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PDE6C phosphodiesterase 6C [ Homo sapiens (human) ]

Gene ID: 5146, updated on 3-Nov-2024

Summary

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Official Symbol
PDE6Cprovided by HGNC
Official Full Name
phosphodiesterase 6Cprovided by HGNC
Primary source
HGNC:HGNC:8787
See related
Ensembl:ENSG00000095464 MIM:600827; AllianceGenome:HGNC:8787
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
COD4; ACHM5; PDEA2
Summary
This gene encodes the alpha-prime subunit of cone phosphodiesterase, which is composed of a homodimer of two alpha-prime subunits and 3 smaller proteins of 11, 13, and 15 kDa. Mutations in this gene are associated with cone dystrophy type 4 (COD4). [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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See PDE6C in Genome Data Viewer
Location:
10q23.33
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (93612537..93666010)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (94492491..94545941)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (95372294..95425767)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902485 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:95341272-95341477 Neighboring gene free fatty acid receptor 4 Neighboring gene retinol binding protein 4 Neighboring gene FRA10A associated CGG repeat 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3786 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:95474242-95474394 Neighboring gene fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) Neighboring gene uncharacterized LOC101927013 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:95505761-95506512 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:95508859-95509841

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 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. Isolation and characterization of a cDNA encoding the alpha' subunit of human cone cGMP-phosphodiesterase. Viczian AS, et al. Gene, 1995 Dec 12. PMID 8543163
  2. Human cone-specific cGMP phosphodiesterase alpha' subunit: complete cDNA sequence and gene arrangement. Feshchenko EA, et al. FEBS Lett, 1996 Feb 26. PMID 8641425
  3. Screening of the gene encoding the alpha'-subunit of cone cGMP-PDE in patients with retinal degenerations. Gao YQ, et al. Invest Ophthalmol Vis Sci, 1999 Jul. PMID 10393054
  4. PDE6C: Novel Mutations, Atypical Phenotype, and Differences Among Children and Adults. Daich Varela M, et al. Invest Ophthalmol Vis Sci, 2020 Oct 1. PMID 33001157, Free PMC Article
  5. Two novel PDE6C gene mutations in Chinese family with achromatopsia. Yuan S, et al. Ophthalmic Genet, 2020 Dec. PMID 32787476

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Clinical characterizations and molecular genetic study of two co-segregating variants in PDZD7 and PDE6C genes leading simultaneously to non-syndromic hearing loss and achromatopsia.
    Title: Clinical characterizations and molecular genetic study of two co-segregating variants in PDZD7 and PDE6C genes leading simultaneously to non-syndromic hearing loss and achromatopsia.
  2. Reconstitution of the phosphodiesterase 6 maturation process important for photoreceptor cell function.
    Title: Reconstitution of the phosphodiesterase 6 maturation process important for photoreceptor cell function.
  3. An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas.
    Title: An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas.
  4. Two novel PDE6C gene mutations in Chinese family with achromatopsia.
    Title: Two novel PDE6C gene mutations in Chinese family with achromatopsia.
  5. PDE6C: Novel Mutations, Atypical Phenotype, and Differences Among Children and Adults.
    Title: PDE6C: Novel Mutations, Atypical Phenotype, and Differences Among Children and Adults.
  6. Novel Bi-allelic PDE6C Variant Leads to Congenital Achromatopsia.
    Title: Novel Bi-allelic PDE6C Variant Leads to Congenital Achromatopsia.
  7. Three novel homozygous variants were detected in CNGA3, two novel variants were found in PDE6C. All patients had nonrecordable full-field electroretinography 30-Hz flicker responses, reduced single-flash cone responses but preserved rod responses.
    Title: Novel causative variants in patients with achromatopsia.
  8. This study reveals two general mechanisms of missense PDE6C mutations underlying retinal diseases: (a) inability of AIPL1 to fold mutant PDE6C proteins leading to complete catalytic inactivity and (b) failure of P gamma regulatory subunit to serve as co-chaperone with AIPL1 in folding of mutant PDE6C.
    Title: Mechanisms of mutant PDE6 proteins underlying retinal diseases.
  9. A novel homozygous PDE6C mutation was identified as the cause of ACHM. In addition, we identified an OPN1SW mutation in the sibling with complete achromatopsia.
    Title: Congenital Achromatopsia and Macular Atrophy Caused by a Novel Recessive PDE6C Mutation (p.E591K).
  10. Expression of PDE6 in rod photoreceptors show that the cone PDE6 isoform is responsible for the difference in light adaptation between rods and cones.
    Title: Exchange of Cone for Rod Phosphodiesterase 6 Catalytic Subunits in Rod Photoreceptors Mimics in Part Features of Light Adaptation.
Submit: New GeneRIF Correction See all GeneRIFs (20)

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
not available
Cone dystrophy 4
MedGen: C2751308 OMIM: 613093 GeneReviews: Achromatopsia
not available

EBI GWAS Catalog

Description
A genome-wide association meta-analysis of preschool internalizing problems.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

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 cGMP binding IEA
Inferred from Electronic Annotation
more info
  
enables calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
  
enables calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity IEA
Inferred from Electronic Annotation
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 phototransduction, visible light IEA
Inferred from Electronic Annotation
more info
  
involved_in retinal cone cell development IEA
Inferred from Electronic Annotation
more info
  
involved_in visual perception IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
Names
cGMP phosphodiesterase 6C
phosphodiesterase 6C, cGMP-specific, cone, alpha prime
NP_006195.3

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_016752.1 RefSeqGene

    Range
    4950..58423
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_006204.4 → NP_006195.3  cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'

    See identical proteins and their annotated locations for NP_006195.3

    Status: REVIEWED

    Source sequence(s)
    AL157396, AL356214, BG206143, BG220856, U31973
    Consensus CDS
    CCDS7429.1
    UniProtKB/Swiss-Prot
    A6NCR6, P51160, Q5VY29
    Related
    ENSP00000360502.3, ENST00000371447.4
    Conserved Domains (2) summary
    smart00065
    Location:80 → 231
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:561 → 806
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    93612537..93666010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    94492491..94545941
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P51160.2 GenPept UniProtKB/Swiss-Prot:P51160

Gene LinkOut

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