterygii si:dkey-31j3.9 30
  • 51.16 (n)
GDPD2 31
  • 41 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 24 (a)
OneToMany
Species where no ortholog for GDPD2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • 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)
  • worm (Caenorhabditis elegans)

Evolution for GDPD2 Gene

ENSEMBL:
Gene Tree for GDPD2 (if available)
TreeFam:
Gene Tree for GDPD2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for GDPD2: view image

Paralogs for GDPD2 Gene

Paralogs for GDPD2 Gene

(2) SIMAP similar genes for GDPD2 Gene using alignment to 1 proteins:

  • GDPD2_HUMAN
genes like me logo Genes that share paralogs with GDPD2: view

Variants for GDPD2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for GDPD2 Gene

SNP ID Clinical significance and condition Chr 0X pos Variation AA Info Type
rs775565226 Benign: Abnormality of neuronal migration 70,426,402(+) C/T MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for GDPD2 Gene

Structural Variations from Database of Genomic Variants (DGV) for GDPD2 Gene

Variant ID Type Subtype PubMed ID
esv1584074 OTHER inversion 17803354
esv33082 CNV loss 17666407
nsv6950 CNV insertion 18451855

Variation tolerance for GDPD2 Gene

Residual Variation Intolerance Score: 67.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.03; 21.09% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for GDPD2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
GDPD2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for GDPD2 Gene

Disorders for GDPD2 Gene

MalaCards: The human disease database

(1) MalaCards diseases for GDPD2 Gene - From: DISEASES

Disorder Aliases PubMed IDs
epidermolysis bullosa, junctional, non-herlitz type
  • epidermolysis bullosa junctionalis, non-herlitz type
- elite association - COSMIC cancer census association via MalaCards
Search GDPD2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for GDPD2

genes like me logo Genes that share disorders with GDPD2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for GDPD2 Gene

Publications for GDPD2 Gene

  1. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 2 3 4 54
  2. The DNA sequence of the human X chromosome. (PMID: 15772651) Ross MT … Bentley DR (Nature 2005) 3 4 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. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  5. Novel membrane protein containing glycerophosphodiester phosphodiesterase motif is transiently expressed during osteoblast differentiation. (PMID: 12933806) Yanaka N … Sakurai N (The Journal of biological chemistry 2003) 3 4 54

Products for GDPD2 Gene

Sources for GDPD2 Gene