PLCD1 (phospholipase C delta 1)

Gene

• Entrez ID: 5333
• Gene name: Phospholipase C delta 1
• Gene symbol: PLCD1
• Synonyms: NDNC3, PLC-III
• Chromosome: 3
• Chromosome location: 3p22.2
• Summary: This gene encodes a member of the phospholipase C family. Phospholipase C isozymes play critical roles in intracellular signal transduction by catalyzing the hydrolysis of phosphatidylinositol 4,5-bisphosphate (PIP2) into the second messengers diacylglyce

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs375683615	C>T	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs397514470	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs397514471	A>G	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs1210583991	CACTACAGGC>-	Pathogenic	Coding sequence variant, splice acceptor variant, non coding transcript variant, intron variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT018905	hsa-miR-335-5p	Microarray	18185580
MIRT1239777	hsa-miR-1258	CLIP-seq
MIRT1239778	hsa-miR-1321	CLIP-seq
MIRT1239779	hsa-miR-15a	CLIP-seq
MIRT1239780	hsa-miR-15b	CLIP-seq
MIRT1239781	hsa-miR-16	CLIP-seq
MIRT1239782	hsa-miR-1827	CLIP-seq
MIRT1239783	hsa-miR-1915	CLIP-seq
MIRT1239784	hsa-miR-195	CLIP-seq
MIRT1239785	hsa-miR-2355-5p	CLIP-seq
MIRT1239786	hsa-miR-3117-5p	CLIP-seq
MIRT1239787	hsa-miR-3166	CLIP-seq
MIRT1239788	hsa-miR-3612	CLIP-seq
MIRT1239789	hsa-miR-378g	CLIP-seq
MIRT1239790	hsa-miR-424	CLIP-seq
MIRT1239791	hsa-miR-4270	CLIP-seq
MIRT1239792	hsa-miR-4281	CLIP-seq
MIRT1239793	hsa-miR-4441	CLIP-seq
MIRT1239794	hsa-miR-4515	CLIP-seq
MIRT1239795	hsa-miR-4739	CLIP-seq
MIRT1239796	hsa-miR-4756-5p	CLIP-seq
MIRT1239797	hsa-miR-497	CLIP-seq
MIRT1239798	hsa-miR-650	CLIP-seq
MIRT1239799	hsa-miR-922	CLIP-seq
MIRT1239778	hsa-miR-1321	CLIP-seq
MIRT1239782	hsa-miR-1827	CLIP-seq
MIRT1239783	hsa-miR-1915	CLIP-seq
MIRT1239785	hsa-miR-2355-5p	CLIP-seq
MIRT1239788	hsa-miR-3612	CLIP-seq
MIRT1239791	hsa-miR-4270	CLIP-seq
MIRT1239792	hsa-miR-4281	CLIP-seq
MIRT1239793	hsa-miR-4441	CLIP-seq
MIRT1239795	hsa-miR-4739	CLIP-seq
MIRT1239796	hsa-miR-4756-5p	CLIP-seq
MIRT1239798	hsa-miR-650	CLIP-seq
MIRT1239778	hsa-miR-1321	CLIP-seq
MIRT1239782	hsa-miR-1827	CLIP-seq
MIRT1239783	hsa-miR-1915	CLIP-seq
MIRT1239785	hsa-miR-2355-5p	CLIP-seq
MIRT1239788	hsa-miR-3612	CLIP-seq
MIRT1239791	hsa-miR-4270	CLIP-seq
MIRT1239792	hsa-miR-4281	CLIP-seq
MIRT1239793	hsa-miR-4441	CLIP-seq
MIRT1239795	hsa-miR-4739	CLIP-seq
MIRT1239796	hsa-miR-4756-5p	CLIP-seq
MIRT1239798	hsa-miR-650	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001786	Function	Phosphatidylserine binding	IEA
GO:0004435	Function	Phosphatidylinositol phospholipase C activity	IBA	21873635
GO:0004435	Function	Phosphatidylinositol phospholipase C activity	IDA	9188725
GO:0005509	Function	Calcium ion binding	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005546	Function	Phosphatidylinositol-4,5-bisphosphate binding	IDA	9188725, 11001876
GO:0005737	Component	Cytoplasm	IDA	15702972
GO:0005886	Component	Plasma membrane	TAS
GO:0006644	Process	Phospholipid metabolic process	TAS	9588182
GO:0016042	Process	Lipid catabolic process	IEA
GO:0032794	Function	GTPase activating protein binding	IPI	18434237
GO:0043647	Process	Inositol phosphate metabolic process	TAS
GO:0046488	Process	Phosphatidylinositol metabolic process	IDA	9188725
GO:0048015	Process	Phosphatidylinositol-mediated signaling	IBA	21873635
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0070300	Function	Phosphatidic acid binding	IEA

Other IDs

• MIM: 602142
• HGNC: 9060
• e!Ensembl: ENSG00000187091

Protein

• UniProt ID: P51178
• Protein name: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-1 (EC 3.1.4.11) (Phosphoinositide phospholipase C-delta-1) (Phospholipase C-III) (PLC-III) (Phospholipase C-delta-1) (PLC-delta-1)
• Protein function: The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes (PubMed:9188725). Essential for trophoblast and placental
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF09279	EF-hand_like	204 → 289	Phosphoinositide-specific phospholipase C, efhand-like	Domain
  PF00388	PI-PLC-X	298 → 441	Phosphatidylinositol-specific phospholipase C, X domain	Family
  PF00387	PI-PLC-Y	492 → 607	Phosphatidylinositol-specific phospholipase C, Y domain	Family
  PF00168	C2	629 → 737	C2 domain	Domain

• Sequence:

  MDSGRDFLTLHGLQDDEDLQALLKGSQLLKVKSSSWRRERFYKLQEDCKTIWQESRKVMR
  TPESQLFSIEDIQEVRMGHRTEGLEKFARDVPEDRCFSIVFKDQRNTLDLIAPSPADAQH
  WVLGLHKIIHHSGSMDQRQKLQHWIHSCLRKADKNKDNKMSFKELQNFLKELNIQVDDSY
  ARKIFRECDHSQTDSLEDEEIEAFYKMLTQRVEIDRTFAEAAGSGETLSVDQLVTFLQHQ
  QREEAAGPALALSLIERYEPSETAKAQRQMTKDGFLMYLLSADGSAFSLAHRRVYQDMGQ
  PLSHYLVSSSHNTYLLEDQLAGPSSTEAYIRALCKGCRCLELDCWDGPNQEPIIYHGYTF
  TSKILFCDVLRAIRDYAFKASPYPVILSLENHCTLEQQRVMARHLHAILGPMLLNRPLDG
  VTNSLPSPEQLKGKILLKGKKLGGLLPPGGEGGPEATVVSDEDEAAEMEDEAVRSRVQHK
  PKEDKLRLAQELSDMVIYCKSVHFGGFSSPGTPGQAFYEMASFSENRALRLLQESGNGFV
  RHNVGHLSRIYPAGWRTDSSNYSPVEMWNGGCQIVALNFQTPGPEMDVYQGRFQDNGACG
  YVLKPAFLRDPNGTFNPRALAQGPWWARKRLNIRVISGQQLPKVNKNKNSIVDPKVTVEI
  HGVSRDVASRQTAVITNNGFNPWWDTEFAFEVVVPDLALIRFLVEDYDASSKNDFIGQST
  IPLNSLKQGYRHVHLMSKNGDQHPSATLFVKISLQD

• Sequence length: 756

Pathways

KEGG:

Inositol phosphate metabolism
Metabolic pathways
Calcium signaling pathway
Phosphatidylinositol signaling system
Thyroid hormone signaling pathway
AGE-RAGE signaling pathway in diabetic complications
Shigellosis

Reactome:

Synthesis of IP3 and IP4 in the cytosol

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Arthritis	Degenerative polyarthritis	rs1594890601, rs1594882933, rs184370809, rs776489319, rs1594883470	18784066
Diabetes mellitus	Diabetes Mellitus, Non-Insulin-Dependent	rs587776515, rs61730328, rs606231121, rs606231122, rs79020217, rs77625743, rs78378398, rs606231123, rs4402960, rs1362648752, rs3745368, rs3792267, rs3842570, rs5030952, rs2975760, rs119489103, rs7903146, rs12255372, rs11196205, rs104893649, rs80356624, rs80356616, rs80356625, rs80356611, rs104894237, rs80356613, rs137852740, rs137852786, rs387906407, rs151344623, rs28938469, rs28936371, rs137852672, rs80356637, rs80356642, rs80356653, rs137852673, rs137852674, rs80356634, rs80356651, rs193929360, rs137853334, rs137853335, rs137853336, rs1600731198, rs137853338, rs121964882, rs121964883, rs387906511, rs121964884, rs121964885, rs2147483647, rs387906512, rs121964887, rs121964888, rs121964889, rs121964890, rs121964891, rs28934878, rs74315383, rs121964893, rs886037620, rs886037621, rs80356663, rs121434593, rs121913150, rs587776825, rs137853236, rs2135842335, rs137853237, rs137853238, rs2135818776, rs1566092470, rs1463923467, rs137853243, rs137853244, rs2135839114, rs137853245, rs2135847417, rs121918407, rs104894005, rs104894006, rs80356655, rs104894008, rs104894009, rs104894010, rs104894011, rs80356654, rs104894016, rs193929376, rs193929374, rs193929375, rs193929373, rs80356666, rs80356669, rs80356664, rs193929366, rs1048095, rs193929355, rs193929356, rs1259467443, rs104893642, rs387906777, rs387906779, rs141804752, rs182349376, rs184917682, rs193922396, rs193922400, rs193922401, rs137852676, rs193922407, rs193922638, rs193922257, rs193922258, rs193922259, rs193922260, rs193922261, rs193922262, rs193922263, rs193922264, rs193922265, rs193922268, rs193921338, rs193922269, rs193922272, rs193922273, rs193922275, rs193922278, rs193922279, rs193922280, rs193922281, rs193922282, rs193922283, rs193922284, rs193922286, rs193922287, rs193922289, rs193922291, rs193922295, rs193922297, rs193922300, rs193922302, rs193922303, rs193922308, rs193922313, rs193922314, rs144723656, rs193922315, rs193922316, rs193922317, rs148311934, rs193922319, rs193922320, rs193922326, rs193922329, rs193922330, rs193922331, rs193922335, rs193922336, rs193922338, rs193922340, rs193922341, rs193922471, rs193922475, rs193922476, rs193922479, rs193922355, rs193922356, rs193922576, rs193922578, rs193922582, rs193922588, rs193922592, rs193922594, rs193922596, rs386134267, rs193922598, rs193922599, rs193922600, rs193922604, rs193922605, rs397514580, rs397515519, rs267601516, rs587780343, rs587780345, rs587780346, rs587780347, rs587780357, rs148954387, rs61736969, rs587783673, rs587783672, rs587783669, rs786204676, rs794727236, rs151344624, rs794727775, rs794727839, rs199946797, rs869320673, rs796065047, rs759072800, rs797045595, rs797045209, rs797045207, rs797045213, rs797045623, rs863225280, rs149703259, rs864321656, rs139964066, rs777870079, rs878853246, rs769268803, rs886039380, rs886041392, rs886041391, rs886042610, rs143064649, rs1057516192, rs746480424, rs1057516281, rs576684889, rs754728827, rs1057520291, rs1057520779, rs893256143, rs1057520504, rs1057524790, rs1057524902, rs1057524904, rs1057524905, rs764232985, rs1064793998, rs1064794268, rs769086289, rs369429452, rs1085307913, rs1131691416, rs765432081, rs1131692182, rs748749585, rs1554335441, rs762263694, rs1312678560, rs767565869, rs1375656631, rs1554335391, rs1360415315, rs1554335616, rs1554335752, rs1554909277, rs769518471, rs757171524, rs768951263, rs762703502, rs1555212248, rs1555212359, rs1555813319, rs1555816654, rs1553638903, rs1553638909, rs948820149, rs371977235, rs1553784995, rs76474829, rs200998587, rs1415041911, rs1554334894, rs1260178539, rs1554335421, rs1555211904, rs779184183, rs1554335564, rs200670692, rs1400535021, rs1554334872, rs1555212749, rs1553876668, rs1553878211, rs954727530, rs1554924035, rs372307320, rs925231098, rs1554913069, rs1554933565, rs766431403, rs746714109, rs751279984, rs770664202, rs1008906426, rs758844607, rs1554924540, rs1566092307, rs753998395, rs1565885935, rs1167124132, rs1376796469, rs556436603, rs1562715657, rs1486280029, rs1564869850, rs755259997, rs769569410, rs1172328722, rs1286294151, rs1375557127, rs1568731279, rs1562715426, rs556581174, rs1564865302, rs1565886545, rs776793516, rs1568724014, rs1392795567, rs781260712, rs1562719705, rs1382448285, rs1564977373, rs750586210, rs1598842892, rs1583592247, rs780612692, rs1593060859, rs1476637197, rs751279776, rs1593060890, rs1191912908, rs1167675604, rs1583601110, rs1593058932, rs778611627, rs753296261

Unknown
Disease name	Disease term	dbSNP ID	References
Adenoma sebaceum	Fibrous skin tumor of tuberous sclerosis
Leukonychia totalis	Leukonychia totalis
Nephrolithiasis	Nephrolithiasis
Osteoarthrosis deformans	Osteoarthrosis Deformans		18784066