PDE6C phosphodiesterase 6C [Homo sapiens (human)] - Gene

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: mouse all
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Genomic context

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_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
Two novel PDE6C gene mutations in Chinese family with achromatopsia.
Title: Two novel PDE6C gene mutations in Chinese family with achromatopsia.
PDE6C: Novel Mutations, Atypical Phenotype, and Differences Among Children and Adults.
Title: PDE6C: Novel Mutations, Atypical Phenotype, and Differences Among Children and Adults.
Novel Bi-allelic PDE6C Variant Leads to Congenital Achromatopsia.
Title: Novel Bi-allelic PDE6C Variant Leads to Congenital Achromatopsia.
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.
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.
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).
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.
The majority (n = 12) of patients were either homozygotes or compound heterozygotes for known achromatopsia alleles, two in CNGB3 (p.T383fsX and p.T296YfsX9) and three in CNGA3 (p.R283Q, p.R427C and p.L527R).
Title: Molecular genetics of achromatopsia in Newfoundland reveal genetic heterogeneity, founder effects and the first cases of Jalili syndrome in North America.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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
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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH79144 (e-PCR)
- UniSTS:65392

PDE6C-1 (e-PCR)
- UniSTS:512643

SHGC-31657 (e-PCR)
- UniSTS:65719

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 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

EC 3.1.4.35

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

NG_016752.1 RefSeqGene

Range

4950..58423

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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