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PDE6H Gene(Protein Coding)

Phosphodiesterase 6H

GCID:
GC12P014980
GIFtS:
60
Genes Participants
UDN Logo

Aliases for PDE6H Gene

Aliases for PDE6H Gene

  • Phosphodiesterase 6H 2 3 5
  • Phosphodiesterase 6H, CGMP-Specific, Cone, Gamma 2 3
  • GMP-PDE Gamma 3 4
  • Retinal Cone Rhodopsin-Sensitive CGMP 3,5-Cyclic Phosphodiesterase Subunit Gamma 3
  • EC 3.1.4.17 61
  • EC 3.1.4.35 4
  • ACHM6 3
  • RCD3 3

External Ids for PDE6H Gene

Previous GeneCards Identifiers for PDE6H Gene

  • GC12P014865
  • GC12P015270
  • GC12P015026
  • GC12P015017
  • GC12P015125
  • GC12P014975
  • GC12P014976
  • GC12P014977
  • GC12P014978
  • GC12P014979

Summaries for PDE6H Gene

Entrez Gene Summary for PDE6H Gene

  • This gene encodes the inhibitory (or gamma) subunit of the cone-specific cGMP phosphodiesterase, which is a tetramer composed of two catalytic chains (alpha and beta), and two inhibitory chains (gamma). It is specifically expressed in the retina, and is involved in the transmission and amplification of the visual signal. Mutations in this gene are associated with retinal cone dystrophy type 3A (RCD3A). [provided by RefSeq, Mar 2010]

GeneCards Summary for PDE6H Gene

PDE6H (Phosphodiesterase 6H) is a Protein Coding gene. Diseases associated with PDE6H include Retinal Cone Dystrophy 3 and Achromatopsia. Among its related pathways are Phototransduction and Purine metabolism (KEGG). GO annotations related to this gene include enzyme inhibitor activity and cGMP binding. An important paralog of this gene is PDE6G.

UniProtKB/Swiss-Prot for PDE6H Gene

  • Participates in processes of transmission and amplification of the visual signal. cGMP-PDEs are the effector molecules in G-protein-mediated phototransduction in vertebrate rods and cones.

Tocris Summary for PDE6H 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.

No data available for CIViC summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDE6H Gene

Genomics for PDE6H Gene

Products:

  1. Regulatory Element

Regulatory Elements for PDE6H Gene

Enhancers for PDE6H 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
GH12G014945 1.9 FANTOM5 Ensembl ENCODE dbSUPER 16.1 -17.7 -17709 19.1 HDGF PKNOX1 ATF1 FOXA2 WRNIP1 SIN3A YBX1 YY1 ZNF766 GATA2 ARHGDIB ERP27 PDE6H WBP11 ART4 HIST4H4 H2AFJ SMCO3 C12orf60 ENSG00000256339
GH12G014883 1 Ensembl ENCODE 15.6 -88.1 -88051 3.2 PKNOX1 NFIB CTBP1 GATA3 GATA2 CBX5 POLR2A RCOR1 IKZF2 MTA2 ENSG00000256339 ERP27 PDE6H ART4 SMCO3 ARHGDIB H2AFJ HIST4H4 WBP11 C12orf60
GH12G014937 1.1 Ensembl ENCODE dbSUPER 10.9 -34.5 -34543 2.7 CTCF RAD21 EP300 MAFF SMC3 ZNF143 BCL6 MAFK SPI1 ERP27 ARHGDIB PDE6H HIST4H4 ENSG00000256339 MGP C12orf60 GC12M014903
GH12G014896 1 Ensembl ENCODE 9.6 -76.3 -76310 1.3 TAL1 FOSL1 TCF12 ZNF316 GATA2 NCOR1 FOS NFE2 TRIM24 CEBPB ERP27 ART4 SMCO3 ENSG00000256339 PDE6H GC12M014889 GC12M014903
GH12G014927 0.9 Ensembl ENCODE 10.2 -44.0 -44048 2.4 STAT1 ZSCAN4 ZHX2 DPF2 RAD21 ZNF217 JUND GATA3 CTBP1 RCOR1 ERP27 MGP C12orf60 ARHGDIB PDE6H ENSG00000256339 GC12M014903
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDE6H on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the PDE6H gene promoter:

Genomic Location for PDE6H Gene

Chromosome:
12
Start:
14,973,022 bp from pter
End:
14,981,865 bp from pter
Size:
8,844 bases
Orientation:
Plus strand

Genomic View for PDE6H Gene

Genes around PDE6H on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDE6H Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDE6H Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PDE6H Gene

Proteins for PDE6H Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for PDE6H Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13956-CNCG_HUMAN
    Recommended name:
    Retinal cone rhodopsin-sensitive cGMP 3,5-cyclic phosphodiesterase subunit gamma
    Protein Accession:
    Q13956
    Secondary Accessions:
    • Q52LY7

    Protein attributes for PDE6H Gene

    Size:
    83 amino acids
    Molecular mass:
    9074 Da
    Quaternary structure:
    • Tetramer composed of two catalytic chains (alpha and beta), and two inhibitory chains (gamma).

neXtProt entry for PDE6H Gene

Selected DME Specific Peptides for PDE6H Gene

Q13956:
  • TPRKGPPKFKQRQTRQFKSKPPKKGV
  • HLELHELAQ
  • GFGDDIPGMEGLGTDITVICPWEAF

Post-translational modifications for PDE6H Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDE6H Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for PDE6H Gene

Gene Families for PDE6H Gene

HGNC:
IUPHAR :

Protein Domains for PDE6H Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PDE6H Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q13956

UniProtKB/Swiss-Prot:

CNCG_HUMAN :
  • The C-terminal region is important in conferring inhibition.
  • Belongs to the rod/cone cGMP-PDE gamma subunit family.
Domain:
  • The C-terminal region is important in conferring inhibition.
Family:
  • Belongs to the rod/cone cGMP-PDE gamma subunit family.
genes like me logo Genes that share domains with PDE6H: view

Function for PDE6H Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for PDE6H Gene

GENATLAS Biochemistry:
cGMP specific nucleotide phosphodiesterase,gamma subunit,cone phosphoreceptor
UniProtKB/Swiss-Prot CatalyticActivity:
Guanosine 3,5-cyclic phosphate + H(2)O = guanosine 5-phosphate.
UniProtKB/Swiss-Prot Function:
Participates in processes of transmission and amplification of the visual signal. cGMP-PDEs are the effector molecules in G-protein-mediated phototransduction in vertebrate rods and cones.

Enzyme Numbers (IUBMB) for PDE6H Gene

Gene Ontology (GO) - Molecular Function for PDE6H Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004114 3,5-cyclic-nucleotide phosphodiesterase activity IEA --
GO:0004857 enzyme inhibitor activity TAS 8786098
GO:0005515 protein binding IPI 25416956
GO:0016787 hydrolase activity IEA --
GO:0030553 cGMP binding IEA --
genes like me logo Genes that share ontologies with PDE6H: view
genes like me logo Genes that share phenotypes with PDE6H: view

Human Phenotype Ontology for PDE6H Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PDE6H Gene

MGI Knock Outs for PDE6H:

Animal Model Products

CRISPR Products

miRNA for PDE6H Gene

miRTarBase miRNAs that target PDE6H

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Transcription Factor Targets and HOMER Transcription for PDE6H Gene

Localization for PDE6H Gene

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 PDE6H gene
Compartment Confidence
nucleus 2
cytosol 2
mitochondrion 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for PDE6H Gene

Pathways & Interactions for PDE6H Gene

genes like me logo Genes that share pathways with PDE6H: view

Pathways by source for PDE6H Gene

1 BioSystems pathway for PDE6H Gene
1 KEGG pathway for PDE6H Gene

Gene Ontology (GO) - Biological Process for PDE6H Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000187 activation of MAPK activity IEA --
GO:0007601 visual perception TAS,IEA --
GO:0043086 negative regulation of catalytic activity IEA --
GO:0045742 positive regulation of epidermal growth factor receptor signaling pathway IEA --
GO:0045745 positive regulation of G-protein coupled receptor protein signaling pathway IEA --
genes like me logo Genes that share ontologies with PDE6H: view

No data available for SIGNOR curated interactions for PDE6H Gene

Drugs & Compounds for PDE6H Gene

Products:

  1. Drug

(11) Drugs for PDE6H Gene - From: DrugBank, HMDB, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vardenafil Approved Pharma Target, allosteric modulator PDE5 inhibitor 0
Sildenafil Approved, Investigational Pharma Inhibition, Inhibitor, Target, inhibitor PDE5 inhibitor, selective 0
Water Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
cyclic amp Experimental Pharma 0

(1) Additional Compounds for PDE6H Gene - From: Tocris

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

(5) Tocris Compounds for PDE6H 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 PDE6H: view

Transcripts for PDE6H Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for PDE6H Gene

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

Unigene Clusters for PDE6H Gene

Phosphodiesterase 6H, cGMP-specific, cone, gamma:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDE6H Gene

No ASD Table

Relevant External Links for PDE6H Gene

GeneLoc Exon Structure for
PDE6H
ECgene alternative splicing isoforms for
PDE6H

Expression for PDE6H Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDE6H Gene

mRNA expression in normal human tissues for PDE6H Gene
mRNA expression by BioGPS for PDE6H GenemRNA expression by GTEx for PDE6H Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDE6H Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x7.7), Brain - Cortex (x6.8), Whole Blood (x6.0), and Brain - Anterior cingulate cortex (BA24) (x4.6).

NURSA nuclear receptor signaling pathways regulating expression of PDE6H Gene:

PDE6H

SOURCE GeneReport for Unigene cluster for PDE6H Gene:

Hs.54471

Evidence on tissue expression from TISSUES for PDE6H Gene

  • Eye(4.5)
  • Nervous system(4.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDE6H Gene

Germ Layers:
  • ectoderm
Systems:
  • nervous
Organs:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • eyelid
  • head
General:
  • peripheral nervous system
genes like me logo Genes that share expression patterns with PDE6H: view

Primer Products

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for PDE6H Gene

Orthologs for PDE6H Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDE6H Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PDE6H 34 35
  • 99.2 (n)
dog
(Canis familiaris)
 Mammalia PDE6H 34 35
  • 90.76 (n)
oppossum
(Monodelphis domestica)
 Mammalia PDE6H 35
  • 90 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia PDE6H 34 35
  • 88.76 (n)
rat
(Rattus norvegicus)
 Mammalia Pde6h 34
  • 85.94 (n)
mouse
(Mus musculus)
 Mammalia Pde6h 34 16 35
  • 85.54 (n)
chicken
(Gallus gallus)
 Aves PDE6H 34 35
  • 80.32 (n)
lizard
(Anolis carolinensis)
 Reptilia PDE6H 35
  • 81 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia pde6h 34
  • 76.89 (n)
zebrafish
(Danio rerio)
 Actinopterygii zgc:112320 35
  • 70 (a)
 ManyToMany
zgc:73359 34
  • 67.08 (n)
Species where no ortholog for PDE6H 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 PDE6H Gene

ENSEMBL:
Gene Tree for PDE6H (if available)
TreeFam:
Gene Tree for PDE6H (if available)

Paralogs for PDE6H Gene

Paralogs for PDE6H Gene

(1) SIMAP similar genes for PDE6H Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PDE6H: view

Variants for PDE6H Gene

Sequence variations from dbSNP and Humsavar for PDE6H Gene

SNP ID Clin Chr 12 pos Sequence Context AA Info Type
rs200311463 Pathogenic 14,978,047(+) AGCTT(C/G)AAACC intron-variant, reference, stop-gained
rs114575851 Likely benign 14,977,984(+) AAAGG(C/G)AAACA intron-variant, utr-variant-5-prime
rs3748304 Likely benign 14,981,795(+) AATAG(C/T)AGACT intron-variant, utr-variant-3-prime
rs77796036 Likely benign 14,981,777(+) TAGGC(A/G)TTCAT intron-variant, utr-variant-3-prime
rs144778897 Uncertain significance 14,981,547(+) TCTGC(C/T)GGAGT intron-variant, utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for PDE6H Gene

Variant ID Type Subtype PubMed ID
dgv1394n100 CNV gain 25217958
esv3628659 CNV gain 21293372
nsv951333 CNV duplication 24416366

Variation tolerance for PDE6H Gene

Residual Variation Intolerance Score: 59.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.42; 9.24% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDE6H Gene

Human Gene Mutation Database (HGMD)
PDE6H
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDE6H

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDE6H Gene

Disorders for PDE6H Gene

MalaCards: The human disease database

(5) MalaCards diseases for PDE6H Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
retinal cone dystrophy 3
  • achromatopsia 6
achromatopsia
  • achm
cone dystrophy
  • retinal cone dystrophy
cone dystrophy-3
  • cone-rod dystrophy 14
color blindness
  • blindness color
- elite association - COSMIC cancer census association via MalaCards
Search PDE6H in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CNCG_HUMAN
  • Cone dystrophy, retinal 3A (RCD3A) [MIM:610024]: A rare form of cone dystrophy associated with supernormal rod responses. The disorder is characterized by reduced visual acuity, photoaversion, night blindness, and abnormal color vision. At an early age, the retina shows subtle depigmentation at the macula and, later, more obvious areas of atrophy. {ECO:0000269 PubMed:15629837}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PDE6H

Genetic Association Database (GAD)
PDE6H
Human Genome Epidemiology (HuGE) Navigator
PDE6H
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDE6H
genes like me logo Genes that share disorders with PDE6H: view

No data available for Genatlas for PDE6H Gene

Publications for PDE6H Gene

  1. Isolation and chromosomal localization of the human cone cGMP phosphodiesterase gamma cDNA (PDE6H). (PMID: 8786098) Shimizu-Matsumoto A. … Okubo K. (Genomics 1996) 2 3 4 22 64
  2. A substitution of G to C in the cone cGMP-phosphodiesterase gamma subunit gene found in a distinctive form of cone dystrophy. (PMID: 15629837) Piri N. … Farber D.B. (Ophthalmology 2005) 3 4 22 64
  3. 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
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T. … Vidal M. (Cell 2014) 3 64

Products for PDE6H Gene

Sources for PDE6H Gene

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