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PDE6B phosphodiesterase 6B [ Homo sapiens (human) ]

Gene ID: 5158, updated on 11-Apr-2024

Summary

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Official Symbol
PDE6Bprovided by HGNC
Official Full Name
phosphodiesterase 6Bprovided by HGNC
Primary source
HGNC:HGNC:8786
See related
Ensembl:ENSG00000133256 MIM:180072; AllianceGenome:HGNC:8786
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
rd1; PDEB; RP40; CSNB3; CSNBAD2; GMP-PDEbeta
Summary
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]
Expression
Broad expression in brain (RPKM 2.0), thyroid (RPKM 1.1) and 19 other tissues See more
Orthologs
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Genomic context

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See PDE6B in Genome Data Viewer
Location:
4p16.3
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (625573..670782)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (586384..670456)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (619362..664571)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374338 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:581897-583096 Neighboring gene uncharacterized LOC124900162 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:604697-605456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:617058-618048 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:619038-620027 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:620028-621016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:628544-629044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:644363-645316 Neighboring gene PDE6B antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:657162-657754 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:668197-668954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:674515-675154 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15103 Neighboring gene ATP synthase membrane subunit e Neighboring gene solute carrier family 49 member 3 Neighboring gene myosin light chain 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A novel homozygous missense substitution p.Thr313Ile in the PDE6B gene underlies autosomal recessive retinitis pigmentosa in a consanguineous Pakistani family. Aziz N, et al. BMC Ophthalmol, 2023 Mar 23. PMID 36959549, Free PMC Article
  2. Identification of a novel large multigene deletion and a frameshift indel in PDE6B as the underlying cause of early-onset recessive rod-cone degeneration. Sangermano R, et al. Cold Spring Harb Mol Case Stud, 2022 Dec. PMID 36376065, Free PMC Article
  3. PDE6B Mutation-associated Inherited Retinal Disease. Marconi S, et al. Int Ophthalmol Clin, 2021 Oct 1. PMID 34584050
  4. Clinical Phenotype of PDE6B-Associated Retinitis Pigmentosa. Kuehlewein L, et al. Int J Mol Sci, 2021 Feb 27. PMID 33673512, Free PMC Article
  5. Clinical characteristics and disease progression of retinitis pigmentosa associated with PDE6B mutations in Korean patients. Kim YN, et al. Sci Rep, 2020 Nov 11. PMID 33177553, Free PMC Article

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A Novel Intronic Deletion in PDE6B Causes Autosomal Recessive Retinitis Pigmentosa by Interfering with RNA Splicing.
    Title: A Novel Intronic Deletion in PDE6B Causes Autosomal Recessive Retinitis Pigmentosa by Interfering with RNA Splicing.
  2. A novel homozygous missense substitution p.Thr313Ile in the PDE6B gene underlies autosomal recessive retinitis pigmentosa in a consanguineous Pakistani family.
    Title: A novel homozygous missense substitution p.Thr313Ile in the PDE6B gene underlies autosomal recessive retinitis pigmentosa in a consanguineous Pakistani family.
  3. Identification of a novel large multigene deletion and a frameshift indel in PDE6B as the underlying cause of early-onset recessive rod-cone degeneration.
    Title: Identification of a novel large multigene deletion and a frameshift indel in PDE6B as the underlying cause of early-onset recessive rod-cone degeneration.
  4. Photoreceptor Phosphodiesterase (PDE6): Structure, Regulatory Mechanisms, and Implications for Treatment of Retinal Diseases.
    Title: Photoreceptor Phosphodiesterase (PDE6): Structure, Regulatory Mechanisms, and Implications for Treatment of Retinal Diseases.
  5. Novel variants in PDE6A and PDE6B genes and its phenotypes in patients with retinitis pigmentosa in Chinese families.
    Title: Novel variants in PDE6A and PDE6B genes and its phenotypes in patients with retinitis pigmentosa in Chinese families.
  6. Clinical and genetic investigations of three Moroccan families with retinitis pigmentosa phenotypes.
    Title: Clinical and genetic investigations of three Moroccan families with retinitis pigmentosa phenotypes.
  7. PDE6B Mutation-associated Inherited Retinal Disease.
    Title: PDE6B Mutation-associated Inherited Retinal Disease.
  8. Clinical Phenotype of PDE6B-Associated Retinitis Pigmentosa.
    Title: Clinical Phenotype of PDE6B-Associated Retinitis Pigmentosa.
  9. Clinical characteristics and disease progression of retinitis pigmentosa associated with PDE6B mutations in Korean patients.
    Title: Clinical characteristics and disease progression of retinitis pigmentosa associated with PDE6B mutations in Korean patients.
  10. Mutations in PDE6A and PDE6B accounted for 1.6% and 2.4%, respectively, in a cohort of French patients with rod-cone dystrophy (RCD)
    Title: Longitudinal Clinical Follow-up and Genetic Spectrum of Patients With Rod-Cone Dystrophy Associated With Mutations in PDE6A and PDE6B.
Submit: New GeneRIF Correction See all GeneRIFs (29)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3',5'-cyclic-AMP phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 3',5'-cyclic-GMP phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cAMP-mediated signaling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in entrainment of circadian clock by photoperiod ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in phototransduction, visible light TAS
Traceable Author Statement
more info
 PubMed 
involved_in retina development in camera-type eye IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retinal cell apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in visual perception IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in photoreceptor disc membrane TAS
Traceable Author Statement
more info
  
is_active_in photoreceptor outer segment membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
Names
GMP-PDE beta
phosphodiesterase 6B, cGMP-specific, rod, beta
rod cGMP-phosphodiesterase beta-subunit
NP_000274.3
NP_001138763.2
NP_001138764.2
NP_001337083.1
NP_001337084.1
NP_001366175.1
NP_001366176.1
XP_011511775.2
XP_047271728.1
XP_047271729.1
XP_047271730.1
XP_047271731.1
XP_047271732.1
XP_047271733.1
XP_054206142.1
XP_054206143.1
XP_054206144.1
XP_054206145.1
XP_054206146.1
XP_054206147.1
XP_054206148.1
XP_054206149.1
XP_054206150.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_009839.2 RefSeqGene

    Range
    5002..50211
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000283.4 → NP_000274.3  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC107464
    Consensus CDS
    CCDS33932.1
    UniProtKB/Swiss-Prot
    B7Z9T9, E7ETT3, P35913, Q53XN5, Q9BWH5, Q9UD49
    Related
    ENSP00000420295.1, ENST00000496514.6
    Conserved Domains (2) summary
    smart00065
    Location:71 → 230
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:556 → 800
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  2. NM_001145291.2 → NP_001138763.2  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks one amino acid near the C-terminus, compared to isoform 1.
    Source sequence(s)
    AC107464
    Consensus CDS
    CCDS54703.1
    Related
    ENSP00000255622.6, ENST00000255622.10
    Conserved Domains (2) summary
    smart00065
    Location:71 → 230
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:556 → 801
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  3. NM_001145292.2 → NP_001138764.2  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents use of an alternate promoter and 5' UTR, and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a substantially shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC107464
    Consensus CDS
    CCDS46993.1
    UniProtKB/TrEMBL
    B4DHV7
    Related
    ENSP00000406334.2, ENST00000429163.6
    Conserved Domains (2) summary
    smart00065
    Location:52 → 160
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:277 → 522
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  4. NM_001350154.3 → NP_001337083.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) represents the use of an alternate promoter. It differs in the 5' UTR, uses a downstream start codon and contains multiple coding region differences, compared to variant 1. It encodes isoform 4, which is shorter than isoform 1.
    Source sequence(s)
    AC107464
    UniProtKB/TrEMBL
    B4DHV7
    Conserved Domains (2) summary
    smart00065
    Location:52 → 160
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:277 → 517
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  5. NM_001350155.3 → NP_001337084.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) represents the use of an alternate promoter. It differs in the 5' UTR, uses a downstream start codon and contains multiple coding region differences, resulting in a frameshift and an early stop codon, compared to variant 1. It encodes isoform 5, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC107464
    Conserved Domains (2) summary
    smart00065
    Location:1 → 54
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:171 → 411
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  6. NM_001379246.1 → NP_001366175.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC107464
    Consensus CDS
    CCDS46993.1
    UniProtKB/TrEMBL
    B4DHV7
    Conserved Domains (2) summary
    smart00065
    Location:52 → 160
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:277 → 522
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  7. NM_001379247.1 → NP_001366176.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC107464
    Consensus CDS
    CCDS46993.1
    UniProtKB/TrEMBL
    B4DHV7
    Conserved Domains (2) summary
    smart00065
    Location:52 → 160
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:277 → 522
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    625573..670782
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047415773.1 → XP_047271729.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X2

  2. XM_047415772.1 → XP_047271728.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X1

  3. XM_011513473.4 → XP_011511775.2  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X3

  4. XM_047415774.1 → XP_047271730.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X4

  5. XM_047415775.1 → XP_047271731.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X5

  6. XM_047415776.1 → XP_047271732.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X5

  7. XM_047415777.1 → XP_047271733.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    586384..670456
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350168.1 → XP_054206143.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X7

  2. XM_054350167.1 → XP_054206142.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X6

  3. XM_054350171.1 → XP_054206146.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X9

  4. XM_054350170.1 → XP_054206145.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X8

  5. XM_054350172.1 → XP_054206147.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X10

  6. XM_054350169.1 → XP_054206144.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X1

  7. XM_054350173.1 → XP_054206148.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X5

  8. XM_054350174.1 → XP_054206149.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X5

  9. XM_054350175.1 → XP_054206150.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X5

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P35913.2 GenPept UniProtKB/Swiss-Prot:P35913

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