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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
  • Retinal Rod Rhodopsin-Sensitive CGMP 3,5-Cyclic Phosphodiesterase Subunit Delta 3
  • 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 Orofaciodigital Syndrome Vi. 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

Additional gene information for PDE6D Gene

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

Genomics for PDE6D Gene

Regulatory Elements for PDE6D Gene

Enhancers for PDE6D 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
GH02H231049 1.5 FANTOM5 ENCODE dbSUPER 5.3 +735.9 735946 2.4 FOXA2 ATF1 MLX ZFP64 ARID4B DMAP1 YY1 SLC30A9 PAF1 SP5 C2orf72 RPL28P2 PDE6D GC02P231047 PIR41760 ENSG00000261829
GH02H231785 1.2 ENCODE 0.7 -0.2 -198 1.8 ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC ZC3H11A DIS3L2 RPL28P2 GIGYF2 NCL RPL23AP26 ENSG00000233538 ENSG00000261096 ENSG00000251485 COPS7B LOC100289360
GH02H231780 1.1 ENCODE 0.7 +4.6 4562 2.3 PKNOX1 ARID4B SIN3A YBX1 YY1 ZNF766 ZNF143 FOS SP3 ZHX2 GIGYF2 RPL28P2 DIS3L2 COPS7B PDE6D
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDE6D on UCSC Golden Path with GeneCards custom track

Promoters for PDE6D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000131875 -528 1201 ZFP64 FEZF1 DMAP1 YY1 ZNF416 ZNF143 ZNF548 SP3 NFYC ZC3H11A

Genomic Locations for PDE6D Gene

Genomic Locations for PDE6D Gene
chr2:231,732,425-231,786,272
(GRCh38/hg38)
Size:
53,848 bases
Orientation:
Minus strand
chr2:232,597,135-232,650,982
(GRCh37/hg19)

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

Post-translational modifications for PDE6D Gene

  • Ubiquitination at posLast=2929
  • Modification sites at PhosphoSitePlus

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

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

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).

Phenotypes From GWAS Catalog for PDE6D Gene

Gene Ontology (GO) - Molecular Function for PDE6D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004114 3,5-cyclic-nucleotide phosphodiesterase activity IEA --
GO:0005095 GTPase inhibitor activity ISS,IEA --
GO:0005515 protein binding IPI 9712853
GO:0017137 Rab GTPase binding IPI 9712853
genes like me logo Genes that share ontologies with PDE6D: view
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

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , 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
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 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:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
GO:0005929 cilium TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PDE6D: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDE6D Gene

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 TAS,IEA --
GO:0034260 negative regulation of GTPase activity IEA --
GO:0050896 response to stimulus 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

(10) Drugs for PDE6D Gene - From: ApexBio and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Cilostazol Approved Pharma PDE3 inhibitor 110
Water Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
cyclic amp Experimental Pharma 0
Cyclic GMP Experimental Pharma 0

(1) Additional Compounds for PDE6D Gene - From:

Name Synonyms Role CAS Number PubChem IDs PubMed IDs

(5) Tocris Compounds for PDE6D Gene

Compound Action Cas Number
Eggmanone Potent and selective PDE4 inhibitor; suppresses hedgehog signaling 505068-32-6
Etazolate hydrochloride PDE4 inhibitor 35838-58-5
IBMX PDE inhibitor (non-selective) 28822-58-4
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

Drug Products

Transcripts for PDE6D Gene

Unigene Clusters for PDE6D Gene

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

CRISPR Products

Inhibitory RNA Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for PDE6D Gene



Protein tissue co-expression partners for PDE6D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDE6D Gene:

PDE6D

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.

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDE6D Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • hypothalamus
  • jaw
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • nose
  • outer ear
  • pituitary gland
  • skull
  • tongue
  • tooth
Thorax:
  • heart
  • lung
  • rib
  • rib cage
Abdomen:
  • kidney
Pelvis:
  • pelvis
  • testicle
  • ureter
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • nail
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • blood
  • blood vessel
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
  • white blood cell
genes like me logo Genes that share expression patterns with PDE6D: view

No data available for mRNA differential expression in normal tissues and Evidence on tissue expression from 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
chimpanzee
(Pan troglodytes)
Mammalia PDE6D 33 34
  • 99.78 (n)
oppossum
(Monodelphis domestica)
Mammalia PDE6D 34
  • 98 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDE6D 34
  • 96 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDE6D 33 34
  • 93.56 (n)
cow
(Bos Taurus)
Mammalia PDE6D 33 34
  • 93.33 (n)
mouse
(Mus musculus)
Mammalia Pde6d 33 16 34
  • 93.33 (n)
rat
(Rattus norvegicus)
Mammalia Pde6d 33
  • 91.6 (n)
chicken
(Gallus gallus)
Aves PDE6D 33 34
  • 85.96 (n)
lizard
(Anolis carolinensis)
Reptilia PDE6D 34
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pde6d 33
  • 77.7 (n)
Str.14984 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.16708 33
zebrafish
(Danio rerio)
Actinopterygii pde6d 33 34
  • 80.22 (n)
Dr.21566 33
fruit fly
(Drosophila melanogaster)
Insecta PrBP 34 33
  • 64 (n)
OneToOne
CG9296 35
  • 61 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta PDE6D_ANOGA 33
  • 62.04 (n)
worm
(Caenorhabditis elegans)
Secernentea pdl-1 33 34 35
  • 66.2 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.4899 34
  • 76 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13889 33
Species where no ortholog for PDE6D 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 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
rs587777156 Pathogenic 231,738,139(+) ACGGG(C/T)TGGTA splice-acceptor-variant
rs1000034235 -- 231,760,644(+) ACTCA(C/T)GATCC intron-variant
rs1000084577 -- 231,779,031(+) ACATT(A/T)ATTTT intron-variant, nc-transcript-variant, utr-variant-5-prime
rs1000150134 -- 231,777,694(+) AAAAA(A/C)CCTAT intron-variant
rs1000185232 -- 231,771,861(+) TCAAA(G/T)AATTG intron-variant

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

Variant ID Type Subtype PubMed ID
nsv834568 CNV loss 17160897
nsv428408 CNV gain+loss 18775914
nsv1114179 CNV deletion 24896259
esv3594633 CNV loss 21293372
esv3594632 CNV loss 21293372
esv2759117 CNV gain+loss 17122850
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

Human Gene Mutation Database (HGMD)
PDE6D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDE6D

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

Disorders for PDE6D Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
joubert syndrome 22
  • jbts22
orofaciodigital syndrome vi
  • joubert syndrome with orofaciodigital defect
pde6d-related joubert syndrome
  • joubert syndrome 22
retinitis pigmentosa 3
  • rp3
retinitis pigmentosa 26
  • rp26
- 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 22 60
  2. Cloning and gene structure of the rod cGMP phosphodiesterase delta subunit gene (PDED) in man and mouse. (PMID: 9781033) Lorenz B … Meitinger T (European journal of human genetics : EJHG 1998) 3 4 22 60
  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) Ershova G … de Gunzburg J (Cytogenetics and cell genetics 1997) 2 3 4 60
  4. A homozygous PDE6D mutation in Joubert syndrome impairs targeting of farnesylated INPP5E protein to the primary cilium. (PMID: 24166846) Thomas S … Attié-Bitach T (Human mutation 2014) 3 4 60
  5. The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo. (PMID: 23559067) Wätzlich D … Ismail S (EMBO reports 2013) 3 4 60

Products for PDE6D Gene

Sources for PDE6D Gene

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