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PDE6A phosphodiesterase 6A [ Homo sapiens (human) ]

Gene ID: 5145, updated on 27-Nov-2024

Summary

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Official Symbol
PDE6Aprovided by HGNC
Official Full Name
phosphodiesterase 6Aprovided by HGNC
Primary source
HGNC:HGNC:8785
See related
Ensembl:ENSG00000132915 MIM:180071; AllianceGenome:HGNC:8785
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
PDEA; RP43; CGPR-A
Summary
This gene encodes the cyclic-GMP (cGMP)-specific phosphodiesterase 6A alpha subunit, expressed in cells of the retinal rod outer segment. The phosphodiesterase 6 holoenzyme is a heterotrimer composed of an alpha, beta, and two gamma subunits. cGMP is an important regulator of rod cell membrane current, and its dynamic concentration is established by phosphodiesterase 6A cGMP hydrolysis and guanylate cyclase cGMP synthesis. The protein is a subunit of a key phototransduction enzyme and participates in processes of transmission and amplification of the visual signal. Mutations in this gene have been identified as one cause of autosomal recessive retinitis pigmentosa. [provided by RefSeq, Jul 2008]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

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See PDE6A in Genome Data Viewer
Location:
5q32
Exon count:
24
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (149857953..149944793, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150394428..150481347, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149237516..149324356, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:149109472-149110122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16502 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16501 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16500 Neighboring gene RNA, 7SL, cytoplasmic 868, pseudogene Neighboring gene PPARG coactivator 1 beta Neighboring gene microRNA 378a Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149138890-149139607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149143045-149143915 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149152433-149153272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23387 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23388 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23389 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149183799-149184608 Neighboring gene NFE2L2 motif-containing MPRA enhancer 202 Neighboring gene melanoma risk locus-associated MPRA allelic enhancer 5:149195389 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149198738-149199254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23391 Neighboring gene Sharpr-MPRA regulatory region 12732 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149318171-149318672 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149318673-149319172 Neighboring gene Sharpr-MPRA regulatory region 12514 Neighboring gene MFF pseudogene 2 Neighboring gene NANOG hESC enhancer GRCh37_chr5:149338737-149339340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16504 Neighboring gene solute carrier family 26 member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23393 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:149379441-149380229 Neighboring gene tigger transposable element derived 6

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. Central Visual Function and Genotype-Phenotype Correlations in PDE6A-Associated Retinitis Pigmentosa. Kuehlewein L, et al. Invest Ophthalmol Vis Sci, 2022 May 2. PMID 35533076, Free PMC Article
  2. The molecular genetics of retinal photoreceptor proteins involved in cGMP metabolism. Pittler SJ, et al. Prog Clin Biol Res, 1991. PMID 1672236
  3. Visual transduction in rod outer segments. Takemoto DJ, et al. Cell Signal, 1990. PMID 2169289
  4. Clinical Phenotype and Course of PDE6A-Associated Retinitis Pigmentosa Disease, Characterized in Preparation for a Gene Supplementation Trial. Kuehlewein L, et al. JAMA Ophthalmol, 2020 Dec 1. PMID 33057649, Free PMC Article
  5. Autosomal recessive retinitis pigmentosa caused by mutations in the alpha subunit of rod cGMP phosphodiesterase. Huang SH, et al. Nat Genet, 1995 Dec. PMID 7493036

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Central Visual Function and Genotype-Phenotype Correlations in PDE6A-Associated Retinitis Pigmentosa.
    Title: Central Visual Function and Genotype-Phenotype Correlations in PDE6A-Associated Retinitis Pigmentosa.
  2. Photoreceptor Phosphodiesterase (PDE6): Structure, Regulatory Mechanisms, and Implications for Treatment of Retinal Diseases.
    Title: Photoreceptor Phosphodiesterase (PDE6): Structure, Regulatory Mechanisms, and Implications for Treatment of Retinal Diseases.
  3. Novel variants in PDE6A and PDE6B genes and its phenotypes in patients with retinitis pigmentosa in Chinese families.
    Title: Novel variants in PDE6A and PDE6B genes and its phenotypes in patients with retinitis pigmentosa in Chinese families.
  4. Clinical Phenotype and Course of PDE6A-Associated Retinitis Pigmentosa Disease, Characterized in Preparation for a Gene Supplementation Trial.
    Title: Clinical Phenotype and Course of PDE6A-Associated Retinitis Pigmentosa Disease, Characterized in Preparation for a Gene Supplementation Trial.
  5. Mutations in PDE6A and PDE6B accounted for 1.6% and 2.4%, respectively, in a cohort of French patients with rod-cone dystrophy (RCD)
    Title: Longitudinal Clinical Follow-up and Genetic Spectrum of Patients With Rod-Cone Dystrophy Associated With Mutations in PDE6A and PDE6B.
  6. Co-Existence of Novel PDE6A Mutations and A Recurrent RPGR Mutation: A Potential Explanation for Phenotypic Diversity in Female RPGR Mutation Carriers.
    Title: Co-Existence of Novel PDE6A Mutations and A Recurrent RPGR Mutation: A Potential Explanation for Phenotypic Diversity in Female RPGR Mutation Carriers.
  7. Mutation in PDE6A gene is associated with autosomal recessive retinitis pigmentosa disease progression.
    Title: Structural disease progression in PDE6-associated autosomal recessive retinitis pigmentosa.
  8. By using targeted next-generation sequencing (NGS) method, we identified a compound heterozygous mutation in PDE6A gene that is associated with retinitis pigmentosa in a Chinese family.
    Title: Targeted next-generation sequencing reveals that a compound heterozygous mutation in phosphodiesterase 6a gene leads to retinitis pigmentosa in a Chinese family.
  9. this is the first phenotypic description of arRP due to homozygous IVS6+1G>A mutations in PDE6A and these seem here to be associated with severe RP leading to early extinction of rod responses as well as reduced macular function.
    Title: Increased Plasma cGMP in a Family With Autosomal Recessive Retinitis Pigmentosa Due to Homozygous Mutations in the PDE6A Gene.
  10. report two splice acceptor site variations in PDE6A in consanguineous Pakistani families who manifested cardinal symptoms of autosomal recessive retinitis pigmentosa
    Title: Splice-site mutations identified in PDE6A responsible for retinitis pigmentosa in consanguineous Pakistani families.
Submit: New GeneRIF Correction See all GeneRIFs (18)

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 43
MedGen: C3151139 OMIM: 613810 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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 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 retina development in camera-type eye IBA
Inferred from Biological aspect of Ancestor
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
rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
Names
GMP-PDE alpha
PDE V-B1
cGMP phosphodiesterase alpha subunit
phosphodiesterase 6A, cGMP-specific, rod, alpha
retinitis pigmentosa type 43
rod photoreceptor cGMP phosphodiesterase alpha subunit
NP_000431.2
NP_001397717.1
XP_011535952.1
XP_011535953.1
XP_011535955.1
XP_011535956.1
XP_054208777.1
XP_054208778.1
XP_054208779.1
XP_054208780.1

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_009102.1 RefSeqGene

    Range
    5001..91841
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000440.3 → NP_000431.2  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform 1

    See identical proteins and their annotated locations for NP_000431.2

    Status: REVIEWED

    Source sequence(s)
    AC008427, AC008545, BC035909, BU734142, M26061
    Consensus CDS
    CCDS4299.1
    UniProtKB/Swiss-Prot
    P16499, Q0P638
    Related
    ENSP00000255266.5, ENST00000255266.10
    Conserved Domains (2) summary
    smart00065
    Location:254 → 441
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:558 → 802
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  2. NM_001410788.1 → NP_001397717.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC008427, AC008545
    Consensus CDS
    CCDS93802.1
    UniProtKB/TrEMBL
    F1T0K3
    Related
    ENSP00000478060.1, ENST00000613228.1

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    149857953..149944793 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011537650.3 → XP_011535952.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X1

    Conserved Domains (2) summary
    smart00065
    Location:40 → 146
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:263 → 507
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  2. XM_011537651.2 → XP_011535953.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X2

    Conserved Domains (2) summary
    smart00065
    Location:7 → 92
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:209 → 453
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  3. XM_011537654.2 → XP_011535956.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X3

    See identical proteins and their annotated locations for XP_011535956.1

    Conserved Domains (2) summary
    smart00065
    Location:11 → 82
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:199 → 443
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

  4. XM_011537653.2 → XP_011535955.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X3

    See identical proteins and their annotated locations for XP_011535955.1

    Conserved Domains (2) summary
    smart00065
    Location:11 → 82
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:199 → 443
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    150394428..150481347 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352802.1 → XP_054208777.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X1

  2. XM_054352803.1 → XP_054208778.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X2

  3. XM_054352805.1 → XP_054208780.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X3

  4. XM_054352804.1 → XP_054208779.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P16499.4 GenPept UniProtKB/Swiss-Prot:P16499

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