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PDE6H phosphodiesterase 6H [ Homo sapiens (human) ]

Gene ID: 5149, updated on 5-Mar-2024

Summary

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Official Symbol
PDE6Hprovided by HGNC
Official Full Name
phosphodiesterase 6Hprovided by HGNC
Primary source
HGNC:HGNC:8790
See related
Ensembl:ENSG00000139053 MIM:601190; AllianceGenome:HGNC:8790
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
RCD3; ACHM6
Summary
This gene encodes the inhibitory (or gamma) subunit of the cone-specific cGMP phosphodiesterase, which is a tetramer composed of two catalytic chains (alpha and beta), and two inhibitory chains (gamma). It is specifically expressed in the retina, and is involved in the transmission and amplification of the visual signal. Mutations in this gene are associated with retinal cone dystrophy type 3A (RCD3A). [provided by RefSeq, Mar 2010]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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Location:
12p12.3
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (14973042..14981865)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (14850375..14859197)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (15125976..15134799)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6059 Neighboring gene endoplasmic reticulum protein 27 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6060 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr12:15103381-15104580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6061 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6062 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6063 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6064 Neighboring gene Rho GDP dissociation inhibitor beta Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4277 Neighboring gene long intergenic non-protein coding RNA 1489 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:15191267-15191767 Neighboring gene RERG intronic transcript 1 Neighboring gene RAS like estrogen regulated growth inhibitor

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 nonsense mutation in PDE6H causes autosomal-recessive incomplete achromatopsia. Kohl S, et al. Am J Hum Genet, 2012 Sep 7. PMID 22901948, Free PMC Article
  2. A substitution of G to C in the cone cGMP-phosphodiesterase gamma subunit gene found in a distinctive form of cone dystrophy. Piri N, et al. Ophthalmology, 2005 Jan. PMID 15629837
  3. Isolation and chromosomal localization of the human cone cGMP phosphodiesterase gamma cDNA (PDE6H). Shimizu-Matsumoto A, et al. Genomics, 1996 Feb 15. PMID 8786098
  4. A phosphodiesterase inhibitor specific to a subset of bovine retinal cones. Hamilton SE, et al. J Biol Chem, 1990 Jul 5. PMID 2162841
  5. Three-dimensional structure of non-activated cGMP phosphodiesterase 6 and comparison of its image with those of activated forms. Kajimura N, et al. J Struct Biol, 2002 Jul. PMID 12372317

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. These findings add PDE6H to the set of genes involved in autosomal-recessive cone disorders and demonstrate the importance of the inhibitory gamma subunit in cone phototransduction
    Title: A nonsense mutation in PDE6H causes autosomal-recessive incomplete achromatopsia.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. Our results indicate that mutations in the PDE6H gene are not common, because only 1 of 240 patients with cone dystrophy showed a single nucleotide substitution in the 5' UTR of PDE6H mRNA
    Title: A substitution of G to C in the cone cGMP-phosphodiesterase gamma subunit gene found in a distinctive form of cone dystrophy.
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
Achromatopsia
MedGen: C0152200 GeneReviews: Achromatopsia
Compare labs
Retinal cone dystrophy 3A
MedGen: C1864900 OMIM: 610024 GeneReviews: Achromatopsia
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

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 
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
is_active_in photoreceptor outer segment membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
retinal cone rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma
Names
GMP-PDE gamma
phosphodiesterase 6H, cGMP-specific, cone, gamma
NP_006196.1

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_016859.1 RefSeqGene

    Range
    5021..13844
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_006205.3 → NP_006196.1  retinal cone rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit gamma

    See identical proteins and their annotated locations for NP_006196.1

    Status: REVIEWED

    Source sequence(s)
    BU729922, D45399, EL946662
    Consensus CDS
    CCDS8672.1
    UniProtKB/Swiss-Prot
    Q13956, Q52LY7
    Related
    ENSP00000266395.2, ENST00000266395.3
    Conserved Domains (1) summary
    pfam04868
    Location:2 → 83
    PDE6_gamma; Retinal cGMP phosphodiesterase, gamma subunit

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_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    14973042..14981865
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    14850375..14859197
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13956.1 GenPept UniProtKB/Swiss-Prot:Q13956

Gene LinkOut

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