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Aliases for PDE6D Gene

Aliases for PDE6D Gene

  • Phosphodiesterase 6D 2 3 5
  • Phosphodiesterase 6D, CGMP-Specific, Rod, Delta 2 3
  • GMP-PDE Delta 3 4
  • Protein P17 3 4
  • PDED 3 4
  • JBTS22 3

External Ids for PDE6D Gene

Previous GeneCards Identifiers for PDE6D Gene

  • GC02M230656
  • GC02M231328
  • GC02M232561
  • GC02M232799
  • GC02M232422
  • GC02M232305
  • GC02M224440
  • GC02M232597

Summaries for PDE6D Gene

Entrez Gene Summary for PDE6D Gene

  • This gene encodes the delta subunit of rod-specific photoreceptor phosphodiesterase (PDE), a key enzyme in the phototransduction cascade. A similar protein in cow functions in solubilizing membrane-bound PDE. In addition to its role in the PDE complex, the encoded protein is thought to bind to prenyl groups of proteins to target them to subcellular organelles called cilia. Mutations in this gene are associated with Joubert syndrome-22. Alternative splicing results in multiple splice variants. [provided by RefSeq, Mar 2014]

GeneCards Summary for PDE6D Gene

PDE6D (Phosphodiesterase 6D) is a Protein Coding gene. Diseases associated with PDE6D include joubert syndrome 22 and pde6d-related joubert syndrome. Among its related pathways are Organelle biogenesis and maintenance and Pyrimidine metabolism (KEGG). GO annotations related to this gene include Rab GTPase binding and GTPase inhibitor activity.

UniProtKB/Swiss-Prot for PDE6D Gene

  • Promotes the release of prenylated target proteins from cellular membranes (PubMed:9712853). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22002721, PubMed:23698361). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (PubMed:24166846). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (By similarity). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation rate (By similarity).

Tocris Summary for PDE6D Gene

  • Phosphodiesterases (PDEs) are a family of phosphohydrolyases that catalyze the hydrolysis of 3' cyclic phosphate bonds in adenosine and/or guanine 3',5' cyclic monophosphate (cAMP and/or cGMP). PDEs regulate the second messengers by controlling their degradation.

Gene Wiki entry for PDE6D Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDE6D Gene

Genomics for PDE6D Gene

Genomic Location for PDE6D Gene

Chromosome:
2
Start:
231,732,425 bp from pter
End:
231,786,272 bp from pter
Size:
53,848 bases
Orientation:
Minus strand

Genomic View for PDE6D Gene

Genes around PDE6D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDE6D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDE6D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDE6D Gene

Proteins for PDE6D Gene

  • Protein details for PDE6D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O43924-PDE6D_HUMAN
    Recommended name:
    Retinal rod rhodopsin-sensitive cGMP 3,5-cyclic phosphodiesterase subunit delta
    Protein Accession:
    O43924
    Secondary Accessions:
    • O43250

    Protein attributes for PDE6D Gene

    Size:
    150 amino acids
    Molecular mass:
    17420 Da
    Quaternary structure:
    • Interacts with the prenylated catalytic subunits of PDE6, an oligomer composed of two catalytic chains (PDE6A and PDE6B) and two inhibitory chains (gamma); has no effect on enzyme activity but promotes the release of the prenylated enzyme from cell membrane (By similarity). Interacts with prenylated GRK1 and GRK7 (By similarity). Interacts with prenylated Ras family members, including RAP2A and RAP2C (By similarity). Interacts with prenylated RHEB and NRAS (PubMed:22002721). Interacts with prenylated HRAS and KRAS. Interacts with RAB13 (prenylated form); dissociates RAB13 from membranes (PubMed:9712853). Interacts with prenylated INPP5E (PubMed:24166846). Interacts with RPGR (PubMed:9990021, PubMed:24166846, PubMed:23559067). Interacts with ARL2 (PubMed:24166846, PubMed:22002721). Interacts with ARL3; the interaction occurs specifically with the GTP-bound form of ARL3 (PubMed:24166846). Interaction with ARL2 and ARL3 promotes release of farnesylated cargo proteins (PubMed:22002721).

    Three dimensional structures from OCA and Proteopedia for PDE6D Gene

neXtProt entry for PDE6D Gene

Proteomics data for PDE6D Gene at MOPED

Post-translational modifications for PDE6D Gene

Other Protein References for PDE6D Gene

No data available for DME Specific Peptides for PDE6D Gene

Domains & Families for PDE6D Gene

Gene Families for PDE6D Gene

Protein Domains for PDE6D Gene

Suggested Antigen Peptide Sequences for PDE6D Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O43924

UniProtKB/Swiss-Prot:

PDE6D_HUMAN :
  • Belongs to the PDE6D/unc-119 family.
Family:
  • Belongs to the PDE6D/unc-119 family.
genes like me logo Genes that share domains with PDE6D: view

Function for PDE6D Gene

Molecular function for PDE6D Gene

GENATLAS Biochemistry:
cGMP specific nucleotide phosphodiesterase,class VI,delta subunit,17kDa,expressed in retinal rod cells,binding specifically to RAB13,putatively involved in the control of the dynamic of RAB13 association with cellular membranes,also binding to RPGR
UniProtKB/Swiss-Prot Function:
Promotes the release of prenylated target proteins from cellular membranes (PubMed:9712853). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22002721, PubMed:23698361). Required for normal ciliary targeting of farnesylated target proteins, such as INPP5E (PubMed:24166846). Modulates the subcellular location of target proteins by acting as a GTP specific dissociation inhibitor (GDI) (By similarity). Increases the affinity of ARL3 for GTP by several orders of magnitude. Stabilizes ARL3-GTP by decreasing the nucleotide dissociation rate (By similarity).
genes like me logo Genes that share phenotypes with PDE6D: view

Human Phenotype Ontology for PDE6D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PDE6D Gene

MGI Knock Outs for PDE6D:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for PDE6D Gene

Localization for PDE6D Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDE6D Gene

Cytoplasm, cytosol. Cytoplasmic vesicle membrane; Peripheral membrane protein. Cytoplasm, cytoskeleton, cilium basal body.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDE6D Gene COMPARTMENTS Subcellular localization image for PDE6D gene
Compartment Confidence
cytosol 5
cytoskeleton 3

Gene Ontology (GO) - Cellular Components for PDE6D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005856 cytoskeleton IEA --
GO:0030659 cytoplasmic vesicle membrane IEA --
genes like me logo Genes that share ontologies with PDE6D: view

Pathways & Interactions for PDE6D Gene

genes like me logo Genes that share pathways with PDE6D: view

Pathways by source for PDE6D Gene

Gene Ontology (GO) - Biological Process for PDE6D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007601 visual perception IEA --
genes like me logo Genes that share ontologies with PDE6D: view

No data available for SIGNOR curated interactions for PDE6D Gene

Drugs & Compounds for PDE6D Gene

(7) Drugs for PDE6D Gene - From: HMDB, ApexBio, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cilostazol Approved Pharma PDE3 inhibitor, PDE3A inhibitor. Also adenosine uptake inhibitor 100
Adenosine monophosphate Approved Nutra 0
Dipyridamole Approved Pharma Inhibition, Inhibitor Adenosine transport inhibitor 76
cyclic amp Experimental Pharma 0
Cyclic GMP Experimental Pharma 0

(5) Additional Compounds for PDE6D Gene - From: HMDB and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
Etazolate hydrochloride
35838-58-5
MMPX
78033-08-6
MY-5445
78351-75-4
Ro 20-1724
29925-17-5

(5) Tocris Compounds for PDE6D Gene

Compound Action Cas Number
Dipyridamole Adenosine transport inhibitor 58-32-2
Etazolate hydrochloride PDE4 inhibitor 35838-58-5
MMPX PDE1 inhibitor 78033-08-6
MY-5445 PDE5 inhibitor 78351-75-4
Ro 20-1724 PDE4 inhibitor 29925-17-5

(2) ApexBio Compounds for PDE6D Gene

Compound Action Cas Number
Cilostazol PDE3 inhibitor 73963-72-1
Sildenafil Citrate Treat erectile dysfunction and PAH 171599-83-0
genes like me logo Genes that share compounds with PDE6D: view

Transcripts for PDE6D Gene

Unigene Clusters for PDE6D Gene

Phosphodiesterase 6D, cGMP-specific, rod, delta:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PDE6D Gene

No ASD Table

Relevant External Links for PDE6D Gene

GeneLoc Exon Structure for
PDE6D
ECgene alternative splicing isoforms for
PDE6D

Expression for PDE6D Gene

mRNA expression in normal human tissues for PDE6D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDE6D Gene

This gene is overexpressed in Bone (18.7) and Retina (16.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PDE6D Gene



SOURCE GeneReport for Unigene cluster for PDE6D Gene Hs.516808

mRNA Expression by UniProt/SwissProt for PDE6D Gene

O43924-PDE6D_HUMAN
Tissue specificity: Widely expressed. Detected in various tissues including spleen, prostate gland, testis, ovary, small intestine, colon, retina, and peripheral blood.
genes like me logo Genes that share expression patterns with PDE6D: view

Protein tissue co-expression partners for PDE6D Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for PDE6D Gene

Orthologs for PDE6D Gene

This gene was present in the common ancestor of animals.

Orthologs for PDE6D Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PDE6D 35
  • 93.33 (n)
  • 99.33 (a)
PDE6D 36
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDE6D 35
  • 93.56 (n)
  • 98.67 (a)
PDE6D 36
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pde6d 35
  • 93.33 (n)
  • 98 (a)
Pde6d 16
Pde6d 36
  • 98 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PDE6D 35
  • 99.78 (n)
  • 100 (a)
PDE6D 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pde6d 35
  • 91.6 (n)
  • 97.71 (a)
oppossum
(Monodelphis domestica)
Mammalia PDE6D 36
  • 98 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDE6D 36
  • 96 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDE6D 35
  • 85.96 (n)
  • 96.99 (a)
PDE6D 36
  • 95 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDE6D 36
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pde6d 35
  • 77.7 (n)
  • 93.92 (a)
Str.14984 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.16708 35
zebrafish
(Danio rerio)
Actinopterygii pde6d 35
  • 80.22 (n)
  • 90 (a)
pde6d 36
  • 90 (a)
OneToOne
Dr.21566 35
fruit fly
(Drosophila melanogaster)
Insecta CG9296 37
  • 61 (a)
PrBP 36
  • 61 (a)
OneToOne
PrBP 35
  • 64 (n)
  • 62 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta PDE6D_ANOGA 35
  • 62.04 (n)
  • 66.67 (a)
worm
(Caenorhabditis elegans)
Secernentea pdl-1 37
  • 69 (a)
pdl-1 35
  • 66.2 (n)
  • 70.83 (a)
pdl-1 36
  • 63 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13889 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4899 36
  • 76 (a)
OneToOne
Species with no ortholog for PDE6D:
  • 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 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 PDE6D Gene

ENSEMBL:
Gene Tree for PDE6D (if available)
TreeFam:
Gene Tree for PDE6D (if available)

Paralogs for PDE6D Gene

No data available for Paralogs for PDE6D Gene

Variants for PDE6D Gene

Sequence variations from dbSNP and Humsavar for PDE6D Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs8165 -- 231,732,765(-) AAGCC(A/G/T)CCATC utr-variant-3-prime
rs838414 -- 231,735,190(-) atctc(A/G)gctca intron-variant
rs838415 -- 231,735,146(-) tcctg(C/T)ctcag intron-variant
rs838416 -- 231,735,122(-) tggga(C/T)tacag intron-variant
rs838417 -- 231,735,069(-) gagac(A/G)gggtt intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDE6D Gene

Variant ID Type Subtype PubMed ID
nsv834568 CNV Loss 17160897
dgv1291e1 CNV Complex 17122850
dgv1292e1 CNV Complex 17122850
nsv428408 CNV Gain+Loss 18775914
dgv1293e1 CNV Complex 17122850
nsv875969 CNV Loss 21882294
esv2657431 CNV Deletion 23128226

Variation tolerance for PDE6D Gene

Residual Variation Intolerance Score: 54.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.09; 22.11% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDE6D Gene

HapMap Linkage Disequilibrium report
PDE6D
Human Gene Mutation Database (HGMD)
PDE6D

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDE6D Gene

Disorders for PDE6D Gene

MalaCards: The human disease database

(8) MalaCards diseases for PDE6D Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
joubert syndrome 22
  • jbts22
pde6d-related joubert syndrome
  • joubert syndrome 22
joubert syndrome with orofaciodigital defect
  • orofaciodigital syndrome vi
retinitis pigmentosa 3
  • retinitis pigmentosa 15
primary syphilis
  • early symptomatic syphilis
- elite association - COSMIC cancer census association via MalaCards
Search PDE6D in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PDE6D_HUMAN
  • Joubert syndrome 22 (JBTS22) [MIM:615665]: A disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly. {ECO:0000269 PubMed:24166846}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PDE6D

Genetic Association Database (GAD)
PDE6D
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDE6D
genes like me logo Genes that share disorders with PDE6D: view

No data available for Genatlas for PDE6D Gene

Publications for PDE6D Gene

  1. Characterization of human and mouse rod cGMP phosphodiesterase delta subunit (PDE6D) and chromosomal localization of the human gene. (PMID: 9570951) Li N. … Baehr W. (Genomics 1998) 2 3 4 23 67
  2. Cloning and gene structure of the rod cGMP phosphodiesterase delta subunit gene (PDED) in man and mouse. (PMID: 9781033) Lorenz B. … Meitinger T. (Eur. J. Hum. Genet. 1998) 3 23
  3. cDNA sequence, genomic organization and mapping of PDE6D, the human gene encoding the delta subunit of the cGMP phosphodiesterase of retinal rod cells to chromosome 2q36. (PMID: 9533031) Erchova G. … de Gunzburg J. (Cytogenet. Cell Genet. 1997) 2 3
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  5. Prenylation defects in inherited retinal diseases. (PMID: 24401286) Roosing S. … Siemiatkowska A.M. (J. Med. Genet. 2014) 3

Products for PDE6D Gene

Sources for PDE6D Gene

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