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PDE6G phosphodiesterase 6G [ Homo sapiens (human) ]

Gene ID: 5148, updated on 5-Mar-2024

Summary

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Official Symbol
PDE6Gprovided by HGNC
Official Full Name
phosphodiesterase 6Gprovided by HGNC
Primary source
HGNC:HGNC:8789
See related
Ensembl:ENSG00000185527 MIM:180073; AllianceGenome:HGNC:8789
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
PDEG; RP57
Summary
This gene encodes the gamma subunit of cyclic GMP-phosphodiesterase, which is composed of alpha- and beta- catalytic subunits and two identical, inhibitory gamma subunits. This gene is expressed in rod photoreceptors and functions in the phototransduction signaling cascade. It is also expressed in a variety of other tissues, and has been shown to regulate the c-Src protein kinase and G-protein-coupled receptor kinase 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2009]
Expression
Biased expression in spleen (RPKM 3.3), lymph node (RPKM 1.9) and 12 other tissues See more
Orthologs
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Genomic context

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Location:
17q25.3
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (81650459..81663127, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (82567389..82580038, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (79617489..79630157, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904085 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79525737-79526238 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:79526239-79526738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12972 Neighboring gene NPL4 homolog, ubiquitin recognition factor Neighboring gene ReSE screen-validated silencer GRCh37_chr17:79537592-79537800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12974 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79585853-79586396 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:79586397-79586940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9140 Neighboring gene tetraspanin 10 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79630511-79631145 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12975 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79632831-79633752 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:79633753-79634674 Neighboring gene coiled-coil domain containing 137 Neighboring gene oxidoreductase like domain containing 1

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. Phosphodiesterase 6 subunits are expressed and altered in idiopathic pulmonary fibrosis. Nikolova S, et al. Respir Res, 2010 Oct 27. PMID 20979602, Free PMC Article
  2. Autosomal-recessive early-onset retinitis pigmentosa caused by a mutation in PDE6G, the gene encoding the gamma subunit of rod cGMP phosphodiesterase. Dvir L, et al. Am J Hum Genet, 2010 Aug 13. PMID 20655036, Free PMC Article
  3. Determinants for phosphodiesterase 6 inhibition by its gamma-subunit. Zhang Z, et al. Biochemistry, 2010 May 11. PMID 20397626, Free PMC Article
  4. Physical and genetic localization of the gamma subunit of the cyclic GMP phosphodiesterase on the long arm of chromosome 17 (17q25). Dollfus H, et al. Genomics, 1993 Aug. PMID 8406511
  5. Evaluation of the gene encoding the gamma subunit of rod phosphodiesterase in retinitis pigmentosa. Hahn LB, et al. Invest Ophthalmol Vis Sci, 1994 Mar. PMID 8125719

See all (29) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Collectively, we report previously unrecognized PDE6 expression in human lungs, significant alterations of the PDE6D and PDE6G/H subunits in IPF lungs.
    Title: Phosphodiesterase 6 subunits are expressed and altered in idiopathic pulmonary fibrosis.
  2. These findings demonstrate the positive role of the gamma subunit in maintaining phosphodiesterase activity and confirm the contribution of PDE6G to the etiology of retinitis pigmentosa in humans.
    Title: Autosomal-recessive early-onset retinitis pigmentosa caused by a mutation in PDE6G, the gene encoding the gamma subunit of rod cGMP phosphodiesterase.
  3. The C-terminus of PED gamma occludes the active site of PDE6, thereby preventing hydrolysis of cGMP.
    Title: Determinants for phosphodiesterase 6 inhibition by its gamma-subunit.
  4. Crystal structures of a chimaeric PDE5/PDE6 catalytic domain (PDE5/6cd) complexed with sildenafil or 3-isobutyl-1-methylxanthine and the Pgamma-inhibitory peptide Pgamma(70-87) have been determined at 2.9 and 3.0 A, respectively.
    Title: Structural basis of phosphodiesterase 6 inhibition by the C-terminal region of the gamma-subunit.
  5. PDEG functions to link c-Src and G-protein-coupled receptor kinase 2 in a signaling unit that regulates p42/p44 mitogen-activated protein kinase by epidermal growth factor
    Title: The inhibitory gamma subunit of the type 6 retinal cGMP phosphodiesterase functions to link c-Src and G-protein-coupled receptor kinase 2 in a signaling unit that regulates p42/p44 mitogen-activated protein kinase by epidermal growth factor.
Submit: New GeneRIF Correction

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

Associated conditions

Description Tests
Retinitis pigmentosa
MedGen: C0035334 OMIM: 268000 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
Compare labs
Retinitis pigmentosa 57
MedGen: C3150821 OMIM: 613582 GeneReviews: Not available
Compare labs

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

Clone Names

  • MGC125749, DKFZp686C0587

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3',5'-cyclic-GMP phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
  
enables cGMP binding IEA
Inferred from Electronic Annotation
more info
  
enables enzyme inhibitor activity TAS
Traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables spectrin binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in positive regulation of G protein-coupled receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of MAPK cascade IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of epidermal growth factor receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in response to stimulus 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
retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
Names
GMP-PDE gamma
phosphodiesterase 6G, cGMP-specific, rod, gamma
rod cG-PDE G
NP_001352653.1
NP_001352654.1
NP_002593.1
XP_016880225.1
XP_054172375.1

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_009834.2 RefSeqGene

    Range
    11877..17960
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001365724.1 → NP_001352653.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 3, and 4 all encode the same protein.
    Source sequence(s)
    AC139530, EL945892
    Consensus CDS
    CCDS11783.1
    UniProtKB/Swiss-Prot
    P18545, Q3KP63, Q7Z3U8
    Related
    ENSP00000458167.1, ENST00000571224.5
    Conserved Domains (1) summary
    pfam04868
    Location:5 → 87
    PDE6_gamma; Retinal cGMP phosphodiesterase, gamma subunit

  2. NM_001365725.1 → NP_001352654.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 3, and 4 all encode the same protein.
    Source sequence(s)
    AC139530
    Consensus CDS
    CCDS11783.1
    UniProtKB/Swiss-Prot
    P18545, Q3KP63, Q7Z3U8
    Related
    ENSP00000461464.1, ENST00000571004.1
    Conserved Domains (1) summary
    pfam04868
    Location:5 → 87
    PDE6_gamma; Retinal cGMP phosphodiesterase, gamma subunit

  3. NM_002602.4 → NP_002593.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma

    See identical proteins and their annotated locations for NP_002593.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 3, and 4 all encode the same protein.
    Source sequence(s)
    AC139530, BC106884, BQ639132, BX647779
    Consensus CDS
    CCDS11783.1
    UniProtKB/Swiss-Prot
    P18545, Q3KP63, Q7Z3U8
    Related
    ENSP00000328412.5, ENST00000331056.10
    Conserved Domains (1) summary
    pfam04868
    Location:5 → 87
    PDE6_gamma; Retinal cGMP phosphodiesterase, gamma subunit

RNA

  1. NR_026872.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC139530, BX647779
    Related
    ENST00000574024.1

  2. NR_158591.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' end compared to variant 1. This variant (2) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
    Source sequence(s)
    AC139530, BM685565, EL945892

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    81650459..81663127 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017024736.2 → XP_016880225.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma isoform X1

    UniProtKB/Swiss-Prot
    P18545, Q3KP63, Q7Z3U8
    Conserved Domains (1) summary
    pfam04868
    Location:5 → 87
    PDE6_gamma; Retinal cGMP phosphodiesterase, gamma subunit

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    82567389..82580038 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316400.1 → XP_054172375.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma isoform X1

    UniProtKB/Swiss-Prot
    P18545, Q3KP63, Q7Z3U8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P18545.1 GenPept UniProtKB/Swiss-Prot:P18545

Gene LinkOut

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