PLCB2
protein-codingphospholipase C beta 2, the group of Phospholipases|C2 domain containing phospholipases
Gene summary
The protein encoded by this gene is a phosphodiesterase that catalyzes the hydrolysis of phosphatidylinositol 4,5-bisphosphate to the second messengers inositol 1,4,5-trisphosphate (IP3) and diacylglycerol. The encoded protein is activated by G proteins and has been shown to be involved in the type 2 taste receptor signal transduction pathway. In addition, nuclear factor kappa B can regulate the transcription of this gene, whose protein product is also an important regulator of platelet responses. [provided by RefSeq, Jan 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~29.8 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 PLCB2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004573.3. 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 | 1 | 2 | 3 | |||
| missense | 155 | 8 | 1 | 164 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 161 | 8 | 4 | 173 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004564.2 | 32 | MANE Select | |
| Ensembl | ENSP00000260402.3 | 32 | MANE Select | |
| RefSeq | NP_001271226.1 | 32 | Standard | |
| RefSeq | NP_001271227.1 | 31 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Inflammatory mediator regulation of TRP channels - Homo sapiens (human)
- Platelet activation - Homo sapiens (human)
- Cortisol synthesis and secretion - Homo sapiens (human)
- Relaxin signaling pathway - Homo sapiens (human)
- Aldosterone synthesis and secretion - Homo sapiens (human)
Biological Process
- phospholipid metabolic process
- G protein-coupled receptor signaling pathway
- activation of phospholipase C activity
- Wnt signaling pathway, calcium modulating pathway
- lipid catabolic process
Molecular Function
- phosphatidylinositol phospholipase C activity
- phospholipase C activity
- calcium ion binding
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000260402
- Coding exons
- 32
- Length
- 29760
- Individuals with no LoFs
- 125095
- Homozygous LoFs
- 6
- Heterozygous LoFs
- 478
- Defined
- 125579
- p
- 0.00193
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.51 | 583 | 695 | 0.838 | 0.0000401 | 7753 |
| Missense (PolyPhen) | 212 | 292.57 | 0.7246 | 3236 | ||
| Synonymous | 0.754 | 262 | 278 | 0.942 | 0.0000168 | 2220 |
| Loss of Function | 2.51 | 41 | 62.4 | 0.657 | 0.00000301 | 746 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00078 | 0.00075 | rare |
| Latino/Admixed American | 0.00075 | 0.00075 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.014 | 0.014 | notable |
| European (Non-Finnish) | 0.00077 | 0.00074 | rare |
| South Asian | 0.0012 | 0.0012 | notable |
| Other | 0.0036 | 0.0036 | notable |
dbNSFP Gene Annotations
Source:
- Function
- 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. {ECO:0000269|PubMed:1644792}.;
Recessive Scores
- pRec
- 0.185
Intolerance Scores
- LoFtool
- 0.855
- RVIS EVS
- -0.7
- RVIS percentile EVS
- 14.81
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.695
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |