PDE6D (phosphodiesterase 6D)

Gene

• Entrez ID: 5147
• Gene name: Phosphodiesterase 6D
• Gene symbol: PDE6D
• Synonyms (NCBI Gene): JBTS22, PDED
• Chromosome: 2
• Chromosome location: 2q37.1
• 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, th

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs587777156	C>T	Pathogenic	Genic downstream transcript variant, splice acceptor variant
rs1559307932	->C	Likely-pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT048274	hsa-miR-196a-5p	CLASH	23622248
MIRT444844	hsa-miR-8083	PAR-CLIP	22100165
MIRT444843	hsa-miR-4728-3p	PAR-CLIP	22100165
MIRT444842	hsa-miR-204-3p	PAR-CLIP	22100165
MIRT444840	hsa-miR-4646-5p	PAR-CLIP	22100165
MIRT444841	hsa-miR-4786-5p	PAR-CLIP	22100165
MIRT444839	hsa-miR-769-5p	PAR-CLIP	22100165
MIRT444838	hsa-miR-4731-5p	PAR-CLIP	22100165
MIRT444837	hsa-miR-5589-5p	PAR-CLIP	22100165
MIRT444836	hsa-miR-4533	PAR-CLIP	22100165
MIRT444834	hsa-miR-4747-5p	PAR-CLIP	22100165
MIRT444835	hsa-miR-5196-5p	PAR-CLIP	22100165
MIRT444833	hsa-miR-3672	PAR-CLIP	22100165
MIRT444832	hsa-miR-6864-3p	PAR-CLIP	22100165
MIRT444831	hsa-miR-675-3p	PAR-CLIP	22100165
MIRT440014	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT440014	hsa-miR-218-5p	HITS-CLIP	23212916
MIRT444844	hsa-miR-8083	PAR-CLIP	22100165
MIRT444843	hsa-miR-4728-3p	PAR-CLIP	22100165
MIRT444842	hsa-miR-204-3p	PAR-CLIP	22100165
MIRT444840	hsa-miR-4646-5p	PAR-CLIP	22100165
MIRT444841	hsa-miR-4786-5p	PAR-CLIP	22100165
MIRT444839	hsa-miR-769-5p	PAR-CLIP	22100165
MIRT444838	hsa-miR-4731-5p	PAR-CLIP	22100165
MIRT444837	hsa-miR-5589-5p	PAR-CLIP	22100165
MIRT444836	hsa-miR-4533	PAR-CLIP	22100165
MIRT444834	hsa-miR-4747-5p	PAR-CLIP	22100165
MIRT444835	hsa-miR-5196-5p	PAR-CLIP	22100165
MIRT444833	hsa-miR-3672	PAR-CLIP	22100165
MIRT444832	hsa-miR-6864-3p	PAR-CLIP	22100165
MIRT444831	hsa-miR-675-3p	PAR-CLIP	22100165
MIRT1220873	hsa-miR-128	CLIP-seq
MIRT1220874	hsa-miR-2054	CLIP-seq
MIRT1220875	hsa-miR-27a	CLIP-seq
MIRT1220876	hsa-miR-27b	CLIP-seq
MIRT1220877	hsa-miR-380	CLIP-seq
MIRT1220878	hsa-miR-3924	CLIP-seq
MIRT1220879	hsa-miR-4495	CLIP-seq
MIRT1220880	hsa-miR-4712-3p	CLIP-seq
MIRT1220881	hsa-miR-889	CLIP-seq
MIRT2063729	hsa-miR-765	CLIP-seq
MIRT2456118	hsa-miR-1238	CLIP-seq
MIRT2456119	hsa-miR-1470	CLIP-seq
MIRT2456120	hsa-miR-30a	CLIP-seq
MIRT2456121	hsa-miR-30b	CLIP-seq
MIRT2456122	hsa-miR-30c	CLIP-seq
MIRT2456123	hsa-miR-30d	CLIP-seq
MIRT2456124	hsa-miR-30e	CLIP-seq
MIRT2456125	hsa-miR-3613-3p	CLIP-seq
MIRT2456126	hsa-miR-4469	CLIP-seq
MIRT2456127	hsa-miR-4667-3p	CLIP-seq
MIRT2456128	hsa-miR-4691-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005095	Function	GTPase inhibitor activity	IEA
GO:0005095	Function	GTPase inhibitor activity	ISS
GO:0005515	Function	Protein binding	IPI	9712853, 9990021, 11980706, 16169070, 16189514, 18588884, 21516116, 23559067, 25416956, 25519916, 26455799, 27107012, 27173435, 28514442, 30257685, 31515488, 32296183, 33961781, 35271311
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA	9712853
GO:0005829	Component	Cytosol	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	TAS
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	TAS	9570951
GO:0016020	Component	Membrane	IEA
GO:0030659	Component	Cytoplasmic vesicle membrane	IEA
GO:0031267	Function	Small GTPase binding	IPI	9712853
GO:0031410	Component	Cytoplasmic vesicle	IDA	9712853
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0042995	Component	Cell projection	IEA
GO:0050953	Process	Sensory perception of light stimulus	IEA

Other IDs

• MIM: 602676
• HGNC: 8788
• e!Ensembl: ENSG00000156973

Protein

• UniProt ID: O43924
• Protein name: Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (GMP-PDE delta) (Protein p17)
• Protein function: Promotes the release of prenylated target proteins from cellular membranes (PubMed:9712853). Modulates the activity of prenylated or palmitoylated Ras family members by regulating their subcellular location (PubMed:22002721, PubMed:23698361). Re
• PDB: 1KSG, 1KSH, 1KSJ, 3T5G, 3T5I, 4JHP, 4JV6, 4JV8, 4JVB, 4JVF, 5E80, 5E8F, 5F2U, 5ML2, 5ML3, 5ML4, 5ML6, 5ML8, 5NAL, 5TAR, 5TB5, 5X72, 5X73, 5X74, 5YAV, 5YAW, 7PAC, 7PAD, 7PAE, 7Q9Q, 7Q9R, 7Q9S, 7Q9U, 7QF9, 7QJK
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05351	GMP_PDE_delta	9 → 149	GMP-PDE, delta subunit	Family

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed. Detected in various tissues including spleen, prostate gland, testis, ovary, small intestine, colon, retina, and peripheral blood. {ECO:0000269|PubMed:9712853}.
• Sequence:

  MSAKDERAREILRGFKLNWMNLRDAETGKILWQGTEDLSVPGVEHEARVPKKILKCKAVS
  RELNFSSTEQMEKFRLEQKVYFKGQCLEEWFFEFGFVIPNSTNTWQSLIEAAPESQMMPA
  SVLTGNVIIETKFFDDDLLVSTSRVRLFYV

• Sequence length: 150

Pathways

KEGG:

Purine metabolism
Metabolic pathways

Reactome:

ARL13B-mediated ciliary trafficking of INPP5E

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Joubert syndrome 22	Pathogenic; Likely pathogenic	rs587777156, rs2106261987, rs772392692, rs2106294164, rs536550976, rs2469686850, rs1559307932, rs2048717087	RCV000087137 RCV001945181 RCV001890504 RCV002244302 RCV002595758 RCV002815616 RCV000721961 RCV001175218

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
PDE6D-related disorder	Uncertain significance; Likely benign	rs1448692172, rs2106261935, rs142298615	RCV004758842 RCV004731240 RCV003943048

Associations from Text Mining
Disease Name	Relationship Type	References
Ciliopathies	Associate	32055034
Idiopathic Pulmonary Fibrosis	Inhibit	20979602