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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 4 61
  • PDEB 3 4
  • Congenital Stationary Night Blindness 3, Autosomal Dominant 2
  • Rod CGMP-Specific 3,5-Cyclic Phosphodiesterase Subunit Beta 3
  • Rod CGMP-Phosphodiesterase Beta-Subunit 3
  • EC 3.1.4 61
  • 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 Metabolism of fat-soluble vitamins and Phototransduction. 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 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
GH04F001176 1.4 FANTOM5 Ensembl ENCODE 12 +590.8 590818 2.5 CBX3 THRB RAD21 ZNF48 YY1 GATA2 TBX21 ZNF623 KLF16 SMARCA4 ENSG00000251188 PDE6B CRIPAK ZNF732 RNF212 ENSG00000251639 DGKQ UVSSA GAK ENSG00000273179
GH04F001512 1.2 Ensembl ENCODE 12 +925.7 925739 1.6 ZNF76 YBX1 NFXL1 RAD21 GLIS2 ZNF302 ZNF416 ZNF207 ZNF548 RCOR1 HAUS3 MIR943 CTBP1-AS2 CRIPAK ENSG00000272588 LOC100129917 IDUA PDE6B ENSG00000270195 GC04M001514
GH04F000212 0.6 ENCODE 12 -374.5 -374507 1.6 PKNOX1 CREB3L1 TSC22D4 YBX1 POLR2H POLR2A TARDBP PBX2 ZFX ZNF718 PDE6B ZNF876P PIR59219 GC04P000228 GC04P000229 GC04P000230
GH04F001184 0.6 Ensembl 12 +595.8 595776 0.2 BCOR ZNF366 TARDBP TSC22D4 YBX1 ZNF24 THRB PDE6B ENSG00000251639 ENSG00000273179 LOC101928548
GH04F001045 1.1 Ensembl ENCODE 5.3 +459.7 459716 2.3 HDGF ATF1 PKNOX1 GLIS2 HDAC8 CREB3 ZNF589 MYNN IKZF1 ZNF341 ENSG00000251639 CRIPAK UVSSA PDE6B RNF212 SLBP CTBP1-AS2 LETM1 MAEA PCGF3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PDE6B on UCSC Golden Path with GeneCards custom track

Genomic Location for PDE6B Gene

587,325 bp from pter
670,892 bp from pter
83,568 bases
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:
    Recommended name:
    Rod cGMP-specific 3,5-cyclic phosphodiesterase subunit beta
    Protein Accession:
    Secondary Accessions:
    • B7Z9T9
    • E7ETT3
    • Q53XN5
    • Q9BWH5
    • Q9UD49

    Protein attributes for PDE6B Gene

    854 amino acids
    Molecular mass:
    98336 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.

    Alternative splice isoforms for PDE6B Gene


neXtProt entry for PDE6B Gene

Selected DME Specific Peptides for PDE6B Gene


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



  • Contains 2 GAF domains.
  • Belongs to the cyclic nucleotide phosphodiesterase family.
  • Contains 2 GAF domains.
  • 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

Gene Ontology (GO) - Molecular Function for PDE6B 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:0046872 metal ion binding IEA --
GO:0047555 3,5-cyclic-GMP phosphodiesterase activity IMP 19946729
genes like me logo Genes that share ontologies with PDE6B: view
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 Models for PDE6B Gene

MGI Knock Outs for PDE6B:

Animal Model Products

Flow Cytometry Products

No data available for 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

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 PDE6B gene
Compartment Confidence
plasma membrane 5
nucleus 3
cytosol 3
extracellular 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PDE6B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0097381 photoreceptor disc membrane TAS --
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

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:0007601 visual perception IEA,TAS --
GO:0007603 phototransduction, visible light TAS 8394174
GO:0009583 detection of light stimulus IEA --
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Caffeine Approved Nutra Antagonist, Target, inhibitor, competitive A1 and A2B antagonist. CNS stimulant 380
Cilostazol Approved Pharma PDE3 inhibitor 103
Cafcit Injection Approved September 1999 Pharma 0
Water Approved Pharma 0
Cyclic GMP Experimental Pharma 0

(1) Additional Compounds for PDE6B Gene - From: Tocris

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

(5) Tocris Compounds for PDE6B 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

(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

Flow Cytometry Products

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

No ASD Table

Relevant External Links for PDE6B Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDE6B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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

Protein tissue co-expression partners for PDE6B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDE6B Gene:


SOURCE GeneReport for Unigene cluster for PDE6B Gene:

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

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
(Canis familiaris)
Mammalia PDE6B 34 35
  • 88.68 (n)
(Bos Taurus)
Mammalia PDE6B 34 35
  • 88.43 (n)
(Monodelphis domestica)
Mammalia PDE6B 35
  • 88 (a)
(Rattus norvegicus)
Mammalia Pde6b 34
  • 86.03 (n)
(Ornithorhynchus anatinus)
Mammalia PDE6B 35
  • 86 (a)
(Mus musculus)
Mammalia Pde6b 34 16 35
  • 85.56 (n)
(Gallus gallus)
Aves PDE6B 34 35
  • 76.18 (n)
(Anolis carolinensis)
Reptilia PDE6B 35
  • 78 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100487945 34
  • 70.56 (n)
(Danio rerio)
Actinopterygii pde6b 34 35
  • 70.89 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 29 (a)
Species where no ortholog for PDE6B 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)
  • 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

Gene Tree for PDE6B (if available)
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
rs121918581 Retinitis pigmentosa 40 (RP40) [MIM:613801], Pathogenic 662,188(+) CCTAC(C/T)ACAAC reference, missense
rs121918582 Night blindness, congenital stationary, autosomal dominant 2 (CSNBAD2) [MIM:163500], Pathogenic 653,912(+) AGTTC(A/C)ACAAG nc-transcript-variant, reference, missense, utr-variant-5-prime
rs141563823 Retinitis pigmentosa 40 (RP40) [MIM:613801] 666,588(+) TCATC(A/G)ACTTC reference, missense
rs144590560 Retinitis pigmentosa 40 (RP40) [MIM:613801] 625,846(+) TGGAG(C/T)GCGTG reference, missense
rs527236088 Retinitis pigmentosa 40 (RP40) [MIM:613801], Pathogenic 660,603(+) CCAGA(A/T)CCCCC reference, missense

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

Variant ID Type Subtype PubMed ID
esv24054 CNV loss 19812545
esv1788163 CNV insertion 17803354
esv1748545 CNV deletion 17803354
esv1532305 CNV deletion 17803354
esv1251464 CNV deletion 17803354
dgv41n50 CNV loss 21212237
dgv2911e59 CNV duplication 20981092
nsv293468 CNV deletion 16902084
nsv1139201 CNV deletion 24896259
nsv1133570 CNV deletion 24896259
nsv10412 CNV gain 18304495
esv993737 CNV deletion 20482838
esv3599376 CNV gain 21293372
esv3599375 CNV loss 21293372
esv3563217 CNV deletion 23714750
esv29320 CNV gain 19812545
esv2831458 CNV deletion 24192839
esv2759217 CNV loss 17122850
esv2726683 CNV deletion 23290073
esv2726682 CNV deletion 23290073
esv2726681 CNV deletion 23290073
esv2726680 CNV deletion 23290073
esv2726679 CNV deletion 23290073
esv2675809 CNV deletion 23128226
esv2663678 CNV deletion 23128226
esv2659418 CNV deletion 23128226
esv2588771 CNV insertion 19546169
esv24745 CNV loss 19812545
nsv950325 CNV deletion 24416366
nsv822425 CNV loss 20364138
nsv819707 CNV loss 19587683
nsv593207 CNV loss 21841781
nsv593206 CNV loss 21841781
nsv593205 CNV loss 21841781
nsv508986 CNV insertion 20534489
nsv4194 CNV deletion 18451855

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for PDE6B Gene

MalaCards: The human disease database

(25) 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
  • retinitis pigmentosa 40
pde6b-related retinitis pigmentosa
  • retinitis pigmentosa 40
retinitis pigmentosa
  • retinitis pigmentosa 1
rhyns syndrome
  • retinitis pigmentosa syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PDE6B in MalaCards View complete list of genes associated with diseases


  • 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)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 22 46 64
  2. [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 22 46 64
  3. 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 4 22 64
  4. A novel mutation in exon 17 of the beta-subunit of rod phosphodiesterase in two RP sisters of a consanguineous family. (PMID: 8557257) Valverde D. … Baiget M. (Hum. Genet. 1996) 3 4 22 64
  5. Screening of the PDE6B gene in patients with autosomal dominant retinitis pigmentosa. (PMID: 8698075) Gao Y.Q. … Farber D.B. (Exp. Eye Res. 1996) 3 4 22 64

Products for PDE6B Gene

Sources for PDE6B Gene

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