PDE6C (phosphodiesterase 6C)

Gene

• Entrez ID: 5146
• Gene name: Phosphodiesterase 6C
• Gene symbol: PDE6C
• Synonyms: ACHM5, COD4, PDEA2
• 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

SNPs

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

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004114	Function	3',5'-cyclic-nucleotide phosphodiesterase activity	IBA	21873635
GO:0005886	Component	Plasma membrane	IEA
GO:0007165	Process	Signal transduction	IBA	21873635
GO:0007601	Process	Visual perception	IBA	21873635
GO:0007603	Process	Phototransduction, visible light	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	IEA

Other IDs

• MIM: 600827
• HGNC: 8787
• e!Ensembl: ENSG00000095464

Protein

• UniProt ID: 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

Pathways

KEGG:

Purine metabolism
Metabolic pathways

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Achromatopsia	Achromatopsia, Achromatopsia 5	rs121918344, rs267606739, rs397515360, rs121918537, rs121918538, rs786200908, rs796051871, rs121918539, rs387906401, rs267606936, rs786200909, rs786200910, rs267606934, rs267606937, rs267606935, rs786200911, rs104893612, rs104893613, rs104893614, rs104893615, rs104893616, rs104893617, rs137852608, rs104893619, rs104893620, rs104893621, rs121434585, rs2101121827, rs146640460, rs199474697, rs372006750, rs786204762, rs373862340, rs773372519, rs768345097, rs201794629, rs786204492, rs786204498, rs150115958, rs753625117, rs786205532, rs869320751, rs761357250, rs796065053, rs797045170, rs797045171, rs797045173, rs797045174, rs761129859, rs797045172, rs757470958, rs552069173, rs777509481, rs886063161, rs745557293, rs1057517388, rs1057517454, rs1057516571, rs1057516504, rs1057516825, rs1057516878, rs1057516866, rs1057517167, rs1057517052, rs1057517053, rs748993388, rs1057516791, rs1057517434, rs1057516782, rs376711003, rs1057518098, rs775796581, rs1554604525, rs1554604767, rs1554604833, rs1362472371, rs1554604851, rs1375507464, rs1554607546, rs1554607553, rs964530890, rs1554608319, rs772725807, rs1554609946, rs1554609956, rs768735888, rs773381712, rs999921351, rs373270306, rs201320564, rs1554610279, rs1554610284, rs35010099, rs1026427970, rs1554610655, rs776896038, rs372302139, rs1554610668, rs775038513, rs765574129, rs764742792, rs1385347376, rs1554611860, rs1554612145, rs1554612159, rs1554612805, rs1554612806, rs1201521544, rs1554613998, rs371318766, rs1554614024, rs1554614022, rs6471482, rs1554614038, rs1391492794, rs1174949911, rs1554614131, rs1554614157, rs1554614423, rs1554618404, rs1554618413, rs1554618417, rs1554618420, rs1052078370, rs1554619292, rs1554619303, rs1554619498, rs1554619500, rs1554619509, rs1442286151, rs1554619513, rs1554619514, rs765383904, rs200805087, rs1554888858, rs1554888861, rs1023522305, rs1554890513, rs1554888353, rs756324901, rs1554888848, rs757622521, rs1554888978, rs1554889905, rs1028838062, rs762773298, rs141386891, rs1553450762, rs138958917, rs1553450764, rs1553227755, rs745308973, rs1554609943, rs1554614402, rs1554609978, rs1554604775, rs1554607548, rs1558820471, rs1558022158, rs1558811557, rs1557917535, rs748981899, rs1557917899, rs1557918619, rs1557918635, rs1557918911, rs1403825722, rs1557920291, rs146606352, rs1557918544, rs1557918638, rs777878533, rs1558820134, rs1000861056, rs998703203, rs1585942791, rs750257554, rs374258471, rs1571134523, rs778114016, rs763041373, rs1571143590, rs1570562309, rs1574385431, rs1574390600, rs1464167194, rs1574391103, rs781227859, rs770786127, rs1586003680, rs1233466909, rs1586047969, rs766703340, rs1692739030, rs1692898861, rs371558158, rs1823261605, rs1330263985, rs1574390811, rs1692509021, rs749842881, rs1692921014, rs757167624, rs201782746, rs761969118, rs1823778696, rs1692508715, rs761554853, rs1227761587, rs201747279, rs183838250	19615668
Cone dystrophy	CONE DYSTROPHY 4 (disorder), Progressive cone dystrophy	rs121918537, rs796051871, rs104893967, rs61750172, rs61750173, rs606231180, rs606231181, rs61755783, rs61749668, rs61753046, rs762426409, rs374805348, rs794727197, rs863224908, rs869320709, rs139027297, rs140451304, rs1238632042, rs117522010, rs1023522305, rs531851447, rs1271498710, rs1554186441, rs757622521, rs1028838062, rs1568725951, rs1564801134, rs1557918619, rs1582323732, rs1589705946, rs1589693002, rs1659954489, rs1660447204, rs1660845802, rs1692799480, rs1800113541, rs138924201, rs748084580, rs1883036406, rs1905007623, rs1589690942, rs1589704707, rs1768016995	19615668, 28583373, 21127010
Cone monochromatism	Cone monochromatism	rs104894912, rs121434621, rs104894914
Cone-rod dystrophy	Cone-Rod Dystrophies	rs200691042, rs121908281, rs28940314, rs121434337, rs80338903, rs121909398, rs28937883, rs397515360, rs137853006, rs786205085, rs137853040, rs137853041, rs786205086, rs104894671, rs1568626209, rs104894672, rs61748436, rs2123743692, rs61751408, rs61751374, rs61750200, rs62642560, rs61752410, rs121909206, rs387906388, rs61753033, rs61750172, rs61750173, rs267606857, rs606231180, rs606231181, rs137852551, rs863223294, rs61755792, rs61755786, rs62625014, rs781781440, rs137853932, rs1064792853, rs387907136, rs397517974, rs397517994, rs786200944, rs398123044, rs398122960, rs61752435, rs1800728, rs398124354, rs61749679, rs61750184, rs61755781, rs281865373, rs62653029, rs62635009, rs281865297, rs61748558, rs61749409, rs61750202, rs61750065, rs61751398, rs61750146, rs281865377, rs61751388, rs62646861, rs61750158, rs61751403, rs62646872, rs61750575, rs61751407, rs61750645, rs281865516, rs61751266, rs137853907, rs483353055, rs587777469, rs587777470, rs587777471, rs199882533, rs76216585, rs587777693, rs587777694, rs786205151, rs150115958, rs2723341, rs201422368, rs786205664, rs746559651, rs786205665, rs786205661, rs794727197, rs192003551, rs886041039, rs863224913, rs771214648, rs863225090, rs751163782, rs875989778, rs886044750, rs768278935, rs886044735, rs201471607, rs61752398, rs878853400, rs886037880, rs886037881, rs886039559, rs748706582, rs886039882, rs886041900, rs886042153, rs749526785, rs1057516195, rs1057516199, rs543698823, rs199840367, rs752175052, rs1085307121, rs104893793, rs1064797182, rs1131691378, rs778234759, rs1553193813, rs373331232, rs756678484, rs780667159, rs1557110499, rs1553901823, rs201587670, rs1439202144, rs1555635778, rs1429786931, rs1553187160, rs1553188916, rs1555345387, rs61749412, rs951379922, rs1554186472, rs767528365, rs1210104601, rs776289402, rs750740765, rs544616523, rs75459701, rs759940113, rs1557787559, rs782581701, rs771116776, rs1006935198, rs755733328, rs1560141393, rs121918567, rs752263228, rs775957498, rs1030149008, rs530749007, rs141823837, rs1570393848, rs1571250020, rs1570382663, rs78484040, rs766357803, rs1437021651, rs1601982595, rs1597331616, rs748798324, rs759408031, rs747512450, rs373680665, rs1355802816, rs374017889, rs1589307705, rs376500610, rs1598146173, rs1598149154, rs752619497, rs1571257937, rs1572829866, rs1426009756, rs1464167194, rs1588391640, rs1588865728, rs1589306127, rs1420750126, rs1598150539, rs1598150793, rs1601972449, rs782740998, rs767366723, rs1602653110, rs778456901, rs1662213462, rs1662507319, rs751644763, rs1689012192, rs1667508280, rs1719285721, rs1734066547, rs1800111659, rs1827340429, rs1196886096, rs1882924778, rs2046020472, rs2046113301, rs1594280740, rs1590681805, rs1570373408, rs369973540, rs1005271380, rs368213921, rs535922252, rs745741473, rs138370992, rs772656461, rs749738655, rs1968173024, rs746128841, rs1887576038, rs909373397, rs750116711, rs1659840790, rs1768016995, rs1186795749
Nystagmus	Nystagmus	rs137852207, rs137852208, rs1928435502, rs137852209, rs137852210, rs1929191668, rs137852211, rs137852212, rs2124209414, rs387906720, rs387906721, rs1602791884, rs786205896
Progressive cone dystrophy	Progressive cone dystrophy (without rod involvement)	rs61750173, rs61755783, rs764759172, rs1557106557, rs1306231185, rs536742386, rs1402837406, rs781339303	19615668

Unknown
Disease name	Disease term	dbSNP ID	References
Disorder of eye	Disorder of eye
Dyschromatopsia	Dyschromatopsia
Exotropia	Exotropia
Hyperopia	Hyperopia
Pendular nystagmus	Pendular Nystagmus