# NM_001791.4(CDC42):c.348A>G (p.Gln116=)

https://sugi.bio/variant/cdc42-p-gln116

## Summary

**CDC42 p.Gln116= (c.348A>G)** is classified **Benign** in CDC42 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-12-11). Ultra-rare (popmax 0.0209%, sas).

**At a glance:** Benign · review: Single submitter · rsID rs772882822 · 1 submitter · ultra-rare (popmax 0.0209%, sas)

## For patients & families {#patients}

This is a change in the CDC42 gene that is classified as benign — not considered disease-causing, submitted by 1 submitter.

*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.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [CDC42](https://sugi.bio/atlas/gene/CDC42/) |
| Protein change (HGVS p.) | p.Gln116= |
| Coding change (HGVS c.) | c.348A>G |
| MANE Select transcript | [NM_001791](https://www.ncbi.nlm.nih.gov/nuccore/NM_001791) |
| dbSNP | [rs772882822](https://www.ncbi.nlm.nih.gov/snp/rs772882822/) |
| Variant type | single nucleotide variant |
| Location | chr1:22086728-22086728 (GRCh38) |
| ClinVar | [VCV1900448](https://www.ncbi.nlm.nih.gov/clinvar/variation/1900448/) |

**All HGVS expressions:** `LRG_1326:g.66218A>G`, `LRG_1326t1:c.348A>G`, `LRG_1326t2:c.348A>G`, `NC_000001.10:g.22413221A>G`, `NC_000001.11:g.22086728A>G`, `NG_047042.3:g.66218A>G`, `NM_001039802.2:c.348A>G`, `NM_001791.4:c.348A>G`, `NM_044472.3:c.348A>G`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation and, for splice-region changes, SpliceAI (below), not from a missing predictor score.
- SpliceAI predicts **acceptor gain** (Δ 0.91) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP 1.622, GERP 0.206, phastCons 0.999 — weakly conserved position
- CADD: **PHRED 22.7**. 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.*
- SpliceAI deltas (raw): acceptor loss **0.13**, donor loss **0.00**, acceptor gain **0.91**, donor gain **0.00**. Largest is acceptor gain.
- SpliceAI deltas (masked): acceptor loss **0.00**, donor loss **0.00**, acceptor gain **0.91**, donor gain **0.00**.
- Pangolin: Δ**0.59** (gain), gain 0.59 / loss 0.00. Agrees with SpliceAI. An independent predictor to SpliceAI — a different model trained on different data. *Descriptive; ClinGen's SVI calibration covers SpliceAI, not Pangolin, so no ACMG code is assigned.*
- Population frequency (gnomAD v4.1): grpmax **0.0209%** (sas) · FAF95 0.0136% · FAF99 0.0114% · 19/91,088 in the highest group · 34/1,613,982 alleles overall — ultra-rare (popmax 0.0209%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| South Asian (grpmax) | 0.0209% | 4,794 |
| Middle Eastern | 0.0164% | 6,084 |
| African / African-American | 0.004% | 24,970 |
| Remaining individuals (not grpmax-eligible) | 0.0032% | 31,242 |
| East Asian | 0.00223% | 44,892 |
| Admixed American | 0.00167% | 59,996 |
| European (non-Finnish) | 0.000593% | 168,571 |

*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}

**CDC42** population constraint: LOEUF 0.611, pLI 0.872, missense-Z 2.9049. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **macrothrombocytopenia-lymphedema-developmental delay-facial dysmorphism-camptodactyly syndrome** — Definitive (AD)

## Protein context {#protein}

Residue **116** lies in a binding site.

AlphaFold model confidence (whole protein): pLDDT 93.30, 84% of residues very-high.

**48 experimental structure(s)** (PDB): [1A4R](https://www.rcsb.org/structure/1A4R), [1AJE](https://www.rcsb.org/structure/1AJE), [1AM4](https://www.rcsb.org/structure/1AM4), [1AN0](https://www.rcsb.org/structure/1AN0), [1CEE](https://www.rcsb.org/structure/1CEE), [1CF4](https://www.rcsb.org/structure/1CF4) — incl. mutant structure 1A4R.

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

*Describes the biological roles of CDC42 (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:** CDC42's established molecular role includes GTPase activity. In Reactome, CDC42 is annotated in disease pathway(s) including **FCGR3A-mediated phagocytosis**.

**Disease mechanism (Reactome):** CDC42 loss or alteration is curated in [FCGR3A-mediated phagocytosis](https://reactome.org/content/detail/R-HSA-9664422).

### Pathways affected {#pathways}

CDC42 participates in **30 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [FCGR3A-mediated phagocytosis](https://reactome.org/content/detail/R-HSA-9664422) | electronic |
| [CD28 dependent Vav1 pathway](https://reactome.org/content/detail/R-HSA-389359) | curated |
| [CDC42 GTPase cycle](https://reactome.org/content/detail/R-HSA-9013148) | curated |
| [DCC mediated attractive signaling](https://reactome.org/content/detail/R-HSA-418885) | curated |
| [EGFR downregulation](https://reactome.org/content/detail/R-HSA-182971) | curated |
| [Factors involved in megakaryocyte development and platelet production](https://reactome.org/content/detail/R-HSA-983231) | curated |
| [G beta:gamma signalling through CDC42](https://reactome.org/content/detail/R-HSA-8964616) | curated |
| [GPVI-mediated activation cascade](https://reactome.org/content/detail/R-HSA-114604) | curated |
| [Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation](https://reactome.org/content/detail/R-HSA-8950505) | curated |
| [MAPK6/MAPK4 signaling](https://reactome.org/content/detail/R-HSA-5687128) | curated |
| [RAC1 GTPase cycle](https://reactome.org/content/detail/R-HSA-9013149) | curated |
| [RAC2 GTPase cycle](https://reactome.org/content/detail/R-HSA-9013404) | curated |
| [RAC3 GTPase cycle](https://reactome.org/content/detail/R-HSA-9013423) | curated |
| [RHO GTPases activate IQGAPs](https://reactome.org/content/detail/R-HSA-5626467) | curated |
| [RHO GTPases activate KTN1](https://reactome.org/content/detail/R-HSA-5625970) | curated |
| [RHO GTPases activate PAKs](https://reactome.org/content/detail/R-HSA-5627123) | curated |
| [RHOG GTPase cycle](https://reactome.org/content/detail/R-HSA-9013408) | curated |
| [RHOJ GTPase cycle](https://reactome.org/content/detail/R-HSA-9013409) | curated |
| [RHOQ GTPase cycle](https://reactome.org/content/detail/R-HSA-9013406) | curated |
| [RHOU GTPase cycle](https://reactome.org/content/detail/R-HSA-9013420) | curated |
| [RHOV GTPase cycle](https://reactome.org/content/detail/R-HSA-9013424) | curated |
| [SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST)](https://reactome.org/content/detail/R-HSA-9958810) | curated |
| [VEGFA-VEGFR2 Pathway](https://reactome.org/content/detail/R-HSA-4420097) | curated |
| [Activation of STAT3 by cadherin engagement](https://reactome.org/content/detail/R-HSA-9958825) | electronic |
| [EPHB-mediated forward signaling](https://reactome.org/content/detail/R-HSA-3928662) | electronic |
| [Inactivation of CDC42 and RAC1](https://reactome.org/content/detail/R-HSA-428543) | electronic |
| [Myogenesis](https://reactome.org/content/detail/R-HSA-525793) | electronic |
| [RHO GTPases Activate Formins](https://reactome.org/content/detail/R-HSA-5663220) | electronic |
| [RHO GTPases Activate WASPs and WAVEs](https://reactome.org/content/detail/R-HSA-5663213) | electronic |
| [Regulation of actin dynamics for phagocytic cup formation](https://reactome.org/content/detail/R-HSA-2029482) | electronic |

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

**Molecular function:** GTPase activity, GTP binding, protein kinase binding, thioesterase binding, GBD domain binding, apolipoprotein A-I receptor binding.

**Biological process:** phagocytosis, engulfment, actin filament organization, integrin-mediated signaling pathway, regulation of lamellipodium assembly, positive regulation of lamellipodium assembly, substantia nigra development.

## Clinical significance {#significance}

**Benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2023-12-11.

**Submitter consensus:** unanimous (1/1 Benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Benign | criteria provided, single submitter | clinical testing | 2023-12-11 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Same-residue context {#hotspot}

Residue **116** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [CDC42 p.Gln116Glu](/variant/cdc42-p-gln116glu). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related CDC42 variant pages (same residue, condition, or type): [CDC42 p.Gln116Glu](/variant/cdc42-p-gln116glu), [CDC42 p.Ala159Val](/variant/cdc42-p-ala159val), [CDC42 p.Arg186Cys](/variant/cdc42-p-arg186cys), [CDC42 p.Arg66Gly](/variant/cdc42-p-arg66gly), [CDC42 p.Arg68Gln](/variant/cdc42-p-arg68gln), [CDC42 p.Cys81Phe](/variant/cdc42-p-cys81phe), [CDC42 p.Glu171Lys](/variant/cdc42-p-glu171lys), [CDC42 p.Ser83Pro](/variant/cdc42-p-ser83pro).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-11); gnomAD v4.1 (Broad Institute, built 2026-10-06); 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 2026-07-14); 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 1900448). 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.*