PDE6D phosphodiesterase 6D [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDE6Dprovided by HGNC
Official Full Name: phosphodiesterase 6Dprovided by HGNC
Primary source: HGNC:HGNC:8788
See related: Ensembl:ENSG00000156973 MIM:602676; AllianceGenome:HGNC:8788
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: PDED; JBTS22
Summary: This gene encodes the delta subunit of rod-specific photoreceptor phosphodiesterase (PDE), a key enzyme in the phototransduction cascade. A similar protein in cow functions in solubilizing membrane-bound PDE. In addition to its role in the PDE complex, the encoded protein is thought to bind to prenyl groups of proteins to target them to subcellular organelles called cilia. Mutations in this gene are associated with Joubert syndrome-22. Alternative splicing results in multiple splice variants. [provided by RefSeq, Mar 2014]
Expression: Ubiquitous expression in testis (RPKM 13.2), brain (RPKM 8.3) and 24 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q37.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (231732433..231781282, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (232217003..232265853, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (232597143..232645992, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

PDE6D Mediates Trafficking of Prenylated Proteins NIM1K and UBL3 to Primary Cilia.
Title: PDE6D Mediates Trafficking of Prenylated Proteins NIM1K and UBL3 to Primary Cilia.
Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects.
Title: Validation of a small molecule inhibitor of PDE6D-RAS interaction with favorable anti-leukemic effects.
The variant was confirmed by Sanger sequencing and found at the heterozygous state in both parents. A review of the literature pertaining to the role of PDE6D in Joubert syndrome is discussed.
Title: A novel PDE6D mutation in a patient with Joubert syndrome type 22 (JBTS22).
PDE6delta binds selectively to the C-terminus of RPGR and that this interaction is critical for RPGR's localization to cilia.
Title: Prenylated retinal ciliopathy protein RPGR interacts with PDE6δ and regulates ciliary localization of Joubert syndrome-associated protein INPP5E.
Studies indicate that the binding of UNC119 and PDE6D, to the lipid-modified ciliary cargo and the specific release of the cargo in the cilia by the ciliary small G-protein Arl3 in a GTP-dependent manner.
Title: Shuttling and sorting lipid-modified cargo into the cilia.
Study identifies PDE6D as a novel Joubert syndrome gene and provides the first evidence of prenyl-binding-dependent trafficking in ciliopathies.
Title: A homozygous PDE6D mutation in Joubert syndrome impairs targeting of farnesylated INPP5E protein to the primary cilium.
RPGR is acting as a scaffold protein recruiting cargo-loaded PDE6D and Arl3 to release lipidated cargo into cilia.
Title: The interplay between RPGR, PDEδ and Arl2/3 regulate the ciliary targeting of farnesylated cargo.
findings indicate that ARL13B, INPP5E, PDE6D, and CEP164 form a distinct functional network that is involved in JBTS and NPHP but independent of the ones previously defined by NPHP and MKS proteins
Title: ARL13B, PDE6D, and CEP164 form a functional network for INPP5E ciliary targeting.
Data show that PDEdelta activity augments K/Hras signalling by enriching Ras at the plasma membrane.
Title: The GDI-like solubilizing factor PDEδ sustains the spatial organization and signalling of Ras family proteins.

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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
Joubert syndrome 22 MedGen: C3810278 OMIM: 615665 GeneReviews: Joubert Syndrome	Compare labs

EBI GWAS Catalog

Description
Genetic variants associated with disordered eating. EBI GWAS Catalog EBI GWAS CatalogPubMed
Many sequence variants affecting diversity of adult human height. 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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables GTPase inhibitor activity	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cilium	TAS Traceable Author Statement more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasmic vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info

General protein information

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Preferred Names: retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

Names: GMP-PDE delta; phosphodiesterase 6D, cGMP-specific, rod, delta; protein p17

NP_001277947.1

EC 3.1.4.17

NP_002592.1

EC 3.1.4.17

XP_047300682.1

EC 3.1.4.17

XP_054198493.1

EC 3.1.4.17

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_034064.1 RefSeqGene

Range

5046..53895

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001291018.2 → NP_001277947.1 retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta isoform 2

See identical proteins and their annotated locations for NP_001277947.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region resulting in a frameshift compared to variant 1. The encoded protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1.

Source sequence(s)

AC073476, BC007831, BI754373

Consensus CDS

CCDS77538.1

UniProtKB/TrEMBL

B8ZZK5

Related

ENSP00000387108.1, ENST00000409772.5

Conserved Domains (1) summary

pfam05351
Location:10 → 88

GMP_PDE_delta; GMP-PDE, delta subunit
NM_002601.4 → NP_002592.1 retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta isoform 1

See identical proteins and their annotated locations for NP_002592.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

BC007831, HY037751

Consensus CDS

CCDS33398.1

UniProtKB/Swiss-Prot

O43250, O43924

UniProtKB/TrEMBL

Q6IB24

Related

ENSP00000287600.4, ENST00000287600.9

Conserved Domains (1) summary

pfam05351
Location:10 → 149

GMP_PDE_delta; GMP-PDE, delta subunit

RNA

NR_110994.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks several exons and contains an alternate 3' terminal exon compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.

Source sequence(s)

AK311623, HY037751

Related

ENST00000477748.1