# NM_002661.5(PLCG2):c.2374C>T (p.Arg792Cys)

https://sugi.bio/variant/plcg2-p-arg792cys

## Summary

**PLCG2 p.Arg792Cys (c.2374C>T)** is classified **Uncertain significance** in PLCG2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-07-02). AlphaMissense: likely benign (0.2832); Very rare (popmax 0.00134%, afr); Associated with familial cold autoinflammatory syndrome 3.

**At a glance:** Uncertain significance · review: Multiple submitters · rsID rs983424200 · 2 submitters · 1 linked condition · AlphaMissense likely benign · very rare (popmax 0.00134%, afr)

## For patients & families {#patients}

This is a change in the PLCG2 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 2 submitters, and is linked to familial cold autoinflammatory syndrome 3.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal dominant |
| Age of onset (of this condition) | Infancy, Neonatal |
| Diagnostic panels | PLCG2 is a diagnostic-grade gene on 3 Genomics England panels |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0017369/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PLCG2](https://sugi.bio/atlas/gene/PLCG2/) |
| Protein change (HGVS p.) | p.Arg792Cys |
| Coding change (HGVS c.) | c.2374C>T |
| MANE Select transcript | [NM_002661](https://www.ncbi.nlm.nih.gov/nuccore/NM_002661) |
| dbSNP | [rs983424200](https://www.ncbi.nlm.nih.gov/snp/rs983424200/) |
| Variant type | single nucleotide variant |
| Location | chr16:81923551-81923551 (GRCh38) |
| ClinVar | [VCV1013108](https://www.ncbi.nlm.nih.gov/clinvar/variation/1013108/) |

**All HGVS expressions:** `LRG_376:g.189455C>T`, `NC_000016.10:g.81923551C>T`, `NC_000016.9:g.81957156C>T`, `NG_032019.2:g.189455C>T`, `NM_002661.5:c.2374C>T`

## Computational & population evidence {#evidence}

**Concordance:** ClinVar classifies this **uncertain**; the computational predictors unanimously lean **tolerated** — a triage signal, not a reclassification.

- AlphaMissense **likely benign** (0.2832)
- REVEL 0.27 (benign-leaning) — agrees with AlphaMissense
- SaProt LLR -9.401 (tolerated) — agrees with AlphaMissense
- → **In-silico consensus:** AlphaMissense, REVEL and SaProt all call this tolerated
- Conservation: phyloP 3.084, GERP -0.277, phastCons 1 — highly conserved (differs from AlphaMissense)
- CADD: **PHRED 27.0**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- Regional missense constraint: **o/e 1.09** across the covering region of the MANE Select transcript (81,785,990–81,957,995), spanning 172,005 bp. Chi-square p 0.00029. Describes the region, not this allele; gnomAD v4.1.1's own constrained determination. *Descriptive; no ACMG code applied.*
- SpliceAI: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for PLCG2 (2,380 scored positions, the nearest 12 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency (gnomAD v4.1): grpmax **0.00134%** (afr) · FAF95 0.000247% · FAF99 0.000159% · 1/74,890 in the highest group · 9/1,613,532 alleles overall — very rare (popmax 0.00134%, afr).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Finnish (not grpmax-eligible) | 0.00156% | 63,968 |
| African / African-American (grpmax) | 0.00134% | 74,890 |
| European (non-Finnish) | 0.000593% | 168,524 |

Finnish shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**PLCG2** population constraint: LOEUF 0.461, pLI 0.9987, missense-Z -0.641. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

## Protein context {#protein}

Residue **792** lies in the sh3 domain.

AlphaFold model confidence (whole protein): pLDDT 83.49, 46% of residues very-high.

**8 experimental structure(s)** (PDB): [2K2J](https://www.rcsb.org/structure/2K2J), [2W2W](https://www.rcsb.org/structure/2W2W), [2W2X](https://www.rcsb.org/structure/2W2X), [8JQG](https://www.rcsb.org/structure/8JQG), [8JQH](https://www.rcsb.org/structure/8JQH), [8JQI](https://www.rcsb.org/structure/8JQI).

## What this gene does {#gene-function}

*Describes the biological roles of PLCG2 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** PLCG2's established molecular role includes phosphotyrosine residue binding. p.Arg792Cys falls in the sh3 domain. In Reactome, PLCG2 is annotated in disease pathway(s) including **FCGR3A-mediated IL10 synthesis**, **Potential therapeutics for SARS**.

**Disease mechanism (Reactome):** PLCG2 loss or alteration is curated in [FCGR3A-mediated IL10 synthesis](https://reactome.org/content/detail/R-HSA-9664323), [Potential therapeutics for SARS](https://reactome.org/content/detail/R-HSA-9679191).

### Pathways affected {#pathways}

PLCG2 participates in **15 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [FCGR3A-mediated IL10 synthesis](https://reactome.org/content/detail/R-HSA-9664323) | curated |
| ⚕ [Potential therapeutics for SARS](https://reactome.org/content/detail/R-HSA-9679191) | curated |
| [DAP12 signaling](https://reactome.org/content/detail/R-HSA-2424491) | curated |
| [FCERI mediated MAPK activation](https://reactome.org/content/detail/R-HSA-2871796) | curated |
| [GPVI-mediated activation cascade](https://reactome.org/content/detail/R-HSA-114604) | curated |
| [Generation of second messenger molecules](https://reactome.org/content/detail/R-HSA-202433) | curated |
| [Role of phospholipids in phagocytosis](https://reactome.org/content/detail/R-HSA-2029485) | curated |
| [Synthesis of IP3 and IP4 in the cytosol](https://reactome.org/content/detail/R-HSA-1855204) | curated |
| [Toll Like Receptor 4 (TLR4) Cascade](https://reactome.org/content/detail/R-HSA-166016) | curated |
| [Antigen activates B Cell Receptor (BCR) leading to generation of second messengers](https://reactome.org/content/detail/R-HSA-983695) | electronic |
| [CLEC7A (Dectin-1) signaling](https://reactome.org/content/detail/R-HSA-5607764) | electronic |
| [Dectin-2 family](https://reactome.org/content/detail/R-HSA-5621480) | electronic |
| [Erythropoietin activates Phospholipase C gamma (PLCG)](https://reactome.org/content/detail/R-HSA-9027277) | electronic |
| [FCERI mediated Ca+2 mobilization](https://reactome.org/content/detail/R-HSA-2871809) | electronic |
| [Signaling by CSF1 (M-CSF) in myeloid cells](https://reactome.org/content/detail/R-HSA-9680350) | electronic |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** phosphotyrosine residue binding, phosphatidylinositol-4,5-bisphosphate phospholipase C activity, protein kinase binding, scaffold protein binding, protein tyrosine kinase binding.

**Biological process:** phosphatidylinositol biosynthetic process, positive regulation of gene expression, regulation of lipid metabolic process, calcium-mediated signaling, lipopolysaccharide-mediated signaling pathway, intracellular signal transduction.

## Clinical significance {#significance}

**Uncertain significance** — review status Multiple submitters *(criteria provided, multiple submitters, no conflicts)*, last evaluated 2025-07-02.

**Submitter consensus:** unanimous (2/2 Uncertain significance).

**Submission history:** 2 submissions (2020–2025); classifications have been stable.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2025-07-02 |
| CeGaT Center for Human Genetics Tuebingen | Uncertain significance | criteria provided, single submitter | clinical testing | 2020-10-01 |

## Associated conditions {#conditions}

[familial cold autoinflammatory syndrome 3](https://sugi.bio/atlas/disease/familial-cold-autoinflammatory-syndrome-3/).

**Reported phenotype names (ClinVar):** Familial cold autoinflammatory syndrome 3, not provided, none provided, FAMILIAL ATYPICAL COLD URTICARIA, ANTIBODY DEFICIENCY AND IMMUNE DYSREGULATION, PLCG2-ASSOCIATED.

## Similar variants {#similar}

Related PLCG2 variant pages (same residue, condition, or type): [PLCG2 p.Arg792Pro](/variant/plcg2-p-arg792pro), [PLCG2 p.Ala708Pro](/variant/plcg2-p-ala708pro), [PLCG2 c.1467+3G>A](/variant/plcg2-c-1467-plus-3g-a), [PLCG2 c.1934+1G>A](/variant/plcg2-c-1934-plus-1g-a), [PLCG2 c.2235+3A>G](/variant/plcg2-c-2235-plus-3a-g), [PLCG2 c.2235+5G>A](/variant/plcg2-c-2235-plus-5g-a), [PLCG2 c.2307+4C>T](/variant/plcg2-c-2307-plus-4c-t), [PLCG2 c.2581+5G>A](/variant/plcg2-c-2581-plus-5g-a).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 1013108). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*