PLCD1 (phospholipase C delta 1)

Gene

• Entrez ID: 5333
• Gene name: Phospholipase C delta 1
• Gene symbol: PLCD1
• Synonyms (NCBI Gene): 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-4,5-bisphosphate phospholipase C activity	IBA
GO:0004435	Function	Phosphatidylinositol-4,5-bisphosphate phospholipase C activity	IDA	9188725
GO:0004435	Function	Phosphatidylinositol-4,5-bisphosphate phospholipase C activity	IEA
GO:0004435	Function	Phosphatidylinositol-4,5-bisphosphate phospholipase C activity	TAS	9588182
GO:0004629	Function	Phospholipase C activity	IEA
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	IBA
GO:0005737	Component	Cytoplasm	IDA	15702972
GO:0005737	Component	Cytoplasm	IEA
GO:0005886	Component	Plasma membrane	IBA
GO:0005886	Component	Plasma membrane	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006644	Process	Phospholipid metabolic process	TAS	9588182
GO:0007165	Process	Signal transduction	IEA
GO:0008081	Function	Phosphoric diester hydrolase activity	IEA
GO:0016042	Process	Lipid catabolic process	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0032794	Function	GTPase activating protein binding	IPI	18434237
GO:0035556	Process	Intracellular signal transduction	IEA
GO:0043168	Function	Anion binding	IEA
GO:0046488	Process	Phosphatidylinositol metabolic process	IDA	9188725
GO:0046872	Function	Metal ion binding	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:0070300	Function	Phosphatidic acid binding	IEA
GO:0120548	Function	Phosphatidylinositol phospholipase C activity	IEA
GO:0141212	Process	Phospholipase C/protein kinase C signal transduction	IDA	18434237
GO:1901981	Function	Phosphatidylinositol phosphate 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

• Tissue specificity: TISSUE SPECIFICITY: Strongly expressed in lung, liver and heart. Also expressed at least in pancreas, kidney, skeletal muscle, placenta and brain. {ECO:0000269|PubMed:7890667}.
• Sequence:

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

• Sequence length: 756

Associated diseases

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Nonsyndromic congenital nail disorder 3	Likely pathogenic; Pathogenic	rs201094715, rs397514470, rs1210583991, rs397514471	RCV005362932 RCV002508129 RCV002508130 RCV002508132	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PLCD1-related disorder	Likely pathogenic	rs760879574	RCV003419177	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colon adenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DISORDER OF PILOSEBACEOUS UNIT	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial pancreatic carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS	—	CTD, GWAS catalog CTD, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OSTEOARTHRITIS, HIP	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Primary degenerative dementia of the Alzheimer type, presenile onset	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
SEBACEOUS GLAND DISEASE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alopecia	Alopecia	BEFREE	29793503		★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	23969236		★☆☆☆☆ Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA	Syndromic microphthalmia	BEFREE	31808619		★☆☆☆☆ Found in Text Mining only
Aortic Aneurysm Abdominal	Aortic aneurysm	Pubtator	37228901	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	20657189, 25655282, 28423710, 28576130		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	20657189	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	19448674, 21909432		★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	9345909		★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	31808619	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	36849889	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	25197077		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	21909432, 25197077	Inhibit	★☆☆☆☆ Found in Text Mining only
Coronary Artery Vasospasm	Coronary Artery Vasospasm	BEFREE	20634475, 22265909, 28107550		★☆☆☆☆ Found in Text Mining only
Cystic Fibrosis	Cystic Fibrosis	BEFREE	25477137		★☆☆☆☆ Found in Text Mining only
Degenerative polyarthritis	Arthritis	CTD_human_DG	18784066		★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	Pubtator	31836585	Associate	★☆☆☆☆ Found in Text Mining only
Dermatitis, Irritant	Dermatitis	BEFREE	30791982		★☆☆☆☆ Found in Text Mining only
Dermatologic disorders	Dermatologic Disorders	BEFREE	22805570		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Disruptive, Impulse Control, and Conduct Disorders	Impulse control disorder	BEFREE	30791982		★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down syndrome	Pubtator	27293319	Associate	★☆☆☆☆ Found in Text Mining only
Endometrial Neoplasms	Endometrial neoplasm	Pubtator	32170852	Associate	★☆☆☆☆ Found in Text Mining only
Fibrous skin tumor of tuberous sclerosis	Adenoma sebaceum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	BEFREE	10406008		★☆☆☆☆ Found in Text Mining only
Hypospadias	Hypospadias	Pubtator	32728162	Associate	★☆☆☆☆ Found in Text Mining only
Leukonychia totalis	Leukonychia Totalis	Orphanet			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	20657189, 25655282, 28423710, 28576130		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	9345909		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	19448674		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	25197077		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	LHGDN	11960991		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	25655282		★☆☆☆☆ Found in Text Mining only
Myeloid Leukemia, Chronic	Myeloid Leukemia	BEFREE	22576628		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	18006814, 19448674, 20657189, 22576628, 28423710		★☆☆☆☆ Found in Text Mining only
Nephrolithiasis	Nephrolithiasis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Osteoarthrosis Deformans	Osteoarthrosis Deformans	CTD_human_DG	18784066		★☆☆☆☆ Found in Text Mining only
Psoriasis	Psoriasis	BEFREE	22805570		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	LHGDN	18006814		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	18006814		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	19448674		★☆☆☆☆ Found in Text Mining only
Subarachnoid Hemorrhage	Subarachnoid hemorrhage	BEFREE	10406008		★☆☆☆☆ Found in Text Mining only
Triple Negative Breast Neoplasms	Triple Negative Breast Neoplasms	BEFREE	28576130		★☆☆☆☆ Found in Text Mining only
Tuberous Sclerosis	Tuberous Sclerosis	BEFREE	28455787		★☆☆☆☆ Found in Text Mining only
Type II Mucolipidosis	Mucolipidosis	BEFREE	30791982		★☆☆☆☆ Found in Text Mining only