Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	5147
Gene name Gene Name - the full gene name approved by the HGNC.	Phosphodiesterase 6D
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PDE6D
Synonyms (NCBI Gene) Gene synonyms aliases	JBTS22, PDED
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2q37.1
Summary Summary of gene provided in NCBI Entrez Gene.	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

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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

Show/Hide all(52)

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

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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

MIM	HGNC	e!Ensembl
602676	8788	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

Interactions

View interactions

	KEGG		Reactome
	Purine metabolism Metabolic pathways		ARL13B-mediated ciliary trafficking of INPP5E

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Joubert Syndrome	joubert syndrome 22	rs1559307932, rs587777156	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Orofaciodigital Syndrome	orofaciodigital syndrome type 6	N/A	N/A	GenCC

Show/Hide Text Mining Associations (2)

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

PDE6D (phosphodiesterase 6D)