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PDE6A Gene

protein-coding   GIFtS: 62
GCID: GC05M149220

Phosphodiesterase 6A, CGMP-Specific, Rod, Alpha


(Previous symbol: PDEA)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Phosphodiesterase 6A, CGMP-Specific, Rod, Alpha1 2     CGPR-A2
PDEA1 2 3 5     CGMP Phosphodiesterase Alpha Subunit2
GMP-PDE Alpha2 3     Rod CGMP-Specific 3',5'-Cyclic Phosphodiesterase Subunit Alpha2
PDE V-B12 3     Rod Photoreceptor CGMP Phosphodiesterase Alpha Subunit2
EC 3.1.4.353 8     EC 3.1.48
RP432 5     

External Ids:    HGNC: 87851   Entrez Gene: 51452   Ensembl: ENSG000001329157   OMIM: 1800715   UniProtKB: P164993   

Export aliases for PDE6A gene to outside databases

Previous GC identifers: GC05M149310 GC05M149827 GC05M149268 GC05M144384


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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, cGMP-specific, rod, alpha) is a protein-coding gene. Diseases associated with PDE6A include pde6a-related retinitis pigmentosa, and retinitis pigmentosa 43. GO annotations related to this gene include 3',5'-cyclic-GMP phosphodiesterase activity. An important paralog of this gene is PDE11A.

UniProtKB/Swiss-Prot: PDE6A_HUMAN, P16499
Function: This protein participates in processes of transmission and amplification of the visual signal

summary for PDE6A Gene:
Phosphodiesterases (PDEs) are a family of related phosphohydrolyases that selectively catalyze the
hydrolysis of 3' cyclic phosphate bonds in adenosine and/or guanine 3',5' cyclic monophosphate (cAMP and/or
cGMP). They regulate the cellular levels, localization and duration of action of these second messengers by
controlling the rate of their degradation. There are 11 subtypes of PDEs, named PDE1-11; PDE4, 7 and 8
selectively degrade cAMP, PDE5, 6 and 9 selectively degrade cGMP and PDE1, 2, 3, 10 and 11 degrade both
cyclic nucleotides. PDEs are expressed ubiquitously, with each subtype having a specific tissue
distribution. These enzymes are involved in many signal transduction pathways and their functions include
vascular smooth muscle proliferation and contraction, cardiac contractility, platelet aggregation, hormone
secretion, immune cell activation, and they are involved in learning and memory.

Gene Wiki entry for PDE6A Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000005.10  NT_029289.12  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PDE6A gene promoter:
         GR   p53   AP-2gamma   C/EBPalpha   POU2F1   POU2F1a   AP-2beta   GR-alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPDE6A promoter sequence
   Search Chromatin IP Primers for PDE6A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PDE6A


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 5q31.2-q34   Ensembl cytogenetic band:  5q32   HGNC cytogenetic band: 5q31.2-q34

PDE6A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PDE6A gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05M149220:  view genomic region     (about GC identifiers)

Start:
149,237,519 bp from pter      End:
149,324,356 bp from pter
Size:
86,838 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: PDE6A_HUMAN, P16499 (See protein sequence)
Recommended Name: Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha precursor  
Size: 860 amino acids; 99547 Da
Cofactor: 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 (By similarity)
Subunit: Oligomer composed of two catalytic chains (alpha and beta), an inhibitory chain (gamma) and the delta
chain
Secondary accessions: Q0P638

Explore the universe of human proteins at neXtProt for PDE6A: NX_P16499

Explore proteomics data for PDE6A at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for PDE6A (P16499) (see all 33)
     PIPMMDR  PIVNKKE  LENRKDI  FYKVIDY 


    See PDE6A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_000431.2  
    ENSEMBL proteins: 
     ENSP00000255266  
    Reactome Protein details: P16499

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    PDE: Phosphodiesterases

    IUPHAR Guide to PHARMACOLOGY protein family classification: PDE6A
    Phosphodiesterases, 3',5'-cyclic nucleotide

    5 InterPro protein domains:
     IPR002073 PDEase_catalytic_dom
     IPR003018 GAF
     IPR023174 PDEase_CS
     IPR023088 PDEase
     IPR003607 HD/PDEase_dom

    Graphical View of Domain Structure for InterPro Entry P16499

    ProtoNet protein and cluster: P16499

    UniProtKB/Swiss-Prot: PDE6A_HUMAN, P16499
    Similarity: Belongs to the cyclic nucleotide phosphodiesterase family
    Similarity: Contains 2 GAF domains


    PDE6A for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PDE6A_HUMAN, P16499
    Function: This protein participates in processes of transmission and amplification of the visual signal
    Catalytic activity: Guanosine 3',5'-cyclic phosphate + H(2)O = guanosine 5'-phosphate

         Genatlas biochemistry entry for PDE6A:
    cGMP specific nucleotide phosphodiesterase,class VI,alpha subunit,rod photoreceptor

         Enzyme Numbers (IUBMB): EC 3.1.4.351 2 EC 3.1.42

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003824catalytic activity ----
    GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity ----
    GO:0005515protein binding ----
    GO:0046872metal ion binding IEA--
    GO:00475553',5'-cyclic-GMP phosphodiesterase activity IMP19946729
         
    PDE6A for ontologies           About GeneDecksing


    Phenotypes:
         2 MGI mutant phenotypes (inferred from 2 alleles(MGI details for Pde6a):
     nervous system  vision/eye 

    PDE6A for phenotypes           About GeneDecksing

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PDE6A
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    hsa-miR-138-1* hsa-miR-607 hsa-miR-548b-3p hsa-miR-513c hsa-miR-514b-5p hsa-miR-1205
    SwitchGear 3'UTR luciferase reporter plasmidPDE6A 3' UTR sequence
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PDE6A_HUMAN, P16499: Cell membrane; Lipid-anchor; Cytoplasmic side (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    cytosol3
    nucleus2
    mitochondrion1

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane TAS--
    GO:0097381photoreceptor disc membrane TAS--

    PDE6A for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for PDE6A About   (see all 7)                                                                                              See pathways by source

    SuperPathContained pathways About
    1The phototransduction cascade
    The phototransduction cascade0.51
    Inactivation, recovery and regulation of the phototransduction cascade0.49
    Visual signal transduction- Rods0.51
    Activation of the phototransduction cascade0.00
    Phototransduction0.51
    2beta-catenin independent WNT signaling
    beta-catenin independent WNT signaling0.79
    Ca2+ pathway0.43
    Signaling by Wnt0.79
    3Diseases associated with visual transduction
    Visual phototransduction0.44
    Diseases associated with visual transduction0.43
    4Signaling by GPCR
    Signal Transduction0.58
    5Purine metabolism (KEGG)
    Purine metabolism0.38

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for PDE6A
        Visual Cycle in Retinal Rods

    1 BioSystems Pathway for PDE6A
        Visual signal transduction- Rods

    3 Reactome Pathways for PDE6A
        Activation of the phototransduction cascade
    Ca2+ pathway
    Inactivation, recovery and regulation of the phototransduction cascade


    2 Kegg Pathways  (Kegg details for PDE6A):
        Purine metabolism
    Phototransduction


    PDE6A for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PDE6A
    Interactions:

        GeneGlobe Interaction Network for PDE6A

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for PDE6A (ENSP000002552664) via UniProtKB, MINT, STRING, and/or I2D (see all 60)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ADCY2ENSP000003429524STRING: ENSP00000342952
    CNGA1ENSP000003842644STRING: ENSP00000384264
    GNAT1ENSP000002324614STRING: ENSP00000232461
    GNB5ENSP000002618374STRING: ENSP00000261837
    GUCY1B3ENSP000002644244STRING: ENSP00000264424
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 9):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007165signal transduction ----
    GO:0007596blood coagulation ----
    GO:0007601visual perception IEA--
    GO:0007603phototransduction, visible light TAS--
    GO:0016056rhodopsin mediated signaling pathway TAS--

    PDE6A for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
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      Browse compounds at ApexBio 

    Compounds for PDE6A available from Tocris Bioscience    About this table
    CompoundAction CAS #
    CilostamidePDE3 inhibitor[68550-75-4]
    RolipramPDE4 inhibitor[61413-54-5]
    IBMXPDE inhibitor (non-selective)[28822-58-4]
    Sildenafil citrate Orally active, potent PDE5 inhibitor [171599-83-0]
    (R)-(-)-RolipramPDE4 inhibitor. More active enantiomer of rolipram (Cat. No. 0905)[85416-75-7]

    3 HMDB Compounds for PDE6A    About this table
    CompoundSynonyms CAS #PubMed Ids
    Cyclic GMP3',5'-cyclic GMP (see all 13)7665-99-8--
    Guanosine monophosphate5'-GMP (see all 14)85-32-5--
    WaterDihydrogen oxide (see all 2)7732-18-5--

    1 Novoseek inferred chemical compound relationship for PDE6A gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cgmp 46.4 5 10393062 (2), 7493036 (1)



    PDE6A for compounds           About GeneDecksing



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PDE6A gene: 
    NM_000440.2  

    Unigene Cluster for PDE6A:

    Phosphodiesterase 6A, cGMP-specific, rod, alpha
    Hs.567314  [show with all ESTs]
    Unigene Representative Sequence: NM_000440
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000255266(uc003lrg.4 uc021yfs.1) ENST00000508173 ENST00000512670

    miRNA
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    hsa-miR-138-1* hsa-miR-607 hsa-miR-548b-3p hsa-miR-513c hsa-miR-514b-5p hsa-miR-1205
    SwitchGear 3'UTR luciferase reporter plasmidPDE6A 3' UTR sequence
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    Additional mRNA sequence: 

    AB593141.1 BC035909.1 BC144044.1 BX537592.1 BX648986.1 M26061.1 

    7 DOTS entries:

    DT.413830  DT.40118669  DT.101979897  DT.100774930  DT.40114595  DT.97839786  DT.40248014 

    Selected AceView cDNA sequences (see all 85):

    BM799868 BX648986 BC035909 AL711794 BM690640 BU726255 BX491290 BQ636625 
    AL711622 BQ636485 BU726688 BX491279 BM709653 NM_000440 AA056299 BX490874 
    BG476152 BM686772 BM685895 BU734060 AL713275 BQ638372 AL712994 BE390984 

    GeneLoc Exon Structure

    3 Alternative Splicing Database (ASD) splice patterns (SP) for PDE6A    About this scheme

    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:                                            -                                                                             -                           
    SP2:                                                                                                                                                      
    SP3:                                                                                                                                                      


    ECgene alternative splicing isoforms for PDE6A

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PDE6A expression in normal human tissues (normalized intensities)      PDE6A embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAACACATTC
    PDE6A Expression
    About this image


    PDE6A expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Eye (Sensory Organs)    fully expand to see all 2 entries
             Mature Rod Cells Outer Nuclear Layer
     
     Neurons
             Mature Rod Cells Outer Nuclear Layer
    PDE6A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PDE6A Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.567314
        Custom PCR Arrays for PDE6A
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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDE6A

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for PDE6A gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pde6a1 , 5 phosphodiesterase 6A, cGMP-specific, rod, alpha1, 5 87.83(n)1
    95(a)1
      18 (34.41 cM)5
    2256001  NM_146086.21  NP_666198.11 
     612204825 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia pde6a1 phosphodiesterase 6A, cGMP-specific, rod, alpha 71.83(n)
    78.11(a)
      100489913  XM_002936704.2  XP_002936750.2 
    zebrafish
    (Danio rerio)
    Actinopterygii pde6a1 phosphodiesterase 6A, cGMP-specific, rod, alpha 72.24(n)
    77.54(a)
      368410  NM_001007160.2  NP_001007161.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta Pde66
    Phosphodiesterase 6
    22(a)
    many ↔ many
    3R(10339622-10383694)
    worm
    (Caenorhabditis elegans)
    Secernentea pde-36
    Protein PDE-3, isoform c
    16(a)
    many ↔ many
    II(14919705-14953312) WBGene00008443


    ENSEMBL Gene Tree for PDE6A (if available)
    TreeFam Gene Tree for PDE6A (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PDE6A gene
    PDE11A2  PDE3A2  PDE6B2  PDE6C2  PDE2A2  PDE5A2  PDE10A2  PDE3B2  
    6 SIMAP similar genes for PDE6A using alignment to 3 protein entries:     PDE6A_HUMAN (see all proteins):
    PDE6B    PDE6C    PDE5A    PDE11A    PDE2A    PDE4

    PDE6A for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PDE6A (see all 2130)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0254604
    Retinitis pigmentosa 43 (RP43)4--see VAR_0254602 R H mis40--------
    VAR_0060494
    Retinitis pigmentosa 43 (RP43)4--see VAR_0060492 S R mis40--------
    VAR_0254614
    Retinitis pigmentosa 43 (RP43)4--see VAR_0254612 R S mis40--------
    VAR_0254674
    Retinitis pigmentosa 43 (RP43)4--see VAR_0254672 S P mis40--------
    VAR_0254664
    Retinitis pigmentosa 43 (RP43)4--see VAR_0254662 Q K mis40--------
    rs1219185771,2
    Cpathogenic1149563107(-) GTAAGA/C/TGGTCT 2 R S mis11EU 1203
    rs617333621,2
    C,Funtested1149552118(+) CTCCAG/CTTCTG 2 /L /V mis12Minor allele frequency- C:0.02NS NA 4602
    rs1378538991,2
    Cuntested1149577451(-) TGGCCG/AGTTCT 2 /P syn11Minor allele frequency- A:0.00EU 1323
    rs2514581,2
    C,A--149238390(-) aaaaaA/Gaaaaa 1 -- ut310--------
    rs360434371,2
    C--149240216(+) TTTTTT/-AAGTT 1 -- ut311Minor allele frequency- -:0.00NA 2

    HapMap Linkage Disequilibrium report for PDE6A (149237519 - 149324356 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for PDE6A:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2663162CNV Deletion23128226
    esv2666734CNV Deletion23128226
    esv273743CNV Insertion20981092
    nsv830518CNV Loss17160897
    dgv727n27CNV Gain19166990
    nsv883024CNV Gain21882294
    esv24664CNV Gain+Loss19812545

    Human Gene Mutation Database (HGMD): PDE6A
    Locus Specific Mutation Databases (LSDB): PDE6A

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 180071   
    OMIM disorders: 613810  
    UniProtKB/Swiss-Prot: PDE6A_HUMAN, P16499
  • 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. Note=The disease is caused by mutations
    affecting the gene represented in this entry

  • 13 diseases for PDE6A:    About MalaCards
    pde6a-related retinitis pigmentosa    retinitis pigmentosa 43    cystoid macular edema    retinitis pigmentosa
    rhyns syndrome    pigmentary retinopathy    leber congenital amaurosis    retinitis
    retinal disease    blindness    melanoma    multiple myeloma
    myeloma

    2 diseases from the University of Copenhagen DISEASES database for PDE6A:
    Retinitis pigmentosa     Cystoid macular edema

    PDE6A for disorders           About GeneDecksing

    2 Novoseek inferred disease relationships for PDE6A gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    retinitis pigmentosa 82.4 2 10393062 (1), 10782214 (1)
    atrophy 34.2 2 10782214 (2)

    Genetic Association Database (GAD): PDE6A
    Human Genome Epidemiology (HuGE) Navigator: PDE6A (8 documents)

    Export disorders for PDE6A gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PDE6A gene, integrated from 10 sources (see all 35):
    (articles sorted by number of sources associating them with PDE6A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular characterization of human and bovine rod photoreceptor cGMP phosphodiesterase alpha-subunit and chromosomal localization of the human gene. (PubMed id 2155175)1, 2, 3 Pittler S.J.... Davis R.L. (Genomics 1990)
    2. Frequency of mutations in the gene encoding the alpha subunit of rod cGMP-phosphodiesterase in autosomal recessive retinitis pigmentosa. (PubMed id 10393062)1, 2, 9 Dryja T.P.... Berson E.L. (Invest. Ophthalmol. Vis. Sci. 1999)
    3. Autosomal recessive retinitis pigmentosa caused by mutations in the alpha subunit of rod cGMP phosphodiesterase. (PubMed id 7493036)1, 2, 9 Huang S.H....Dryja T.P. (Nat. Genet. 1995)
    4. A novel mutation and phenotypes in phosphodiesterase 6 deficiency. (PubMed id 18723146)1, 4, 9 Tsang S.H....Allikmets R. (Am. J. Ophthalmol. 2008)
    5. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PubMed id 20801516)1, 4 Booij J.C....Florijn R.J. (Ophthalmology 2011)
    6. Development of a diagnostic genetic test for simplex and autosomal recessive retinitis pigmentosa. (PubMed id 20591486)1, 4 Clark G.R.... Simpson D.A. (Ophthalmology 2010)
    7. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    8. Mutations in the gene encoding the alpha-subunit of rod phosphodiesterase in consanguineous Pakistani families. (PubMed id 17110911)1, 9 Riazuddin S.A....Hejtmancik J.F. (Mol. Vis. 2006)
    9. Functional analysis of the rod photoreceptor cGMP phosphodiesterase alpha-subunit gene promoter: Nrl and Crx are required for full transcriptional activity. (PubMed id 15001570)1, 9 Pittler S.J....White J.B. (J. Biol. Chem. 2004)
    10. Structure and upstream region characterization of the human gene encoding rod photoreceptor cGMP phosphodiesterase alpha-subunit. (PubMed id 9770645)1, 9 Mohamed M.K.... Pittler S.J. (J. Mol. Neurosci. 1998)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 5145 HGNC: 8785 AceView: PDE6A Ensembl:ENSG00000132915 euGenes: HUgn5145
    ECgene: PDE6A Kegg: 5145 H-InvDB: PDE6A

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PDE6A Pharmacogenomics, SNPs, Pathways
    Mutations of the PDE6A/B/G geneshttp://www.retina-international.org/files/sci-news/pdemut.htm
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=PDE6A[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PDE6A gene:
    Search GeneIP for patents involving PDE6A

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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