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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
    mouse all
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    Genomic context

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    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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