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PDE6C phosphodiesterase 6C [ Homo sapiens (human) ]

Gene ID: 5146, updated on 23-Nov-2023

Summary

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

See PDE6C in Genome Data Viewer
Location:
10q23.33
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (93612537..93666010)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (94492491..94545941)
105.20220307 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Achromatopsia
MedGen: C0152200 GeneReviews: Achromatopsia
Compare labs
Cone dystrophy 4
MedGen: C2751308 OMIM: 613093 GeneReviews: Achromatopsia
Compare labs

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 3',5'-cyclic-GMP phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
enables cGMP binding 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

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)

NEW Try the new Transcript table

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_006204.4NP_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:80231
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:561806
    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_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)