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Aliases for PDE6A Gene

Aliases for PDE6A Gene

  • Phosphodiesterase 6A 2 3 5
  • Phosphodiesterase 6A, CGMP-Specific, Rod, Alpha 2 3
  • GMP-PDE Alpha 3 4
  • PDE V-B1 3 4
  • PDEA 3 4
  • Rod CGMP-Specific 3,5-Cyclic Phosphodiesterase Subunit Alpha 3
  • Rod Photoreceptor CGMP Phosphodiesterase Alpha Subunit 3
  • CGMP Phosphodiesterase Alpha Subunit 3
  • EC 4
  • CGPR-A 3
  • RP43 3

External Ids for PDE6A Gene

Previous HGNC Symbols for PDE6A Gene

  • PDEA

Previous GeneCards Identifiers for PDE6A Gene

  • GC05M149310
  • GC05M149827
  • GC05M149268
  • GC05M149220
  • GC05M144384

Summaries for PDE6A Gene

Entrez Gene Summary for PDE6A Gene

  • This gene encodes the cyclic-GMP (cGMP)-specific phosphodiesterase 6A alpha subunit, expressed in cells of the retinal rod outer segment. The phosphodiesterase 6 holoenzyme is a heterotrimer composed of an alpha, beta, and two gamma subunits. cGMP is an important regulator of rod cell membrane current, and its dynamic concentration is established by phosphodiesterase 6A cGMP hydrolysis and guanylate cyclase cGMP synthesis. The protein is a subunit of a key phototransduction enzyme and participates in processes of transmission and amplification of the visual signal. Mutations in this gene have been identified as one cause of autosomal recessive retinitis pigmentosa. [provided by RefSeq, Jul 2008]

GeneCards Summary for PDE6A Gene

PDE6A (Phosphodiesterase 6A) is a Protein Coding gene. Diseases associated with PDE6A include Retinitis Pigmentosa 43 and Retinitis Pigmentosa. Among its related pathways are Pyrimidine metabolism (KEGG) and Signaling by Wnt. 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 PDE6B.

UniProtKB/Swiss-Prot for PDE6A Gene

  • This protein participates in processes of transmission and amplification of the visual signal.

Tocris Summary for PDE6A 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 PDE6A Gene

Additional gene information for PDE6A Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDE6A Gene

Genomics for PDE6A Gene

GeneHancer (GH) Regulatory Elements for PDE6A Gene

Promoters and enhancers for PDE6A Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J149956 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 650.7 -0.1 -131 6.7 HDGF PKNOX1 CLOCK SMAD1 FOXA2 MLX ZFP64 ARID4B SIN3A FEZF1 SLC26A2 PDE6A HMGXB3 TCOF1 TIGD6 ZNF300 RPL7P1 CSNK1A1 ZNF300P1 PDGFRB
GH05J149935 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 650.4 +18.2 18184 12.4 PKNOX1 SMAD1 FOXA2 ARNT SIN3A FEZF1 POLR2B ZNF766 FOS JUNB GC05M149941 ENSG00000200334 PDE6A SLC26A2 PPARGC1B CSNK1A1 CD74 HMGXB3
GH05J149885 Enhancer 1.4 FANTOM5 Ensembl ENCODE 14.9 +72.7 72665 3.2 HDGF PKNOX1 ATF1 ARNT FEZF1 TCF12 GATA2 ZFP91 NCOA1 MEF2D GC05P149886 GC05P149885 PDE6A HMGXB3 GC05P149903
GH05J149631 Enhancer 1.4 Ensembl ENCODE dbSUPER 10.2 +325.4 325350 5.8 HDGF ATF1 ARNT SIN3A IRF4 TCF12 ZNF121 ZNF766 GATA2 ZNF143 PIR47540 RNU6-588P SLC26A2 TIGD6 HMGXB3 ENSG00000200334 PDE6A CSF1R MIR143 CARMN
GH05J149800 Enhancer 1.4 Ensembl ENCODE dbSUPER 10 +155.0 155023 9 HDGF PKNOX1 SMAD1 ARNT SIN3A YBX1 ZNF2 IRF4 ZNF766 CBX5 RNU6-588P ENSG00000200334 PDE6A GRPEL2-AS1 GC05P149853 PPARGC1B GC05P149733
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDE6A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDE6A gene promoter:
  • p53
  • GR-alpha
  • GR
  • AP-2gamma
  • C/EBPalpha
  • POU2F1
  • POU2F1a
  • AP-2alphaA
  • AP-2beta

Genomic Locations for PDE6A Gene

Genomic Locations for PDE6A Gene
101,564 bases
Minus strand
86,838 bases
Minus strand

Genomic View for PDE6A Gene

Genes around PDE6A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDE6A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDE6A Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDE6A Gene

Proteins for PDE6A Gene

  • Protein details for PDE6A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Rod cGMP-specific 3,5-cyclic phosphodiesterase subunit alpha
    Protein Accession:
    Secondary Accessions:
    • Q0P638

    Protein attributes for PDE6A Gene

    860 amino acids
    Molecular mass:
    99547 Da
    Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
    Quaternary structure:
    • Oligomer composed of two catalytic chains (alpha and beta), an inhibitory chain (gamma) and the delta chain.

neXtProt entry for PDE6A Gene

Post-translational modifications for PDE6A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PDE6A Gene

Domains & Families for PDE6A Gene

Gene Families for PDE6A Gene

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

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the cyclic nucleotide phosphodiesterase family.
  • Belongs to the cyclic nucleotide phosphodiesterase family.
genes like me logo Genes that share domains with PDE6A: view

Function for PDE6A Gene

Molecular function for PDE6A Gene

UniProtKB/Swiss-Prot Function:
This protein participates in processes of transmission and amplification of the visual signal.
UniProtKB/Swiss-Prot CatalyticActivity:
Guanosine 3,5-cyclic phosphate + H(2)O = guanosine 5-phosphate.
GENATLAS Biochemistry:
cGMP specific nucleotide phosphodiesterase,class VI,alpha subunit,rod photoreceptor

Enzyme Numbers (IUBMB) for PDE6A Gene

Phenotypes From GWAS Catalog for PDE6A Gene

Gene Ontology (GO) - Molecular Function for PDE6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0008081 phosphoric diester hydrolase activity IEA --
GO:0016787 hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
GO:0047555 3,5-cyclic-GMP phosphodiesterase activity IEA,IMP 19946729
genes like me logo Genes that share ontologies with PDE6A: view
genes like me logo Genes that share phenotypes with PDE6A: view

Human Phenotype Ontology for PDE6A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

  • Taconic Biosciences Mouse Models for PDE6A

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDE6A

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PDE6A Gene

Localization for PDE6A Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDE6A Gene

Cell membrane; Lipid-anchor; Cytoplasmic side.

Subcellular locations from

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 PDE6A gene
Compartment Confidence
plasma membrane 4
cytosol 3
nucleus 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PDE6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0097381 photoreceptor disc membrane TAS --
genes like me logo Genes that share ontologies with PDE6A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDE6A Gene

Pathways & Interactions for PDE6A Gene

genes like me logo Genes that share pathways with PDE6A: view

Gene Ontology (GO) - Biological Process for PDE6A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007223 Wnt signaling pathway, calcium modulating pathway TAS --
GO:0007601 visual perception IEA --
GO:0016056 rhodopsin mediated signaling pathway TAS --
GO:0022400 regulation of rhodopsin mediated signaling pathway TAS --
genes like me logo Genes that share ontologies with PDE6A: view

No data available for SIGNOR curated interactions for PDE6A Gene

Drugs & Compounds for PDE6A Gene

(7) Drugs for PDE6A Gene - From: DrugBank, FDA Approved Drugs, HMDB, and Novoseek

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

(5) Additional Compounds for PDE6A Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Etazolate hydrochloride
Antagonist 28822-58-4
Ro 20-1724

(5) Tocris Compounds for PDE6A 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 PDE6A: view

Transcripts for PDE6A Gene

Unigene Clusters for PDE6A Gene

Phosphodiesterase 6A, cGMP-specific, rod, alpha:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDE6A

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDE6A Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20 ^ 21 ^ 22
SP1: - -

Relevant External Links for PDE6A Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDE6A Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDE6A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDE6A Gene

This gene is overexpressed in Colon - Transverse (x8.8), Pituitary (x8.6), Testis (x7.8), and Esophagus - Mucosa (x5.5).

Protein differential expression in normal tissues from HIPED for PDE6A Gene

This gene is overexpressed in Retina (64.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for PDE6A Gene

Protein tissue co-expression partners for PDE6A Gene

NURSA nuclear receptor signaling pathways regulating expression of PDE6A Gene:


SOURCE GeneReport for Unigene cluster for PDE6A Gene:


Evidence on tissue expression from TISSUES for PDE6A Gene

  • Eye(4.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDE6A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
  • penis
  • testicle
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with PDE6A: view

No data available for mRNA Expression by UniProt/SwissProt for PDE6A Gene

Orthologs for PDE6A Gene

This gene was present in the common ancestor of animals.

Orthologs for PDE6A Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PDE6A 34 33
  • 99.5 (n)
(Canis familiaris)
Mammalia PDE6A 34 33
  • 91.28 (n)
(Bos Taurus)
Mammalia PDE6A 34 33
  • 90.38 (n)
(Ornithorhynchus anatinus)
Mammalia PDE6A 34
  • 90 (a)
(Rattus norvegicus)
Mammalia Pde6a 33
  • 88.33 (n)
(Mus musculus)
Mammalia Pde6a 16 34 33
  • 87.83 (n)
(Monodelphis domestica)
Mammalia PDE6A 34
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pde6a 33
  • 71.83 (n)
(Danio rerio)
Actinopterygii pde6a 34 33
  • 72.24 (n)
fruit fly
(Drosophila melanogaster)
Insecta Pde6 34
  • 22 (a)
(Caenorhabditis elegans)
Secernentea pde-3 34
  • 16 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 28 (a)
Species where no ortholog for PDE6A 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)
  • chicken (Gallus gallus)
  • 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)
  • lizard (Anolis carolinensis)
  • 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 PDE6A Gene

Gene Tree for PDE6A (if available)
Gene Tree for PDE6A (if available)
Evolutionary constrained regions (ECRs) for PDE6A: view image

Paralogs for PDE6A Gene

(6) SIMAP similar genes for PDE6A Gene using alignment to 3 proteins:

  • F1T0K3_HUMAN
  • O75316_HUMAN
genes like me logo Genes that share paralogs with PDE6A: view

Variants for PDE6A Gene

Sequence variations from dbSNP and Humsavar for PDE6A Gene

SNP ID Clin Chr 05 pos Variation AA Info Type
rs10057110 likely-benign, Retinitis Pigmentosa, Recessive 149,934,000(-) T/C coding_sequence_variant, genic_upstream_transcript_variant, intron_variant, missense_variant
rs1005811542 uncertain-significance, Retinitis Pigmentosa, Recessive 149,859,506(-) A/G 3_prime_UTR_variant
rs10067462 likely-benign, Retinitis Pigmentosa, Recessive 149,863,201(-) C/T coding_sequence_variant, synonymous_variant
rs1060499536 pathogenic, Retinitis pigmentosa 43 149,896,778(-) T/C splice_acceptor_variant
rs112926956 uncertain-significance, Retinitis Pigmentosa, Recessive 149,944,684(-) C/A 5_prime_UTR_variant, genic_upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PDE6A Gene

Variant ID Type Subtype PubMed ID
dgv10112n54 CNV gain 21841781
dgv1147e214 CNV loss 21293372
dgv727n27 CNV gain 19166990
esv24664 CNV gain+loss 19812545
esv2663162 CNV deletion 23128226
esv2666734 CNV deletion 23128226
esv3370145 CNV insertion 20981092
esv3570491 CNV loss 25503493
esv3607153 CNV loss 21293372
esv3607156 CNV gain 21293372
esv3890751 CNV gain 25118596
nsv1023343 CNV gain 25217958
nsv830518 CNV loss 17160897

Variation tolerance for PDE6A Gene

Residual Variation Intolerance Score: 94.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.78; 73.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDE6A Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDE6A Gene

Disorders for PDE6A Gene

MalaCards: The human disease database

(7) MalaCards diseases for PDE6A Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PDE6A in MalaCards View complete list of genes associated with diseases


  • Retinitis pigmentosa 43 (RP43) [MIM:613810]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:10393062, ECO:0000269 PubMed:7493036}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PDE6A

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PDE6A: view

No data available for Genatlas for PDE6A Gene

Publications for PDE6A Gene

  1. A novel mutation and phenotypes in phosphodiesterase 6 deficiency. (PMID: 18723146) Tsang SH … Allikmets R (American journal of ophthalmology 2008) 3 22 44 58
  2. Frequency of mutations in the gene encoding the alpha subunit of rod cGMP-phosphodiesterase in autosomal recessive retinitis pigmentosa. (PMID: 10393062) Dryja TP … Berson EL (Investigative ophthalmology & visual science 1999) 3 4 22 58
  3. Autosomal recessive retinitis pigmentosa caused by mutations in the alpha subunit of rod cGMP phosphodiesterase. (PMID: 7493036) Huang SH … Dryja TP (Nature genetics 1995) 3 4 22 58
  4. Molecular characterization of human and bovine rod photoreceptor cGMP phosphodiesterase alpha-subunit and chromosomal localization of the human gene. (PMID: 2155175) Pittler SJ … Davis RL (Genomics 1990) 2 3 4 58
  5. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij JC … Florijn RJ (Ophthalmology 2011) 3 44 58

Products for PDE6A Gene

Sources for PDE6A Gene

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