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    PDE6A phosphodiesterase 6A [ Homo sapiens (human) ]

    Gene ID: 5145, updated on 2-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
    mouse all
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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 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
    		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-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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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