PLCD3
protein-codingphospholipase C delta 3, the group of C2 domain containing phospholipases|Phospholipases|MicroRNA protein coding host genes
Gene summary
This gene encodes a member of the phospholipase C family, which catalyze the hydrolysis of phosphatidylinositol 4,5-bisphosphate to generate the second messengers diacylglycerol and inositol 1,4,5-trisphosphate (IP3). Diacylglycerol and IP3 mediate a variety of cellular responses to extracellular stimuli by inducing protein kinase C and increasing cytosolic Ca(2+) concentrations. This enzyme localizes to the plasma membrane and requires calcium for activation. Its activity is inhibited by spermine, sphingosine, and several phospholipids. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~24.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PLCD3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_133373.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 119 | 119 | ||||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 124 | 0 | 0 | 124 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_588614.1 | 15 | MANE Select | |
| Ensembl | ENSP00000479636.1 | 15 | MANE Select | |
| Ensembl | ENSP00000440378.1 | 3 | Standard | |
| Ensembl | ENSP00000443079.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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)
Biological Process
- angiogenesis
- lipid catabolic process
- inositol trisphosphate biosynthetic process
- intracellular signal transduction
- regulation of cell population proliferation
Molecular Function
- phosphatidylinositol phospholipase C activity
- metal ion binding
Cellular Component
- cytosol
- plasma membrane
- cleavage furrow
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000322765
- Coding exons
- 16
- Length
- 24387
- Individuals with no LoFs
- 19205
- Homozygous LoFs
- 105056
- Heterozygous LoFs
- 539
- Defined
- 124800
- p
- 0.608
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.59 | 362 | 458 | 0.791 | 0.0000318 | 4959 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.96 | 0.54 | notable |
| Latino/Admixed American | 1.0 | 0.65 | notable |
| Ashkenazi Jewish | 1.0 | 0.70 | notable |
| East Asian | 1.0 | 0.65 | notable |
| Finnish | 1.0 | 0.61 | notable |
| European (Non-Finnish) | 1.0 | 0.59 | notable |
| South Asian | 1.0 | 0.63 | notable |
| Other | 1.0 | 0.64 | notable |
dbNSFP Gene Annotations
Source:
- 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.;
Recessive Scores
- pRec
- 0.116
Essentials
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.573
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |