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Aliases for PDE6C Gene

Aliases for PDE6C Gene

  • Phosphodiesterase 6C, CGMP-Specific, Cone, Alpha Prime 2 3
  • CGMP Phosphodiesterase 6C 3 4
  • EC 3.1.4.35 4 63
  • PDEA2 3 4
  • EC 3.1.4 63
  • ACHM5 3
  • COD4 3

External Ids for PDE6C Gene

Previous GeneCards Identifiers for PDE6C Gene

  • GC10P094265
  • GC10P094606
  • GC10P095503
  • GC10P095036
  • GC10P095362
  • GC10P089000

Summaries for PDE6C Gene

Entrez Gene Summary for PDE6C Gene

  • This gene encodes the alpha-prime subunit of cone phosphodiesterase, which is composed of a homodimer of two alpha-prime subunits and 3 smaller proteins of 11, 13, and 15 kDa. Mutations in this gene are associated with cone dystrophy type 4 (COD4). [provided by RefSeq, Mar 2010]

GeneCards Summary for PDE6C Gene

PDE6C (Phosphodiesterase 6C, CGMP-Specific, Cone, Alpha Prime) is a Protein Coding gene. Diseases associated with PDE6C include achromatopsia and cone-rod dystrophy 4. Among its related pathways are The phototransduction cascade and Pyrimidine metabolism (KEGG). GO annotations related to this gene include 3,5-cyclic-nucleotide phosphodiesterase activity and 3,5-cyclic-GMP phosphodiesterase activity. An important paralog of this gene is PDE6A.

Tocris Summary for PDE6C 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 PDE6C Gene

No data available for UniProtKB/Swiss-Prot , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDE6C Gene

Genomics for PDE6C Gene

Regulatory Elements for PDE6C Gene

Genomic Location for PDE6C Gene

Chromosome:
10
Start:
93,612,588 bp from pter
End:
93,666,010 bp from pter
Size:
53,423 bases
Orientation:
Plus strand

Genomic View for PDE6C Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PDE6C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDE6C Gene

Proteins for PDE6C Gene

  • Protein details for PDE6C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51160-PDE6C_HUMAN
    Recommended name:
    Cone cGMP-specific 3,5-cyclic phosphodiesterase subunit alpha
    Protein Accession:
    P51160
    Secondary Accessions:
    • A6NCR6
    • Q5VY29

    Protein attributes for PDE6C Gene

    Size:
    858 amino acids
    Molecular mass:
    99147 Da
    Cofactor:
    Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240; Note=Binds 2 divalent metal cations per subunit. Site 1 may preferentially bind zinc ions, while site 2 has a preference for magnesium and/or manganese ions.;
    Quaternary structure:
    • Composed of two alpha subunits that are associated with 3 smaller proteins of 11, 13, and 15 kDa

    Three dimensional structures from OCA and Proteopedia for PDE6C Gene

neXtProt entry for PDE6C Gene

Proteomics data for PDE6C Gene at MOPED

Post-translational modifications for PDE6C Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDE6C Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for PDE6C Gene

Gene Families for PDE6C Gene

Protein Domains for PDE6C Gene

Suggested Antigen Peptide Sequences for PDE6C Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P51160

UniProtKB/Swiss-Prot:

PDE6C_HUMAN :
  • Contains 2 GAF domains.
  • Belongs to the cyclic nucleotide phosphodiesterase family.
Domain:
  • Contains 2 GAF domains.
Family:
  • Belongs to the cyclic nucleotide phosphodiesterase family.
genes like me logo Genes that share domains with PDE6C: view

Function for PDE6C Gene

Molecular function for PDE6C Gene

GENATLAS Biochemistry:
cGMP specific nucleotide phosphodiesterase,class VI,alpha subunit,cone photoreceptor
UniProtKB/Swiss-Prot CatalyticActivity:
Guanosine 3,5-cyclic phosphate + H(2)O = guanosine 5-phosphate

Enzyme Numbers (IUBMB) for PDE6C Gene

Gene Ontology (GO) - Molecular Function for PDE6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004114 3,5-cyclic-nucleotide phosphodiesterase activity --
GO:0005515 protein binding --
GO:0008081 phosphoric diester hydrolase activity --
GO:0030553 cGMP binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PDE6C: view
genes like me logo Genes that share phenotypes with PDE6C: view

Animal Model Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PDE6C

In Situ Assay Products

Flow Cytometry Products

No data available for Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PDE6C Gene

Localization for PDE6C Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDE6C Gene

Cell membrane; Lipid-anchor; Cytoplasmic side.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDE6C Gene COMPARTMENTS Subcellular localization image for PDE6C gene
Compartment Confidence
plasma membrane 3

Gene Ontology (GO) - Cellular Components for PDE6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
genes like me logo Genes that share ontologies with PDE6C: view

Pathways & Interactions for PDE6C Gene

genes like me logo Genes that share pathways with PDE6C: view

Pathways by source for PDE6C Gene

1 BioSystems pathway for PDE6C Gene
1 KEGG pathway for PDE6C Gene

Interacting Proteins for PDE6C Gene

Gene Ontology (GO) - Biological Process for PDE6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction --
GO:0007601 visual perception IEA --
GO:0007603 phototransduction, visible light IEA --
GO:0008152 metabolic process IEA --
GO:0046549 retinal cone cell development IEA --
genes like me logo Genes that share ontologies with PDE6C: view

No data available for SIGNOR curated interactions for PDE6C Gene

Drugs & Compounds for PDE6C Gene

(5) Drugs for PDE6C Gene - From: HMDB, DrugBank, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Caffeine Approved Nutra Activator, Target, inhibitor, competitive 317
Cilostazol Approved Pharma PDE3 inhibitor, PDE3A inhibitor. Also adenosine uptake inhibitor 98
Cyclic GMP Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0
Zaprinast Pharma Inhibition, Inhibitor GPR35 agonist 0

(4) Additional Compounds for PDE6C 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
MY-5445
78351-75-4
Ro 20-1724
29925-17-5
genes like me logo Genes that share compounds with PDE6C: view

Transcripts for PDE6C Gene

mRNA/cDNA for PDE6C Gene

(1) REFSEQ mRNAs :
(1) Additional mRNA sequences :
(10) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PDE6C Gene

Phosphodiesterase 6C, cGMP-specific, cone, alpha prime:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PDE6C

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDE6C Gene

No ASD Table

Relevant External Links for PDE6C Gene

GeneLoc Exon Structure for
PDE6C
ECgene alternative splicing isoforms for
PDE6C

Expression for PDE6C Gene

mRNA expression in normal human tissues for PDE6C Gene

mRNA differential expression in normal tissues according to GTEx for PDE6C Gene

This gene is overexpressed in Brain - Cerebellar Hemisphere (x4.2).

Protein differential expression in normal tissues from HIPED for PDE6C Gene

This gene is overexpressed in Cerebrospinal fluid (50.5) and Retina (18.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PDE6C Gene



SOURCE GeneReport for Unigene cluster for PDE6C Gene Hs.658121

genes like me logo Genes that share expression patterns with PDE6C: view

Protein tissue co-expression partners for PDE6C Gene

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for PDE6C Gene

Orthologs for PDE6C Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDE6C Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PDE6C 35
  • 88.86 (n)
  • 89.8 (a)
PDE6C 36
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDE6C 35
  • 88.37 (n)
  • 89.92 (a)
PDE6C 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pde6c 35
  • 84.54 (n)
  • 87.18 (a)
Pde6c 16
Pde6c 36
  • 87 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PDE6C 35
  • 99.53 (n)
  • 99.65 (a)
PDE6C 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pde6c 35
  • 84.23 (n)
  • 86.71 (a)
oppossum
(Monodelphis domestica)
Mammalia PDE6C 36
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDE6C 36
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDE6C 35
  • 78.17 (n)
  • 83.1 (a)
PDE6C 36
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDE6C 36
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pde6c 35
  • 74.4 (n)
  • 77.96 (a)
zebrafish
(Danio rerio)
Actinopterygii pde6c 35
  • 69.43 (n)
  • 70.97 (a)
zgc73085 35
pde6c 36
  • 69 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 28 (a)
OneToMany
Species with no ortholog for PDE6C:
  • 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)
  • 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 PDE6C Gene

ENSEMBL:
Gene Tree for PDE6C (if available)
TreeFam:
Gene Tree for PDE6C (if available)

Paralogs for PDE6C Gene

Paralogs for PDE6C Gene

(4) SIMAP similar genes for PDE6C Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PDE6C: view

Variants for PDE6C Gene

Sequence variations from dbSNP and Humsavar for PDE6C Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type MAF
rs473934 -- 93,632,179(-) GATCC(A/T)TAAAA intron-variant
rs474709 -- 93,622,651(-) aaaaa(A/C)caaaa intron-variant
rs481031 -- 93,637,997(+) TTTGG(C/T)TTTAT intron-variant
rs487161 -- 93,635,970(-) TGAGG(C/T)GTTAG intron-variant
rs503758 -- 93,647,178(-) TTTTT(G/T)GTTTG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDE6C Gene

Variant ID Type Subtype PubMed ID
esv21639 CNV Gain 19812545
nsv825522 CNV Loss 20364138
esv2739651 CNV Deletion 23290073

Variation tolerance for PDE6C Gene

Residual Variation Intolerance Score: 34.16% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 10.63; 91.35% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDE6C Gene

HapMap Linkage Disequilibrium report
PDE6C
Human Gene Mutation Database (HGMD)
PDE6C

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDE6C Gene

Disorders for PDE6C Gene

MalaCards: The human disease database

(10) MalaCards diseases for PDE6C Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
achromatopsia
  • achm
cone-rod dystrophy 4
  • cod4
achromatopsia 5
cone dystrophy 4
  • cod4
oligocone trichromacy
  • oligocone syndrome
- elite association
Search PDE6C in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PDE6C_HUMAN
  • Cone dystrophy 4 (COD4) [MIM:613093]: An early-onset cone dystrophy. Cone dystrophies are retinal dystrophies characterized by progressive degeneration of the cone photoreceptors with preservation of rod function, as indicated by electroretinogram. However, some rod involvement may be present in some cone dystrophies, particularly at late stage. Affected individuals suffer from photophobia, loss of visual acuity, color vision and central visual field. Another sign is the absence of macular lesions for many years. Cone dystrophies are distinguished from the cone-rod dystrophies in which some loss of peripheral vision also occurs. {ECO:0000269 PubMed:19615668}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PDE6C

Genetic Association Database (GAD)
PDE6C
Human Genome Epidemiology (HuGE) Navigator
PDE6C
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDE6C
genes like me logo Genes that share disorders with PDE6C: view

No data available for Genatlas for PDE6C Gene

Publications for PDE6C Gene

  1. Oligocone trichromacy: clinical and molecular genetic investigations. (PMID: 19797231) Andersen M.K. … Rosenberg T. (Invest. Ophthalmol. Vis. Sci. 2010) 23 67
  2. Impaired cone function and cone degeneration resulting from CNGB3 deficiency: down-regulation of CNGA3 biosynthesis as a potential mechanism. (PMID: 19767295) Ding X.Q. … Barlow R.B. (Hum. Mol. Genet. 2009) 23 67
  3. A homologous genetic basis of the murine cpfl1 mutant and human achromatopsia linked to mutations in the PDE6C gene. (PMID: 19887631) Chang B. … Wissinger B. (Proc. Natl. Acad. Sci. U.S.A. 2009) 23 67
  4. Homozygosity mapping reveals PDE6C mutations in patients with early- onset cone photoreceptor disorders. (PMID: 19615668) Thiadens A.A. … Klaver C.C. (Am. J. Hum. Genet. 2009) 23 67
  5. Screening of the gene encoding the alpha'-subunit of cone cGMP-PDE in patients with retinal degenerations. (PMID: 10393054) Gao Y.Q. … Farber D.B. (Invest. Ophthalmol. Vis. Sci. 1999) 23 67

Products for PDE6C Gene

Sources for PDE6C Gene

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