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Aliases for PDE6C Gene

Aliases for PDE6C Gene

  • Phosphodiesterase 6C 2 3 5
  • Phosphodiesterase 6C, CGMP-Specific, Cone, Alpha Prime 2 3
  • CGMP Phosphodiesterase 6C 3 4
  • EC 4 61
  • PDEA2 3 4
  • Cone CGMP-Specific 3,5-Cyclic Phosphodiesterase Subunit Alpha 3
  • EC 3.1.4 61
  • 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) is a Protein Coding gene. Diseases associated with PDE6C include Cone Dystrophy 4 and Achromatopsia. Among its related pathways are Purine metabolism (KEGG) and Phototransduction. 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

Enhancers for PDE6C 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
GH10F093701 0.4 ENCODE 31.3 +89.9 89895 2.3 CREB3L1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF416 ZNF143 ZNF548 ZNF263 RPL17P34 NOC3L ENSG00000273450 PDE6C FRA10AC1
GH10F093074 0.2 ENCODE 13.9 -537.7 -537680 0.3 RING1 MAZ RNF2 SUZ12 CBX2 ZBTB33 EZH2 PDE6C CYP26A1 GC10M093106 NIP7P1
GH10F094361 0.2 ENCODE 13.9 +749.8 749820 2.3 PKNOX1 CREB3L1 MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 NOC3L PDE6C ENSG00000273450 PLCE1-AS1 PLCE1 PIR55864
GH10F093498 0.2 ENCODE 12.8 -114.1 -114125 0.9 ARID1B ZNF202 NCOR1 ZNF658 ZNF366 CEBPB RPL17P34 PDE6C NOC3L CEP55 GC10M093511 RNA5SP323
GH10F092688 1.4 FANTOM5 Ensembl ENCODE 12.7 -917.9 -917870 12.3 PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 FOS PAF1 BTAF1 HHEX KIF11 RPL17P34 PDE6C IDE TNKS2 EIF2S2P3 CYP26C1 GC10M092666
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PDE6C on UCSC Golden Path with GeneCards custom track

Genomic Location for PDE6C Gene

93,612,588 bp from pter
93,666,010 bp from pter
53,423 bases
Plus strand

Genomic View for PDE6C Gene

Genes around PDE6C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDE6C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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:
    Recommended name:
    Cone cGMP-specific 3,5-cyclic phosphodiesterase subunit alpha
    Protein Accession:
    Secondary Accessions:
    • A6NCR6
    • Q5VY29

    Protein attributes for PDE6C Gene

    858 amino acids
    Molecular mass:
    99147 Da
    Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
    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

Selected DME Specific Peptides for PDE6C Gene


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



  • Contains 2 GAF domains.
  • Belongs to the cyclic nucleotide phosphodiesterase family.
  • Contains 2 GAF domains.
  • 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 IEA --
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0016787 hydrolase activity IEA --
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

Human Phenotype Ontology for PDE6C Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for PDE6C

Inhibitory RNA 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

Jensen Localization Image for PDE6C Gene COMPARTMENTS Subcellular localization image for PDE6C gene
Compartment Confidence
cytosol 3
plasma membrane 3
nucleus 2
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for PDE6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
GO:0016020 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

Gene Ontology (GO) - Biological Process for PDE6C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007601 visual perception IEA,TAS --
GO:0007603 phototransduction, visible light IEA --
GO:0046549 retinal cone cell development IEA --
GO:0050896 response to stimulus 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

(9) Drugs for PDE6C Gene - From: DrugBank, FDA Approved Drugs, HMDB, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Caffeine Approved Nutra Antagonist, Target, inhibitor, competitive A1 and A2B antagonist. CNS stimulant 380
Cafcit Injection Approved September 1999 Pharma 0
Water Approved Pharma 0
Cyclic GMP Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0

(1) Additional Compounds for PDE6C Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Antagonist 28822-58-4

(5) Tocris Compounds for PDE6C Gene

Compound Action Cas Number
(R)-(-)-Rolipram PDE4 inhibitor. More active enantiomer of rolipram (Cat. No. 0905) 85416-75-7
IBMX PDE inhibitor (non-selective) 28822-58-4
MDL 12330A hydrochloride Adenylyl cyclase inhibitor; also cyclic nucleotide PDE inhibitor 40297-09-4
Rolipram PDE4 inhibitor 61413-54-5
Sildenafil citrate Orally active, potent PDE5 inhibitor 171599-83-0
genes like me logo Genes that share compounds with PDE6C: view

Transcripts for PDE6C Gene

mRNA/cDNA for PDE6C Gene

(2) 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:

Inhibitory RNA Products

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
ECgene alternative splicing isoforms for

Expression for PDE6C Gene

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

Protein tissue co-expression partners for PDE6C Gene

NURSA nuclear receptor signaling pathways regulating expression of PDE6C Gene:


SOURCE GeneReport for Unigene cluster for PDE6C Gene:

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

Primer 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
(Pan troglodytes)
Mammalia PDE6C 34 35
  • 99.53 (n)
(Bos Taurus)
Mammalia PDE6C 34 35
  • 88.86 (n)
(Canis familiaris)
Mammalia PDE6C 34 35
  • 88.37 (n)
(Mus musculus)
Mammalia Pde6c 34 16 35
  • 84.54 (n)
(Rattus norvegicus)
Mammalia Pde6c 34
  • 84.23 (n)
(Monodelphis domestica)
Mammalia PDE6C 35
  • 81 (a)
(Ornithorhynchus anatinus)
Mammalia PDE6C 35
  • 70 (a)
(Gallus gallus)
Aves PDE6C 34 35
  • 78.17 (n)
(Anolis carolinensis)
Reptilia PDE6C 35
  • 78 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pde6c 34
  • 74.4 (n)
(Danio rerio)
Actinopterygii pde6c 34 35
  • 69.43 (n)
zgc73085 34
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 28 (a)
Species where no ortholog for PDE6C 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)
  • 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

Gene Tree for PDE6C (if available)
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
rs121918537 Cone dystrophy 4 (COD4) [MIM:613093], Pathogenic 93,612,810(+) AGTTG(C/T)GGGTG upstream-variant-2KB, reference, missense
rs121918538 Cone dystrophy 4 (COD4) [MIM:613093], Pathogenic 93,626,667(+) TTGAT(A/T)ACATT reference, missense
rs121918539 Cone dystrophy 4 (COD4) [MIM:613093], Pathogenic 93,635,590(+) AGGAA(A/G)TGCTC reference, missense
rs267606934 Pathogenic 93,640,987(+) CTGCC(A/T)TGATA reference, missense
rs267606935 Pathogenic 93,663,117(+) GAGTA(A/T)GATGC reference, stop-gained

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

Variant ID Type Subtype PubMed ID
esv21639 CNV gain 19812545
esv2739651 CNV deletion 23290073
esv3624241 CNV loss 21293372
nsv1116497 OTHER inversion 24896259
nsv472454 CNV novel sequence insertion 20440878
nsv825522 CNV loss 20364138

Variation tolerance for PDE6C Gene

Residual Variation Intolerance Score: 34.2% 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

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

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

Disorders for PDE6C Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
cone dystrophy 4
  • cod4
  • achm
cone-rod dystrophy 6
  • retinal cone dystrophy 2
achromatopsia 5
cone-rod dystrophy 4
  • cone dystrophy 4
- elite association - COSMIC cancer census association via MalaCards
Search PDE6C in MalaCards View complete list of genes associated with diseases


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

No data available for Genatlas for PDE6C Gene

Publications for PDE6C Gene

  1. 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) 3 4 22 64
  2. 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) 3 4 22 64
  3. Gene structure and amino acid sequence of the human cone photoreceptor cGMP-phosphodiesterase alpha' subunit (PDEA2) and its chromosomal localization to 10q24. (PMID: 7490077) Piriev N.I. … Farber D.B. (Genomics 1995) 3 4 22 64
  4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  5. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey S.D. … Anand S. (Diabetes Care 2010) 3 46 64

Products for PDE6C Gene

Sources for PDE6C Gene

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