PLCG1
protein-codingphospholipase C gamma 1, the group of Phospholipases|Pleckstrin homology domain containing|MicroRNA protein coding host genes|SH2 domain containing|C2 domain containing phospholipases|EF-hand domain containing
Gene summary
The protein encoded by this gene catalyzes the formation of inositol 1,4,5-trisphosphate and diacylglycerol from phosphatidylinositol 4,5-bisphosphate. This reaction uses calcium as a cofactor and plays an important role in the intracellular transduction of receptor-mediated tyrosine kinase activators. For example, when activated by SRC, the encoded protein causes the Ras guanine nucleotide exchange factor RasGRP1 to translocate to the Golgi, where it activates Ras. Also, this protein has been shown to be a major substrate for heparin-binding growth factor 1 (acidic fibroblast growth factor)-activated tyrosine kinase. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
- PLC1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~59.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0957790
Submitter: ClinGen
A monogenic association between PLCG1 and human disease was first reported in 2023 in an individual with an autosomal dominant syndrome featuring autoimmune anemia and thrombocytopenia, bleeding diathesis, and lymphadenopathy (PMID: 37422272). The condition was later termed “Immune Dysregulation, Autoimmunity, Autoinflammation” (OMIM: 620514; MONDO: 0957790). This individual also had multiple autoantibodies (direct antiglobulin, anti-platelet, ANA 1:1000, anti-SSA, anti-nucleosome), decreased NK cells, low C3/C4, and elevated ESR. To date, eight individuals with heterozygous PLCG1 variants have been reported, six with immune phenotypes. All additional cases were described in a case series reporting variable immune, vision, hearing, and cardiac features in autosomal dominant PLCG1 disease (PMID: 40862571). Reported immune manifestations include recurrent respiratory infections, pneumococcal sepsis, severe EBV infection, recurrent immune thrombocytopenia, lymphadenopathy, arthritis/synovitis, recurrent encephalopathy, impaired polysaccharide vaccine responses, and decreased IgA and IgG2. Non-immune features include blindness, sensorineural hearing loss, septal defects, and motor and speech delays. Phenotypic variability is high, including among four related individuals with the same variant, indicating variable expressivity. The mechanism of pathogenicity is gain of function. Multiple patient variants show increased PLCG1 enzymatic activity, elevated inositol phosphate production, hyperactivation of NFAT, NF-κB, and AP-1 pathways, and increased inflammatory cytokines (PMIDs: 37422272, 40862571, 27369867). A PLCG inhibitor rescues these abnormalities, including excess MAPK phosphorylation and cytokine expression (PMID: 37422272). Additional supporting evidence includes PLCG1 expression in many immune cell types (PMIDs: 22837484, 15372077, 1281218) and impaired inositol phosphate production, proliferation, and cytokine responses in PLCG1-deficient T cells (PMID: 20123962). Unscored but relevant evidence comes from a mouse model of constitutive PLCG2 activation (PMID: 15845450). PLCG2 is highly homologous to PLCG1, functions in analogous signaling pathways, and is itself associated with GOF autoinflammatory disease (PLAID and APLAID). PLCG2-GOF mice develop arthritis, uveitis, and glomerulonephritis, and show increased B-cell Ca²⁺ flux and anti-DNA antibodies. In summary, there is moderate evidence linking PLCG1 to an autosomal dominant, gain-of-function disorder with variable expressivity of immune dysregulation, as well as hearing, vision, and cardiac features. Given that “immune dysregulation” encompasses “autoimmunity” and “autoinflammation”, we propose the simplified disease name “PLCG1 Immune Dysregulation.” However, given phenotypic variability and sparsity of published cases, the core immune features of this condition remain incompletely defined, and additional case descriptions with detailed immune phenotyping are needed.
Inheritance Pattern: AD
Disease ID:MONDO:0957790
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0957790
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Allergy/Immunology/Infectious; Hematologic
Intervention: Allergy/Immunology/Infectious; Hematologic
Rationale: The condition has been described as involving immune dysfucntion and hematologic abnormalities, and medical management (eg, with immunosuppressive agents and tranfusions) has been reported as beneficial
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PLCG1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002660.3. 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 | 5 | 7 | 1 | 13 | ||
| missense | 1 | 141 | 7 | 149 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 1 | 0 | 155 | 14 | 1 | 171 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002651.2 | 32 | MANE Select | |
| Ensembl | ENSP00000508698.1 | 32 | MANE Select | |
| RefSeq | NP_877963.1 | 32 | Standard | |
| Ensembl | ENSP00000244007.3 | 32 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| plcg1 | Danio rerio | Structure: nucleate erythrocyte Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Inflammatory mediator regulation of TRP channels - Homo sapiens (human)
- Non-small cell lung cancer - Homo sapiens (human)
- T cell receptor signaling pathway - Homo sapiens (human)
- Fc epsilon RI signaling pathway - Homo sapiens (human)
- Fc gamma R-mediated phagocytosis - Homo sapiens (human)
Biological Process
- in utero embryonic development
- signal transduction
- epidermal growth factor receptor signaling pathway
- activation of phospholipase C activity
- axon guidance
Molecular Function
- phosphatidylinositol phospholipase C activity
- phospholipase C activity
- neurotrophin TRKA receptor binding
- calcium ion binding
- protein binding
Cellular Component
- ruffle
- cytoplasm
- cytosol
- plasma membrane
- cell-cell junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000373272
- Coding exons
- 32
- Length
- 46030
- Individuals with no LoFs
- 125709
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 39
- Defined
- 125748
- p
- 0.000155
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.24 | 520 | 773 | 0.672 | 0.0000498 | 8500 |
| Missense (PolyPhen) | 161 | 326.19 | 0.49357 | 3524 | ||
| Synonymous | -0.0462 | 300 | 299 | 1.00 | 0.0000190 | 2433 |
| Loss of Function | 5.94 | 24 | 82.1 | 0.292 | 0.00000474 | 850 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00014 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Mediates the production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3). Plays an important role in the regulation of intracellular signaling cascades. Becomes activated in response to ligand- mediated activation of receptor-type tyrosine kinases, such as PDGFRA, PDGFRB, FGFR1, FGFR2, FGFR3 and FGFR4. Plays a role in actin reorganization and cell migration. {ECO:0000269|PubMed:17229814}.;
Recessive Scores
- pRec
- 0.633
Intolerance Scores
- LoFtool
- 0.597
- RVIS EVS
- -1.97
- RVIS percentile EVS
- 1.82
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.763
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |