PLCG1

protein-coding

phospholipase 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]

Previous symbols:
  • PLC1

MANE transcript

NM_002660.3

Inheritance

AD

ClinVar variants

P:1U:155B:15

Top phenotype

Immune dysregulation, autoimmunity, and autoinflammation

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr20:41,136,960-41,196,801

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~59.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

immune dysregulation, autoimmunity, and autoinflammationMODERATE

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.

immune dysregulation, autoimmunity, and autoinflammationLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0957790

Submitter: Ambry Genetics

immune dysregulation, autoimmunity, and autoinflammationMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0957790

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Immune dysregulation, autoimmunity, and autoinflammationAD

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

Refs: 37422272Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PLCG1 variants in ClinVar

6 Conditions Cataloged
not specifiedTotal: 120
PLCG1-related disorderTotal: 23
not providedTotal: 10
Immune dysregulation, autoimmunity, and autoinflammationTotal: 4
Multiple endocrine neoplasia, type 1Total: 2
Hereditary breast ovarian cancer syndromeTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
7
clinvar
1
clinvar
13
missense
1
clinvar
141
clinvar
7
clinvar
149
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
8
clinvar
8
Total10155141171
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002660.3RefSeqNP_002651.232MANE Select
ENST00000685551.1EnsemblENSP00000508698.132MANE Select
NM_182811.2RefSeqNP_877963.132Standard
ENST00000244007.7EnsemblENSP00000244007.332Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
plcg1Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense3.245207730.6720.00004988500
Missense (PolyPhen)161326.190.493573524
Synonymous-0.04623002991.000.00001902433
Loss of Function5.942482.10.2920.00000474850

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000370.00037rare
Latino/Admixed American0.000140.00014rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish0.000190.00018rare
European (Non-Finnish)0.000170.00017rare
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.