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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	5147
Gene name	Phosphodiesterase 6D
Gene symbol	PDE6D
Synonyms (NCBI Gene)	JBTS22PDED
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

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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

Show/Hide all (19)

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

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

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Joubert syndrome 22	Pathogenic; Likely pathogenic	rs587777156, rs2106261987, rs772392692, rs2106294164, rs536550976, rs2469686850, rs1559307932, rs2048717087	RCV000087137 RCV001945181 RCV001890504 RCV002244302 RCV002595758 RCV002815616 RCV000721961 RCV001175218 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
FAMILIAL APLASIA OF THE VERMIS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ISOLATED JOUBERT SYNDROME	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME TYPE 6	—	Disgenet, Orphanet Disgenet, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME VI	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PDE6D-related disorder	Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (43)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Bilateral Cryptorchidism	Cryptorchidism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Brachydactyly	Brachydactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	BEFREE	24166846		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathy	Pubtator	32055034	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Clinodactyly of fingers	Clinodactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Conductive hearing loss	Hearing Loss	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital absence of kidneys syndrome	Renal agenesis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Epicanthus	Congenital Epicanthus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Heart Defects	Congenital heart defects	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital hypoplasia of kidney	Renal hypoplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital ocular coloboma (disorder)	Congenital ocular coloboma	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Esotropia	Esotropia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Familial aplasia of the vermis	Cerebellar vermis agenesis	BEFREE	24166846, 30423442		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Frontal bossing	Frontal bossing	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hypothalamic hamartomas	Hypothalamic Hamartomas	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Pulmonary Fibrosis	BEFREE	20979602		★★★★★ ★☆☆☆☆ Found in Text Mining only
Idiopathic Pulmonary Fibrosis	Idiopathic pulmonary fibrosis	Pubtator	20979602	Inhibit	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
JOUBERT SYNDROME 22	Joubert Syndrome	GENOMICS_ENGLAND_DG	24166846, 30423442		★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 22	Joubert Syndrome	CLINVAR_DG			★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Liver carcinoma	Liver carcinoma	BEFREE	30901922		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development, Group II	Malformation of cortical development	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	30901922		★★★★★ ★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	30901922		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Oculomotor apraxia	Oculomotor apraxia	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Orofaciodigital syndrome type 6	Orofaciodigital Syndrome	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OROFACIODIGITAL SYNDROME VI	Orofaciodigital syndrome	ORPHANET_DG	24166846		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Polydactyly	Polydactyly	GENOMICS_ENGLAND_DG	24166846		★★★★★ ★☆☆☆☆ Found in Text Mining only
Polydactyly of toes	Polydactyly Of Toes	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Radial polydactyly	Radial Polydactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Retinal Dysplasia	Retinal Dysplasia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Syndactyly	Syndactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Temporal cortical atrophy	Temporal cortical atrophy	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ulnar polydactyly of fingers	Postaxial hand polydactyly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Ulnar polydactyly of fingers	Postaxial hand polydactyly	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

PDE6D (phosphodiesterase 6D)