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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 3.1.4.35 4 56
  • PDEA2 3 4
  • Cone CGMP-Specific 3,5-Cyclic Phosphodiesterase Subunit Alpha 3
  • EC 3.1.4 56
  • 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 Pyrimidine metabolism (KEGG) and Phototransduction. Gene Ontology (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.

UniProtKB/Swiss-Prot for PDE6C Gene

  • As cone-specific cGMP phosphodiesterase, it plays an essential role in light detection and cone phototransduction by rapidly decreasing intracellular levels of cGMP.

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

Additional gene information for PDE6C Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDE6C Gene

Genomics for PDE6C Gene

GeneHancer (GH) Regulatory Elements for PDE6C Gene

Promoters and enhancers for PDE6C 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
GH10I093612 Promoter 0.5 EPDnew 550.8 -0.1 -70 0.1 PDE6C GC10P093599 GC10P093601
GH10I093701 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 74.4 +89.9 89894 2.3 ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 FRA10AC1 RPL17P34 NOC3L PDE6C ENSG00000273450 MYOF HELLS
GH10I092688 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 25.3 -919.0 -918977 10.1 HDGF PKNOX1 SMAD1 FOXA2 MLX ARNT ARID4B SIN3A FEZF1 DMAP1 HHEX BTAF1 RPL17P34 PDE6C KIF11 IDE TNKS2 EIF2S2P3 GC10M092666
GH10I094361 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 13.9 +749.8 749820 2.3 PKNOX1 CLOCK MLX ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 NOC3L PIR55864 ENSG00000273450 FRA10AC1 PDE6C PIPSL PLCE1-AS1 PLCE1
GH10I093455 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 10.6 -142.7 -142730 28.4 PKNOX1 FOXA2 SIN3A FEZF1 ZNF2 YY1 ZNF143 FOS SP3 JUNB MYOF CEP55 PDE6C GC10M093419 GC10M093427
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PDE6C on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDE6C gene promoter:

Genomic Locations for PDE6C Gene

Genomic Locations for PDE6C Gene
chr10:93,612,588-93,666,010
(GRCh38/hg38)
Size:
53,423 bases
Orientation:
Plus strand
chr10:95,372,345-95,425,767
(GRCh37/hg19)

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:
    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;
    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

P51160:
  • QTMFTLL
  • ERQFHKALYT
  • PIPMMDR
  • PIVNKKE
  • SGLPTYVA
  • GLQNNRVEWK
  • EFWEQGDLERTVL
  • DESLNIFQNLN
  • IDYILHGKE
  • GLLDMTKEKEF
  • TYHNWRHGFNVGQTMF
  • LTQFLGWS
  • VFPLDIG
  • QQPIPMMDR
  • CHDIDHRGTNNLYQMKS
  • MAMMMTACDLSAITKPWEVQS
  • AIIATDLALYFKKRTMFQKIVD
  • LENRKDI
  • SILERHHLE
  • GWVIKNVLS
  • YLNCERYS
  • CHDIDHRGT
  • EVLTRWMYTVRKGYR
  • YYTDLEAFAM
  • ELPKLQVGFIDFVCTFVYKEFSRFH

Post-translational modifications for PDE6C Gene

No Post-translational modifications

Other Protein References for PDE6C Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for PDE6C Gene

Gene Families for PDE6C Gene

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

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 :
  • Belongs to the cyclic nucleotide phosphodiesterase family.
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.
UniProtKB/Swiss-Prot Function:
As cone-specific cGMP phosphodiesterase, it plays an essential role in light detection and cone phototransduction by rapidly decreasing intracellular levels of cGMP.

Enzyme Numbers (IUBMB) for PDE6C Gene

Phenotypes From GWAS Catalog 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

Clone 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
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 PDE6C gene
Compartment Confidence
plasma membrane 3
cytosol 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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDE6C Gene

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 TAS,IEA --
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Trapidil Approved Pharma Target, inhibitor 1
Caffeine Approved Nutra Antagonist, Target 434
Cafcit Injection Approved September 1999 Pharma 0
Water Approved Pharma 0
Cyclic GMP Experimental Pharma 0

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

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

(5) Tocris Compounds for PDE6C 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
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:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP 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:

PDE6C

SOURCE GeneReport for Unigene cluster for PDE6C Gene:

Hs.658121

Evidence on tissue expression from TISSUES for PDE6C Gene

  • Eye(4.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDE6C Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • nervous
  • skeletal muscle
Organs:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • eyelid
  • head
General:
  • peripheral nervous system
genes like me logo Genes that share expression patterns with PDE6C: view

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
chimpanzee
(Pan troglodytes)
Mammalia PDE6C 33 34
  • 99.53 (n)
cow
(Bos Taurus)
Mammalia PDE6C 33 34
  • 88.86 (n)
dog
(Canis familiaris)
Mammalia PDE6C 33 34
  • 88.37 (n)
mouse
(Mus musculus)
Mammalia Pde6c 33 16 34
  • 84.54 (n)
rat
(Rattus norvegicus)
Mammalia Pde6c 33
  • 84.23 (n)
oppossum
(Monodelphis domestica)
Mammalia PDE6C 34
  • 81 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDE6C 34
  • 70 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDE6C 33 34
  • 78.17 (n)
lizard
(Anolis carolinensis)
Reptilia PDE6C 34
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pde6c 33
  • 74.4 (n)
zebrafish
(Danio rerio)
Actinopterygii pde6c 33 34
  • 69.43 (n)
zgc73085 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 28 (a)
OneToMany
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

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

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 Variation AA Info Type
rs1023522305 likely-pathogenic, Achromatopsia 93,622,073(+) G/A/C splice_donor_variant
rs1051926 uncertain-significance, Achromatopsia, Cone-Rod Dystrophy, Recessive 93,663,085(+) A/C coding_sequence_variant, synonymous_variant
rs11187564 benign, likely-benign, not specified, Achromatopsia, Cone-Rod Dystrophy, Recessive 93,635,488(+) C/G/T intron_variant
rs112520932 uncertain-significance, Cone-Rod Dystrophy, Recessive, Achromatopsia 93,665,444(+) A/G 3_prime_UTR_variant, genic_downstream_transcript_variant
rs1131978 benign, likely-benign, uncertain-significance, not specified, Cone-Rod Dystrophy, Recessive, Achromatopsia 93,612,977(+) G/A/T coding_sequence_variant, genic_upstream_transcript_variant, synonymous_variant, upstream_transcript_variant

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)

Additional Variant Information for PDE6C Gene

Human Gene Mutation Database (HGMD)
PDE6C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDE6C

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

Disorders for PDE6C Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
cone dystrophy 4
  • cod4
achromatopsia
  • achm
cone-rod dystrophy 6
  • retinitis pigmentosa 6
cone dystrophy
  • cone dystrophy 3
oligocone trichromacy
  • oligocone syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PDE6C in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PDE6C_HUMAN
  • Achromatopsia 5 (ACHM5) [MIM:613093]: A form of achromatopsia, an ocular stationary disorder due to the absence of functioning cone photoreceptors in the retina. It is characterized by total colorblindness, low visual acuity, photophobia and nystagmus. ACHM5 inheritance is autosomal recessive. {ECO:0000269 PubMed:19615668, ECO:0000269 PubMed:21127010, ECO:0000269 PubMed:28583373}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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.

Additional Disease Information for PDE6C

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 AA … Klaver CC (American journal of human genetics 2009) 3 4 22 58
  2. Screening of the gene encoding the alpha'-subunit of cone cGMP-PDE in patients with retinal degenerations. (PMID: 10393054) Gao YQ … Farber DB (Investigative ophthalmology & visual science 1999) 3 4 22 58
  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 NI … Farber DB (Genomics 1995) 3 4 22 58
  4. Decreased catalytic activity and altered activation properties of PDE6C mutants associated with autosomal recessive achromatopsia. (PMID: 21127010) Grau T … Kohl S (Human molecular genetics 2011) 3 4 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for PDE6C Gene

Sources for PDE6C Gene

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