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Aliases for PDE6B Gene

Aliases for PDE6B Gene

  • Phosphodiesterase 6B 2 3 5
  • Phosphodiesterase 6B, CGMP-Specific, Rod, Beta 2 3
  • GMP-PDE Beta 3 4
  • EC 3.1.4.35 4 63
  • PDEB 3 4
  • Congenital Stationary Night Blindness 3 2
  • Rod CGMP-Phosphodiesterase Beta-Subunit 3
  • Autosomal Dominant 2
  • EC 3.1.4 63
  • CSNBAD2 3
  • CSNB3 3
  • RP40 3
  • Rd1 3

External Ids for PDE6B Gene

Previous HGNC Symbols for PDE6B Gene

  • PDEB

Previous GeneCards Identifiers for PDE6B Gene

  • GC04P000610
  • GC04P000609

Summaries for PDE6B Gene

Entrez Gene Summary for PDE6B Gene

  • Photon absorption triggers a signaling cascade in rod photoreceptors that activates cGMP phosphodiesterase (PDE), resulting in the rapid hydrolysis of cGMP, closure of cGMP-gated cation channels, and hyperpolarization of the cell. PDE is a peripheral membrane heterotrimeric enzyme made up of alpha, beta, and gamma subunits. This gene encodes the beta subunit. Mutations in this gene result in retinitis pigmentosa and autosomal dominant congenital stationary night blindness. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]

GeneCards Summary for PDE6B Gene

PDE6B (Phosphodiesterase 6B) is a Protein Coding gene. Diseases associated with PDE6B include Night Blindness, Congenital Stationary, Autosomal Dominant 2 and Retinitis Pigmentosa-40. Among its related pathways are Phototransduction and Signaling by Wnt. 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 PDE6B Gene

  • This protein participates in processes of transmission and amplification of the visual signal. Necessary for the formation of a functional phosphodiesterase holoenzyme.

Tocris Summary for PDE6B 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 PDE6B Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDE6B Gene

Genomics for PDE6B Gene

Regulatory Elements for PDE6B Gene

Enhancers for PDE6B Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PDE6B on UCSC Golden Path with GeneCards custom track

Genomic Location for PDE6B Gene

Chromosome:
4
Start:
587,325 bp from pter
End:
670,892 bp from pter
Size:
83,568 bases
Orientation:
Plus strand

Genomic View for PDE6B Gene

Genes around PDE6B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDE6B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDE6B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDE6B Gene

Proteins for PDE6B Gene

  • Protein details for PDE6B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P35913-PDE6B_HUMAN
    Recommended name:
    Rod cGMP-specific 3,5-cyclic phosphodiesterase subunit beta
    Protein Accession:
    P35913
    Secondary Accessions:
    • B7Z9T9
    • E7ETT3
    • Q53XN5
    • Q9BWH5
    • Q9UD49

    Protein attributes for PDE6B Gene

    Size:
    854 amino acids
    Molecular mass:
    98336 Da
    Cofactor:
    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.

    Alternative splice isoforms for PDE6B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDE6B Gene

Proteomics data for PDE6B Gene at MOPED

Post-translational modifications for PDE6B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for PDE6B Gene

Gene Families for PDE6B Gene

Protein Domains for PDE6B Gene

Suggested Antigen Peptide Sequences for PDE6B Gene

Graphical View of Domain Structure for InterPro Entry

P35913

UniProtKB/Swiss-Prot:

PDE6B_HUMAN :
  • Contains 2 GAF domains.
  • Belongs to the cyclic nucleotide phosphodiesterase family.
Domain:
  • Contains 2 GAF domains.
Family:
  • Belongs to the cyclic nucleotide phosphodiesterase family.
genes like me logo Genes that share domains with PDE6B: view

Function for PDE6B Gene

Molecular function for PDE6B Gene

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

Enzyme Numbers (IUBMB) for PDE6B Gene

genes like me logo Genes that share phenotypes with PDE6B: view

Human Phenotype Ontology for PDE6B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

No data available for Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for PDE6B Gene

Localization for PDE6B Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDE6B Gene

Membrane; Lipid-anchor.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDE6B Gene COMPARTMENTS Subcellular localization image for PDE6B gene
Compartment Confidence
cytosol 5
plasma membrane 5
nucleus 3
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PDE6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IMP --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with PDE6B: view

Pathways & Interactions for PDE6B Gene

genes like me logo Genes that share pathways with PDE6B: view

Pathways by source for PDE6B Gene

Interacting Proteins for PDE6B Gene

Gene Ontology (GO) - Biological Process for PDE6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007223 Wnt signaling pathway, calcium modulating pathway TAS --
GO:0007603 phototransduction, visible light TAS 8394174
GO:0008152 metabolic process IEA --
GO:0016056 rhodopsin mediated signaling pathway TAS --
genes like me logo Genes that share ontologies with PDE6B: view

No data available for SIGNOR curated interactions for PDE6B Gene

Drugs & Compounds for PDE6B Gene

(9) Drugs for PDE6B Gene - From: DrugBank, ApexBio, HMDB, Tocris, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Caffeine Approved Nutra Antagonist, Target, inhibitor, competitive 349
Cilostazol Approved Pharma PDE3 inhibitor, PDE3A inhibitor. Also adenosine uptake inhibitor 101
Dipyridamole Approved Pharma Inhibition, Inhibitor Adenosine transport inhibitor 78
Cyclic GMP Experimental Pharma 0
Guanosine monophosphate Experimental Pharma 0

(5) Additional Compounds for PDE6B Gene - From: HMDB and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
Etazolate hydrochloride
35838-58-5
MMPX
78033-08-6
MY-5445
78351-75-4
Ro 20-1724
29925-17-5

(5) Tocris Compounds for PDE6B Gene

Compound Action Cas Number
Dipyridamole Adenosine transport inhibitor 58-32-2
Etazolate hydrochloride PDE4 inhibitor 35838-58-5
MMPX PDE1 inhibitor 78033-08-6
MY-5445 PDE5 inhibitor 78351-75-4
Ro 20-1724 PDE4 inhibitor 29925-17-5

(2) ApexBio Compounds for PDE6B Gene

Compound Action Cas Number
Cilostazol PDE3 inhibitor 73963-72-1
Sildenafil Citrate Treat erectile dysfunction and PAH 171599-83-0
genes like me logo Genes that share compounds with PDE6B: view

Transcripts for PDE6B Gene

mRNA/cDNA for PDE6B Gene

Alternative Splicing Database (ASD) splice patterns (SP) for PDE6B Gene

No ASD Table

Relevant External Links for PDE6B Gene

GeneLoc Exon Structure for
PDE6B
ECgene alternative splicing isoforms for
PDE6B

Expression for PDE6B Gene

mRNA expression in normal human tissues for PDE6B Gene

mRNA differential expression in normal tissues according to GTEx for PDE6B Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x6.0), Brain - Substantia nigra (x5.1), Brain - Putamen (basal ganglia) (x4.2), and Brain - Caudate (basal ganglia) (x4.1).

Protein differential expression in normal tissues from HIPED for PDE6B Gene

This gene is overexpressed in Retina (68.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PDE6B Gene



SOURCE GeneReport for Unigene cluster for PDE6B Gene Hs.623810

genes like me logo Genes that share expression patterns with PDE6B: view

Protein tissue co-expression partners for PDE6B Gene

- Elite partner

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for PDE6B Gene

Orthologs for PDE6B Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDE6B Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PDE6B 35
  • 88.43 (n)
  • 92.15 (a)
PDE6B 36
  • 85 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDE6B 35
  • 88.68 (n)
  • 91.45 (a)
PDE6B 36
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pde6b 35
  • 85.56 (n)
  • 93.33 (a)
Pde6b 16
Pde6b 36
  • 93 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pde6b 35
  • 86.03 (n)
  • 92.97 (a)
oppossum
(Monodelphis domestica)
Mammalia PDE6B 36
  • 88 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDE6B 36
  • 86 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDE6B 35
  • 76.18 (n)
  • 82.37 (a)
PDE6B 36
  • 82 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDE6B 36
  • 78 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487945 35
  • 70.56 (n)
  • 80.78 (a)
zebrafish
(Danio rerio)
Actinopterygii pde6b 35
  • 70.89 (n)
  • 76.17 (a)
pde6b 36
  • 76 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 29 (a)
OneToMany
Species with no ortholog for PDE6B:
  • 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)
  • chimpanzee (Pan troglodytes)
  • 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 PDE6B Gene

ENSEMBL:
Gene Tree for PDE6B (if available)
TreeFam:
Gene Tree for PDE6B (if available)

Paralogs for PDE6B Gene

Paralogs for PDE6B Gene

(8) SIMAP similar genes for PDE6B Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with PDE6B: view

Variants for PDE6B Gene

Sequence variations from dbSNP and Humsavar for PDE6B Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
VAR_006050 Retinitis pigmentosa 40 (RP40)
VAR_006051 Retinitis pigmentosa 40 (RP40)
VAR_006052 Retinitis pigmentosa 40 (RP40)
VAR_009283 Retinitis pigmentosa 40 (RP40)
rs115775983 - 634,704(+) CTGAC(A/G)AGCTC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for PDE6B Gene

Variant ID Type Subtype PubMed ID
nsv878245 CNV Loss 21882294
nsv508986 CNV Insertion 20534489
nsv822425 CNV Loss 20364138
nsv878246 CNV Loss 21882294
dgv1564e1 CNV Complex 17122850
nsv878247 CNV Loss 21882294
esv993737 CNV Deletion 20482838
esv29320 CNV Gain 19812545
nsv293468 CNV Loss 16902084
esv2726679 CNV Deletion 23290073
esv2726680 CNV Deletion 23290073
esv2659418 CNV Deletion 23128226
esv2726681 CNV Deletion 23290073
esv2726682 CNV Deletion 23290073
nsv4194 CNV Loss 18451855
esv2675809 CNV Deletion 23128226
esv24054 CNV Loss 19812545
dgv5387n71 CNV Loss 21882294
nsv10412 CNV Gain 18304495
esv2588771 CNV Insertion 19546169
esv1788163 CNV Insertion 17803354
dgv41n50 CNV Loss 21212237
esv24745 CNV Loss 19812545
esv1251464 CNV Deletion 17803354
esv1532305 CNV Deletion 17803354
esv1748545 CNV Deletion 17803354
esv2663678 CNV Deletion 23128226
esv2726683 CNV Deletion 23290073
nsv819707 CNV Loss 19587683

Variation tolerance for PDE6B Gene

Residual Variation Intolerance Score: 87.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.52; 64.72% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDE6B Gene

Human Gene Mutation Database (HGMD)
PDE6B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDE6B Gene

Disorders for PDE6B Gene

MalaCards: The human disease database

(18) MalaCards diseases for PDE6B Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
night blindness, congenital stationary, autosomal dominant 2
  • congenital stationary night blindness, autosomal dominant 2
retinitis pigmentosa-40
  • rp40
pde6b-related retinitis pigmentosa
  • rp40
congenital stationary night blindness
  • congenital essential nyctalopia
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search PDE6B in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PDE6B_HUMAN
  • Night blindness, congenital stationary, autosomal dominant 2 (CSNBAD2) [MIM:163500]: A non-progressive retinal disorder characterized by impaired night vision, often associated with nystagmus and myopia. {ECO:0000269 PubMed:8075643}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa 40 (RP40) [MIM:613801]: 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:22334370, ECO:0000269 PubMed:8394174, ECO:0000269 PubMed:8557257, ECO:0000269 PubMed:8595886, ECO:0000269 PubMed:8698075, ECO:0000269 PubMed:8956055, ECO:0000269 PubMed:9543643}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PDE6B

Genetic Association Database (GAD)
PDE6B
Human Genome Epidemiology (HuGE) Navigator
PDE6B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDE6B
genes like me logo Genes that share disorders with PDE6B: view

No data available for Genatlas for PDE6B Gene

Publications for PDE6B Gene

  1. [A study of PDE6B gene mutation and phenotype in Chinese cases with retinitis pigmentosa]. (PMID: 12760810) Cui Y. … Wang L.M. (Zhonghua Yan Ke Za Zhi 2003) 3 23 48 67
  2. Assignment of the beta-subunit of rod photoreceptor cGMP phosphodiesterase gene PDEB (homolog of the mouse rd gene) to human chromosome 4p16. (PMID: 1313787) Bateman J.B. … Farber D.B. (Genomics 1992) 2 3 23
  3. Identification of two new mutations in the GPR98 and the PDE6B genes segregating in a Tunisian family. (PMID: 18854872) Hmani-Aifa M. … Ayadi H. (Eur. J. Hum. Genet. 2009) 3 23
  4. [Screening gene mutations of the beta subunit of phosphodiesterase in the Chinese retinitis pigmentosa patients]. (PMID: 12778443) Cui Y. … Wang L.M. (Zhonghua Yi Xue Yi Chuan Xue Za Zhi 2003) 3 23
  5. A novel homozygous Ile535Asn mutation in the rod cGMP phosphodiesterase beta-subunit gene in two brothers of a Japanese family with autosomal recessive retinitis pigmentosa. (PMID: 9543643) Saga M. … Shimizu N. (Curr. Eye Res. 1998) 3 23

Products for PDE6B Gene

Sources for PDE6B Gene

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