PLCD3

phospholipase C delta 3, the group of C2 domain containing phospholipases|Phospholipases|MicroRNA protein coding host genes

Basic information

Region (hg38): 17:45108958-45133354

Links

ENSG00000161714 ∙ NCBI:113026 ∙ OMIM:608795 ∙ HGNC:9061 ∙ Uniprot:Q8N3E9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PLCD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PLCD3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			40			40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	0	0

Variants in PLCD3

This is a list of pathogenic ClinVar variants found in the PLCD3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-45112668-G-A		not specified	Uncertain significance (Nov 03, 2023)
17-45112911-T-C		not specified	Uncertain significance (Feb 07, 2023)
17-45112965-G-A		not specified	Uncertain significance (Mar 17, 2023)
17-45113010-A-G		not specified	Uncertain significance (May 02, 2024)
17-45113166-G-A		not specified	Uncertain significance (Mar 29, 2023)
17-45113177-G-C		not specified	Uncertain significance (Jan 29, 2024)
17-45115163-T-C		not specified	Uncertain significance (Aug 21, 2023)
17-45115189-C-T		not specified	Uncertain significance (Sep 22, 2022)
17-45115196-C-T		not specified	Uncertain significance (Mar 01, 2024)
17-45115219-G-A		not specified	Uncertain significance (Sep 26, 2023)
17-45115349-G-A		not specified	Uncertain significance (Dec 15, 2023)
17-45115412-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-45115427-G-A		not specified	Uncertain significance (Mar 20, 2023)
17-45115441-C-T		not specified	Uncertain significance (Apr 12, 2022)
17-45115442-G-A		not specified	Uncertain significance (Apr 04, 2024)
17-45116715-G-A		not specified	Uncertain significance (Mar 29, 2022)
17-45118002-C-A		not specified	Uncertain significance (Mar 25, 2024)
17-45118014-C-T		not specified	Uncertain significance (Jun 29, 2023)
17-45118039-A-C		not specified	Uncertain significance (Dec 14, 2022)
17-45118118-C-T		not specified	Uncertain significance (Aug 28, 2023)
17-45118315-G-C		not specified	Uncertain significance (Nov 13, 2023)
17-45118322-C-T		not specified	Uncertain significance (Dec 15, 2023)
17-45118394-C-T		not specified	Uncertain significance (Apr 25, 2022)
17-45118443-C-A		not specified	Uncertain significance (Dec 28, 2023)
17-45118878-C-T		not specified	Uncertain significance (Apr 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PLCD3	protein_coding	protein_coding	ENST00000322765	16	24387

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-7	0.989	19205	105056	539	124800	0.608

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.59	362	458	0.791	0.0000318	4959
Missense in Polyphen		146	182.82	0.79859		2090
Synonymous	1.75	166	197	0.842	0.0000142	1569
Loss of Function	2.34	16	29.8	0.537	0.00000128	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	1.96	1.54
Ashkenazi Jewish	1.00	0.703
East Asian	1.00	0.653
Finnish	1.00	0.610
European (Non-Finnish)	1.00	0.585
Middle Eastern	1.00	0.653
South Asian	1.00	0.625
Other	0.999	0.636

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes the phosphatidylinositol 4,5-bisphosphate (PIP2) to generate 2 second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3). DAG mediates the activation of protein kinase C (PKC), while IP3 releases Ca(2+) from intracellular stores. Essential for trophoblast and placental development. May participate in cytokinesis by hydrolyzing PIP2 at the cleavage furrow.
• Pathway: Inositol phosphate metabolism - Homo sapiens (human);AGE-RAGE signaling pathway in diabetic complications - Homo sapiens (human);Thyroid hormone signaling pathway - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);Phosphatidylinositol signaling system - Homo sapiens (human);Proton Pump Inhibitor Pathway, Pharmacodynamics;Inositol Metabolism;GPR40 Pathway;D-<i>myo</i>-inositol (1,4,5)-trisphosphate biosynthesis;Inositol phosphate metabolism;Metabolism;phospholipases;D-<i>myo</i>-inositol-5-phosphate metabolism;superpathway of inositol phosphate compounds;Phosphatidylinositol phosphate metabolism;Synthesis of IP3 and IP4 in the cytosol;Inositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.116

Haploinsufficiency Scores

• pHI: 0.146
• hipred: N
• hipred_score: 0.276
• ghis: 0.530

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.573

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Plcd3

Gene ontology

• Biological process: angiogenesis;lipid catabolic process;inositol trisphosphate biosynthetic process;intracellular signal transduction;regulation of cell population proliferation;inositol phosphate metabolic process;labyrinthine layer blood vessel development
• Cellular component: cytosol;plasma membrane;cleavage furrow
• Molecular function: phosphatidylinositol phospholipase C activity;metal ion binding