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

Gene Gene information from NCBI Gene database. Gene SNPs Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	5146
Gene name	Phosphodiesterase 6C
Gene symbol	PDE6C
Synonyms (NCBI Gene)	ACHM5COD4PDEA2
Chromosome	10
Chromosome location	10q23.33
Summary	This gene encodes the alpha-prime subunit of cone phosphodiesterase, which is composed of a homodimer of two alpha-prime subunits and 3 smaller proteins of 11, 13, and 15 kDa. Mutations in this gene are associated with cone dystrophy type 4 (COD4). [provi

Show/Hide all (39)

SNP ID	Visualize variation	Clinical significance	Consequence
rs121918537	C>A,T	Pathogenic	Synonymous variant, missense variant, coding sequence variant
rs121918538	T>A	Pathogenic	Missense variant, coding sequence variant
rs121918539	A>G	Pathogenic	Missense variant, coding sequence variant
rs140524715	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant
rs181296577	T>C	Conflicting-interpretations-of-pathogenicity	Intron variant
rs267606934	A>G,T	Pathogenic	Coding sequence variant, missense variant
rs267606935	T>A	Pathogenic	Coding sequence variant, stop gained
rs267606936	G>A	Pathogenic	Coding sequence variant, missense variant
rs267606937	C>T	Pathogenic	Coding sequence variant, stop gained
rs374805348	G>A	Likely-pathogenic	Intron variant
rs387906401	G>C	Pathogenic	Coding sequence variant, missense variant
rs756324901	G>T	Pathogenic	Coding sequence variant, stop gained
rs757622521	C>T	Pathogenic	Coding sequence variant, stop gained
rs762152984	T>C	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant
rs762426409	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs766703340	T>G	Likely-pathogenic	Coding sequence variant, missense variant
rs786200908	->AG	Pathogenic	Coding sequence variant, frameshift variant
rs786200909	T>A	Pathogenic	Intron variant
rs786200910	A>G	Pathogenic	Splice acceptor variant
rs786200911	->A	Pathogenic	Stop gained, coding sequence variant
rs786205462	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs786205463	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs796051871	GTAAG>-	Pathogenic, likely-pathogenic	Coding sequence variant, intron variant, splice donor variant
rs863224908	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1023522305	G>A,C	Likely-pathogenic	Splice donor variant
rs1028838062	C>T	Pathogenic	Stop gained, coding sequence variant
rs1057518244	G>T	Likely-pathogenic	Splice acceptor variant
rs1554888353	G>-	Pathogenic	Frameshift variant, coding sequence variant
rs1554888848	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs1554888858	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1554888861	G>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1554888978	A>-	Pathogenic	Frameshift variant, coding sequence variant
rs1554889905	G>A	Pathogenic	Splice donor variant
rs1554890513	AAGT>-	Likely-pathogenic	Intron variant, coding sequence variant, splice donor variant
rs1564801134	T>C	Likely-pathogenic	Missense variant, coding sequence variant
rs1589690942	G>A	Pathogenic	Coding sequence variant, stop gained
rs1589693002	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs1589704707	T>G	Pathogenic	Splice donor variant
rs1589705946	G>A	Pathogenic	Coding sequence variant, stop gained

Show/Hide all (21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0004114	Function	3',5'-cyclic-nucleotide phosphodiesterase activity	IEA
GO:0004115	Function	3',5'-cyclic-AMP phosphodiesterase activity	IBA
GO:0005886	Component	Plasma membrane	IEA
GO:0007165	Process	Signal transduction	IEA
GO:0007601	Process	Visual perception	IBA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	IEA
GO:0007601	Process	Visual perception	TAS	8641425
GO:0007603	Process	Phototransduction, visible light	IEA
GO:0008081	Function	Phosphoric diester hydrolase activity	IEA
GO:0016020	Component	Membrane	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0030553	Function	CGMP binding	IEA
GO:0046549	Process	Retinal cone cell development	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0047555	Function	3',5'-cyclic-GMP phosphodiesterase activity	IBA
GO:0047555	Function	3',5'-cyclic-GMP phosphodiesterase activity	IEA
GO:0050953	Process	Sensory perception of light stimulus	IEA
GO:0097381	Component	Photoreceptor disc membrane	IEA
GO:0141162	Process	Negative regulation of cAMP/PKA signal transduction	IBA

MIM	HGNC	e!Ensembl
600827	8787	ENSG00000095464

P51160

Protein name

Cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' (EC 3.1.4.35) (cGMP phosphodiesterase 6C)

Protein function

As cone-specific cGMP phosphodiesterase, it plays an essential role in light detection and cone phototransduction by rapidly decreasing intracellular levels of cGMP.

PDB

3JWQ , 3JWR , 5E8F , 9CXG , 9CXH , 9CXI , 9CXJ

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01590	GAF	75 → 224	GAF domain	Domain
PF01590	GAF	256 → 433	GAF domain	Domain
PF00233	PDEase_I	561 → 806		Domain

Sequence

MGEINQVAVEKYLEENPQFAKEYFDRKLRVEVLGEIFKNSQVPVQSSMSFSELTQVEESA
LCLELLWTVQEEGGTPEQGVHRALQRLAHLLQADRCSMFLCRSRNGIPEVASRLLDVTPT
SKFEDNLVGPDKEVVFPLDIGIVGWAAHTKKTHNVPDVKKNSHFSDFMDKQTGYVTKNLL
ATPIVVGKEVLAVIMAVNKVNASEFSKQDEEVFSKYLNFVSIILRLHHTSYMYNIESRRS
QILMWSANKVFEELTDVERQFHKALYTVRSYLNCERYSIGLLDMTKEKEFYDEWPIKLGE
VEPYKGPKTPDGREVNFYKIIDYILHGKEEIKVIPTPPADHWTLISGLPTYVAENGFICN
MMNAPADEYFTFQKGPVDETGWVIKNVLSLPIVNKKEDIVGVATFYNRKDGKPFDEHDEY
ITETLTQFLGWSLLNTDTYDKMNKLENRKDIAQEMLMNQTKATPEEIKSILKFQEKLNVD
VIDDCEEKQLVAILKEDLPDPRSAELYEFRFSDFPLTEHGLIKCGIRLFFEINVVEKFKV
PVEVLTRWMYTVRKGYRAVTYHNWRHGFNVGQTMFTLLMTGRLKKYYTDLEAFAMLAAAF
CHDIDHRGTNNLYQMKSTSPLARLHGSSILERHHLEYSKTLLQDESLNIFQNLNKRQFET
VIHLFEVAIIATDLALYFKKRTMFQKIVDACEQMQTEEEAIKYVTVDPTKKEIIMAMMMT
ACDLSAITKPWEVQSQVALMVANEFWEQGDLERTVLQQQPIPMMDRNKRDELPKLQVGFI
DFVCTFVYKEFSRFHKEITPMLSGLQNNRVEWKSLADEYDAKMKVIEEEAKKQEGGAEKA
AEDSGGGDDKKSKTCLML

Sequence length

858

Interactions

View interactions

	KEGG
	Purine metabolism Metabolic pathways

305

Show/Hide Causal Diseases (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormality of the eye	Likely pathogenic	rs2134611976	RCV001814390
Achromatopsia	Pathogenic; Likely pathogenic	rs765296989, rs1554888858, rs1554888861, rs1023522305, rs1554890513, rs1554888353, rs756324901, rs1554888848, rs757622521, rs1554888978, rs1554889905, rs1028838062, rs766703340	RCV001591819 RCV000504665 RCV000504786 RCV000504974 RCV000505030 RCV000664193 RCV000664190 RCV000664194 RCV000664191 RCV000664195 RCV000664189 RCV000664192 RCV001003118
Achromatopsia 5	Likely pathogenic; Pathogenic	rs121918537, rs121918538, rs786200908, rs796051871, rs121918539, rs387906401, rs267606936, rs786200909, rs786200910, rs267606934, rs267606937, rs267606935, rs786200911	RCV000761206 RCV000009309 RCV000009310 RCV000009311 RCV000009312 RCV000009313 RCV000009314 RCV000009315 RCV000009316 RCV000009317 RCV000009318 RCV000009319 RCV000009320
Cone dystrophy	Likely pathogenic	rs1589693002	RCV001003117
Cone dystrophy 4	Likely pathogenic; Pathogenic	rs781699886, rs760343056, rs2492492590, rs958171434, rs762426409, rs374805348, rs863224908, rs121918537, rs796051871, rs2492563607, rs1410436651, rs1023522305, rs757622521, rs1028838062, rs1564801134 View all (4 more)	RCV005245836 RCV002250994 RCV003108008 RCV003225999 RCV001781531 RCV005252788 RCV000199969 RCV000009308 RCV002250457 RCV002789992 RCV003314438 RCV001353003 RCV001809677 RCV005231112 RCV000735778 RCV000988436 RCV001029762 RCV001029756 RCV005909000
Isolated macular dystrophy	Pathogenic	rs2492571833	RCV003389579
PDE6C-related disorder	Likely pathogenic; Pathogenic	rs781699886, rs1328017393, rs1236291370	RCV003399199 RCV003401962 RCV003413900
Retinal dystrophy	Likely pathogenic; Pathogenic	rs781699886, rs2492534156, rs796051871, rs2058399145, rs1403661741, rs746820022, rs1236291370, rs2058673701, rs2058440863	RCV004815515 RCV004817178 RCV004814865 RCV001073910 RCV001074365 RCV001073908 RCV001074364 RCV001075121 RCV001075713

Show/Hide Unknown Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Cervical cancer	Benign	rs76999928	RCV005888437
Clear cell carcinoma of kidney	Benign	rs76999928	RCV005888438
Cone-Rod Dystrophy, Recessive	Conflicting classifications of pathogenicity	rs886047483	RCV000388808
Gastric cancer	Benign	rs76999928	RCV005888439
Malignant tumor of esophagus	Benign	rs76999928	RCV005888436
Optic atrophy	Uncertain significance	rs753424342, rs767703174	RCV004815674 RCV004813587

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Achromatopsia incomplete X linked	Associate	31520890
beta Thalassemia	Associate	11074564
Color Vision Defects	Associate	19615668, 22901948, 24148654, 29618791, 30080950, 31237654, 31520890, 31826238, 32306724, 32913385, 33001157, 34360608, 36833446, 36835061, 36980963, 37372476 View all (1 more)
Cone Dystrophy	Associate	19615668, 33001157, 37433860
Cone Rod Dystrophies	Associate	23776498, 33001157
Jet Lag Syndrome	Associate	31826238
Myopia	Associate	31826238, 36980963
Night Blindness	Associate	33001157
Nystagmus Pathologic	Associate	31826238, 33001157
Parkinson Disease	Associate	40240887
Polyendocrinopathies Autoimmune	Associate	37433860
Prostatic Neoplasms	Associate	25979379
Retinal Cone Dystrophy 1	Associate	30080950
Retinal Dystrophies	Associate	37165311
Retinitis	Associate	31826238, 32306724
Retinitis Pigmentosa	Associate	37165311
RHYNS syndrome	Associate	37165311
Usher Syndromes	Associate	37165311
Vision Disorders	Associate	31520890, 36980963

PDE6C (phosphodiesterase 6C)