PLCL2
protein-codingphospholipase C like 2, the group of C2 domain containing phospholipases|MicroRNA protein coding host genes
Gene summary
Enables GABA receptor binding activity. Predicted to be involved in several processes, including gamma-aminobutyric acid signaling pathway; negative regulation of cold-induced thermogenesis; and phosphatidylinositol-mediated signaling. Predicted to act upstream of or within B cell proliferation involved in immune response; B-1a B cell differentiation; and negative regulation of B cell receptor signaling pathway. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]
- PLCE2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~288.0 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 PLCL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001144382.2. 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 | 2 | 8 | 1 | 11 | ||
| missense | 2 | 1 | 3 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 6 | 8 | 2 | 16 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001137854.1 | 6 | MANE Select | |
| Ensembl | ENSP00000478458.1 | 6 | MANE Select | |
| RefSeq | NP_055999.2 | 5 | Standard | |
| Ensembl | ENSP00000404433.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Proton Pump Inhibitor Pathway, Pharmacodynamics
Biological Process
- B cell proliferation involved in immune response
- B-1a B cell differentiation
- lipid metabolic process
- gamma-aminobutyric acid signaling pathway
- regulation of synaptic transmission, GABAergic
Molecular Function
- phosphatidylinositol phospholipase C activity
- GABA receptor binding
- inositol 1,4,5 trisphosphate binding
Cellular Component
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000418129
- Coding exons
- 5
- Length
- 287928
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.33 | 323 | 541 | 0.597 | 0.0000287 | 6684 |
| Missense (PolyPhen) | 64 | 200.95 | 0.31849 | 2546 | ||
| Synonymous | -0.112 | 199 | 197 | 1.01 | 0.0000110 | 1860 |
| Loss of Function | 5.38 | 0 | 33.7 | 0.00 | 0.00000178 | 453 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play an role in the regulation of Ins(1,4,5)P3 around the endoplasmic reticulum. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- RVIS EVS
- -0.62
- RVIS percentile EVS
- 17.31
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.811
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |