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
Disease Acronyms (UniProt) Disease acronyms from UniProt database	JBTS22
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	ISS
GO:0005515	Function	Protein binding	IPI	9712853, 9990021, 11980706, 16169070, 16189514, 18588884, 21516116, 23559067, 25416956, 25519916, 26455799, 27107012, 27173435, 28514442, 30257685, 31515488, 32296183
GO:0005737	Component	Cytoplasm	IBA	21873635
GO:0005829	Component	Cytosol	IDA	9712853
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	TAS
GO:0007601	Process	Visual perception	IEA
GO:0030659	Component	Cytoplasmic vesicle membrane	IEA
GO:0031267	Function	Small GTPase binding	IPI	9712853
GO:0031410	Component	Cytoplasmic vesicle	IDA	9712853
GO:0034260	Process	Negative regulation of GTPase activity	IEA
GO:0050896	Process	Response to 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 (14)

Disease term	Disease name	dbSNP ID	References
Causal
Brachydactyly	Brachydactyly	rs121908949, rs28937580, rs121909082, rs104894122, rs863223289, rs863223290, rs104894121, rs1587657302, rs863223292, rs74315386, rs74315387, rs28936397, rs753691079, rs121909348, rs121917852 View all (22 more)
Cerebellar vermis agenesis	Familial aplasia of the vermis	rs201108965, rs13297509, rs121918129, rs121918130, rs121918197, rs121918198, rs121918199, rs121918203, rs121918204, rs145665129, rs121434348, rs121434349, rs267606641, rs201391050, rs387907003 View all (121 more)
Congenital heart defects	Congenital Heart Defects	rs267607101, rs121434422, rs387906498, rs397509416, rs587777371, rs587777372, rs587777374, rs367537998, rs797044882, rs886041730, rs768027510, rs1064793873, rs1555447012, rs1554263268, rs1554263321 View all (13 more)
Congenital ocular coloboma	Congenital ocular coloboma (disorder)	rs587778875, rs587777249, rs767611891, rs2091986259, rs2091987023, rs2091988799
Cryptorchidism	Bilateral Cryptorchidism	rs121912555, rs104894697, rs104894698, rs398122886
Developmental delay	Global developmental delay	rs28941770, rs199469464, rs281865469, rs143747297, rs398123009, rs587777428, rs786205133, rs606231459, rs797044854, rs797045027, rs864309504, rs878853160, rs886039902, rs886042046, rs886041291 View all (32 more)
Hearing loss	Conductive hearing loss	rs267607135, rs267606855, rs779841884, rs267606854, rs28942097, rs121908073, rs121908076, rs74315289, rs121908144, rs111033313, rs74315437, rs121908348, rs121908349, rs121908350, rs397515359 View all (184 more)
Joubert syndrome	JOUBERT SYNDROME 22	rs201108965, rs13297509, rs121918128, rs121918129, rs121918130, rs2109050324, rs118204052, rs118204053, rs121918197, rs121918198, rs121918199, rs121918200, rs121918204, rs387906243, rs145665129 View all (432 more)	24166846, 30423442
Mental retardation	Intellectual Disability	rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315 View all (1024 more)
Microphthalmos	Microphthalmos	rs794726862, rs1329285216
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Orofaciodigital syndrome	OROFACIODIGITAL SYNDROME VI, Orofaciodigital syndrome type 6	rs122460150, rs312262822, rs312262833, rs312262886, rs312262890, rs2139738553, rs387907273, rs793888507, rs768525869, rs312262863, rs312262868, rs312262887, rs312262821, rs312262834, rs312262845 View all (42 more)	24166846
Polydactyly	Polydactyly	rs1583729398, rs121917709, rs1583734240, rs121917714, rs397507422, rs398122899, rs587776959, rs386833752, rs1057518698, rs1060499558, rs755938967, rs1375768446, rs1309855392, rs1565601979, rs748321474 View all (3 more)	24166846
Syndactyly	Syndactyly	rs878854345, rs104893635, rs28931600, rs587777050, rs587777051, rs606231304

Show/Hide Unknown Diseases (2)

Disease term	Disease name	Source
Unknown
Renal hypoplasia	Congenital hypoplasia of kidney	ClinVar
Orofaciodigital Syndrome	orofaciodigital syndrome type 6	GenCC

Show/Hide Text Mining Associations (2)

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

PDE6D (phosphodiesterase 6D)