# NM_002880.4(RAF1):c.294_295dup (p.Phe99fs)

https://sugi.bio/variant/raf1-p-phe99fs

## Summary

**RAF1 p.Phe99fs (c.294_295dup)** is classified **Uncertain significance** in RAF1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-27). No gnomAD frequency available for this variant; Associated with RASopathy.

**At a glance:** Uncertain significance · review: Single submitter · rsID rs2470403638 · 1 submitter · 1 linked condition · no gnomAD frequency available for this variant

## For patients & families {#patients}

This is a change in the RAF1 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter, and is linked to RASopathy.

*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.*

|  |  |
| --- | --- |
| Clinical trials | 9 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0022213/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [RAF1](https://sugi.bio/atlas/gene/RAF1/) |
| Protein change (HGVS p.) | p.Phe99fs |
| Coding change (HGVS c.) | c.294_295dup |
| MANE Select transcript | [NM_002880](https://www.ncbi.nlm.nih.gov/nuccore/NM_002880) |
| dbSNP | [rs2470403638](https://www.ncbi.nlm.nih.gov/snp/rs2470403638/) |
| Variant type | Microsatellite |
| Location | chr3:12611974-12611975 (GRCh38) |
| ClinVar | [VCV2032882](https://www.ncbi.nlm.nih.gov/clinvar/variation/2032882/) |

**All HGVS expressions:** `LRG_413:g.57202GT[3]`, `LRG_413t1:c.292_293GT[3]`, `LRG_413t2:c.294_295dup`, `NC_000003.11:g.12653474AC[3]`, `NC_000003.12:g.12611975AC[3]`, `NG_007467.1:g.57202GT[3]`, `NM_001354689.3:c.294_295dup`, `NM_001354690.3:c.294_295dup`, `NM_001354691.3:c.78-2643GT[3]`, `NM_001354692.3:c.78-2643GT[3]`, `NM_001354693.3:c.294_295dup`, `NM_001354694.3:c.78-2643GT[3]`, `NM_001354695.3:c.78-2643GT[3]`, `NM_002880.4:c.294_295dup`, `NR_148940.3:n.623GT[3]`, `NR_148941.3:n.623GT[3]`, `NR_148942.3:n.623GT[3]`

## 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 (below), not from a missing predictor score.
- Conservation: phyloP 11.233, GERP 2.77, phastCons 1 — highly conserved position (PP3-type support)
- Molecular consequence: **frameshift** — a predicted loss-of-function variant. the gene is **loss-of-function-intolerant** (LOEUF 0.353, pLI 1), supporting a loss-of-function disease mechanism. *Descriptive; not an applied PVS1 code.*
- Nonsense-mediated decay: the premature termination codon is **in exon 3 of 17**, so the transcript is predicted to undergo NMD.
- SpliceAI: **not assessed** — the release is built from a substitutions-only source, so it holds no microsatellite variants. That is a property of the dataset, not of the variant, and is not evidence against a splicing effect.
- Population frequency: **no gnomAD frequency available for this variant** — rarity (ACMG PM2) and BA1/BS1 cannot be assessed for this variant.

*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}

**RAF1** population constraint: LOEUF 0.353, pLI 1, missense-Z 3.4281. *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):

- **Costello syndrome** — Disputed (AD)
- **Noonan syndrome** — Definitive (AD)
- **cardiofaciocutaneous syndrome** — Disputed (AD)
- **Noonan syndrome with multiple lentigines** — Limited (AD)

## Protein context {#protein}

Residue **99** lies in the rbd domain; a β-strand.

AlphaFold model confidence (whole protein): pLDDT 68.24, 30% of residues very-high.

**76 experimental structure(s)** (PDB): [1C1Y](https://www.rcsb.org/structure/1C1Y), [1FAQ](https://www.rcsb.org/structure/1FAQ), [1FAR](https://www.rcsb.org/structure/1FAR), [1GUA](https://www.rcsb.org/structure/1GUA), [1RFA](https://www.rcsb.org/structure/1RFA), [3CU8](https://www.rcsb.org/structure/3CU8) — incl. mutant structure 1GUA.

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

*Describes the biological roles of RAF1 (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:** RAF1's established molecular role includes protein kinase activity. p.Phe99fs falls in the rbd domain. In Reactome, RAF1 is annotated in disease pathway(s) including **Gain-of-function MRAS complexes activate RAF signaling**, **Paradoxical activation of RAF signaling by kinase inactive BRAF**.

**Disease mechanism (Reactome):** RAF1 loss or alteration is curated in [Gain-of-function MRAS complexes activate RAF signaling](https://reactome.org/content/detail/R-HSA-9726842), [Paradoxical activation of RAF signaling by kinase inactive BRAF](https://reactome.org/content/detail/R-HSA-6802955), [SHOC2 M1731 mutant abolishes MRAS complex function](https://reactome.org/content/detail/R-HSA-9726840).

### Pathways affected {#pathways}

RAF1 participates in **17 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Gain-of-function MRAS complexes activate RAF signaling](https://reactome.org/content/detail/R-HSA-9726842) | curated |
| ⚕ [Paradoxical activation of RAF signaling by kinase inactive BRAF](https://reactome.org/content/detail/R-HSA-6802955) | curated |
| ⚕ [SHOC2 M1731 mutant abolishes MRAS complex function](https://reactome.org/content/detail/R-HSA-9726840) | curated |
| ⚕ [Signaling by BRAF and RAF1 fusions](https://reactome.org/content/detail/R-HSA-6802952) | curated |
| ⚕ [Signaling by RAF1 mutants](https://reactome.org/content/detail/R-HSA-9656223) | curated |
| ⚕ [Signaling by high-kinase activity BRAF mutants](https://reactome.org/content/detail/R-HSA-6802948) | curated |
| ⚕ [Signaling by moderate kinase activity BRAF mutants](https://reactome.org/content/detail/R-HSA-6802946) | curated |
| ⚕ [Signaling downstream of RAS mutants](https://reactome.org/content/detail/R-HSA-9649948) | curated |
| [CD209 (DC-SIGN) signaling](https://reactome.org/content/detail/R-HSA-5621575) | curated |
| [GP1b-IX-V activation signalling](https://reactome.org/content/detail/R-HSA-430116) | curated |
| [IFNG signaling activates MAPKs](https://reactome.org/content/detail/R-HSA-9732724) | curated |
| [MAP2K and MAPK activation](https://reactome.org/content/detail/R-HSA-5674135) | curated |
| [Negative feedback regulation of MAPK pathway](https://reactome.org/content/detail/R-HSA-5674499) | curated |
| [Negative regulation of MAPK pathway](https://reactome.org/content/detail/R-HSA-5675221) | curated |
| [RAF activation](https://reactome.org/content/detail/R-HSA-5673000) | curated |
| [Rap1 signalling](https://reactome.org/content/detail/R-HSA-392517) | curated |
| [Stimuli-sensing channels](https://reactome.org/content/detail/R-HSA-2672351) | curated |

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

**Molecular function:** protein kinase activity, protein serine/threonine kinase activity, adenylate cyclase activator activity, enzyme binding, identical protein binding.

**Biological process:** negative regulation of cell population proliferation, negative regulation of protein-containing complex assembly, positive regulation of peptidyl-serine phosphorylation, negative regulation of apoptotic process, positive regulation of MAPK cascade.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-09-27.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Uncertain significance | criteria provided, single submitter | clinical testing | 2022-09-27 |

## Associated conditions {#conditions}

[RASopathy](https://sugi.bio/atlas/disease/rasopathy/).

**Reported phenotype names (ClinVar):** RASopathy, Noonan spectrum disorder, rasopathies.

## Similar variants {#similar}

Related RAF1 variant pages (same residue, condition, or type): [RAF1 p.Phe99=](/variant/raf1-p-phe99), [RAF1 c.-340_-339GA[1]](/variant/raf1-c-minus-340-minus-339ga-1), [RAF1 c.208-6_208-3del](/variant/raf1-c-208-minus-6-208-minus-3del), [RAF1 p.Asn523del](/variant/raf1-p-asn523del), [RAF1 p.Leu613fs](/variant/raf1-p-leu613fs), [RAF1 c.1668+10_1668+11del](/variant/raf1-c-1668-plus-10-1668-plus-11del), [RAF1 c.423+19_423+23del](/variant/raf1-c-423-plus-19-423-plus-23del), [RAF1 c.424-5_424-3del](/variant/raf1-c-424-minus-5-424-minus-3del).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); 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 2026-10-14); 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 2032882). 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.*