# NM_002880.4(RAF1):c.781C>T (p.Pro261Ser)

https://sugi.bio/variant/raf1-p-pro261ser

## Summary

**RAF1 p.Pro261Ser (c.781C>T)** is classified **Pathogenic** in RAF1 (ClinVar, Expert panel, 15 submitters; last evaluated 2017-04-03). AlphaMissense: likely pathogenic (0.9986); Absent from gnomAD v4.1; Associated with Noonan syndrome.

**At a glance:** Pathogenic · review: Expert panel · rsID rs121434594 · 15 submitters · 6 linked conditions · AlphaMissense likely pathogenic · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the RAF1 gene that is considered disease-causing, submitted by 15 submitters, and is linked to Noonan syndrome.

*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 | 27 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0010955/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.Pro261Ser |
| Coding change (HGVS c.) | c.781C>T |
| MANE Select transcript | [NM_002880](https://www.ncbi.nlm.nih.gov/nuccore/NM_002880) |
| dbSNP | [rs121434594](https://www.ncbi.nlm.nih.gov/snp/rs121434594/) |
| Variant type | single nucleotide variant |
| Location | chr3:12604189-12604189 (GRCh38) |
| ClinVar | [VCV13958](https://www.ncbi.nlm.nih.gov/clinvar/variation/13958/) |

**All HGVS expressions:** `LRG_413:g.64991C>T`, `LRG_413t1:c.781C>T`, `LRG_413t2:c.781C>T`, `NC_000003.11:g.12645688G>A`, `NC_000003.12:g.12604189G>A`, `NG_007467.1:g.64991C>T`, `NM_001354689.1:c.781C>T`, `NM_001354689.3:c.781C>T`, `NM_001354690.3:c.781C>T`, `NM_001354691.3:c.538C>T`, `NM_001354692.3:c.538C>T`, `NM_001354693.3:c.682C>T`, `NM_001354694.3:c.538C>T`, `NM_001354695.3:c.439C>T`, `NM_002880.4:c.781C>T`, `NR_148940.3:n.1112C>T`, `NR_148941.3:n.1112C>T`, `NR_148942.3:n.1112C>T`

## Computational & population evidence {#evidence}

**Concordance:** 1 independent predictor **concordant** with the ClinVar classification.

- AlphaMissense **likely pathogenic** (0.9986) — concordant with the pathogenic call
- REVEL 0.823 (moderately pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -5.361 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense and REVEL call this damaging; SaProt does not
- Conservation: phyloP 11.908, GERP 2.77, phastCons 1 — highly conserved (agrees)
- AlphaMissense ranks this among the **top 10%** most-pathogenic-predicted substitutions in RAF1 (of 3,821 modeled).
- CADD: **PHRED 29.6**. 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: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*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 **261** lies in the 'disordered' region; a UniProt-annotated variant site (in ns5; shows in vitro greater kinase activity and enhanced mapk1 activation than wild-type); a UniProt-annotated variant site (in ns5; shows greater kinase activity and enhanced mapk1 activation than wild-type); an α-helix.

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.Pro261Ser falls in the disordered region. 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}

**Pathogenic** — review status Expert panel *(reviewed by expert panel)*, last evaluated 2017-04-03.

**Submitter consensus:** unanimous (16/16 Pathogenic).

**Submission history:** 16 submissions (2007–2026); classifications have been stable.

**ClinGen expert panel:** Pathogenic — RASopathy VCEP (Noonan syndrome). *Expert-panel curated (ACMG); the highest ClinVar review tier.*
**Applied ACMG criteria (met):** `PM2`, `PM6_Strong`, `PS3`, `PM1`, `PP2`.
Inheritance: Autosomal dominant inheritance.

> **Curation rationale (ClinGen, verbatim):** The c.781C>T (p.Pro261Ser) variant in RAF1 has been reported in the literature in at least 2 unconfirmed de novo occurrences in patients with clinical features of a RASopathy (PM6_Strong; PMID 17603482, 20683980). In vitro functional studies provide some evidence that the p.Pro261Leu variant may impact protein function (PS3; PMID 17603483, 17603482). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of RAF1 (PM1; PMID 29493581). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PP2, PM1, PM2, PS3, PM6_Strong.
*Source: https://cspec.clinicalgenome.org/cspec/ui/svi/affiliation/50021 · approved 2017-04-03 · [ClinGen Evidence Repository](https://erepo.genome.network/evrepo/ui/classification/563677cb-406b-41f7-9c7d-7fc9d73cbbe2).*
*These are ClinGen's applied codes, reported verbatim — Sugi Variant does not re-tally or combine them into its own classification.*

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Genome Diagnostics Laboratory, The Hospital for Sick Children | Pathogenic | criteria provided, single submitter | clinical testing | 2020-06-01 |
| Ambry Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2022-06-02 |
| Ambry Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2016-04-12 |
| 3billion | Pathogenic | criteria provided, single submitter | clinical testing | 2024-09-28 |
| Labcorp Genetics (formerly Invitae), Labcorp | Pathogenic | criteria provided, single submitter | clinical testing | 2025-12-15 |
| OMIM | Pathogenic | no assertion criteria provided | literature only | 2007-08-01 |
| Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Pathogenic | criteria provided, single submitter | clinical testing | 2018-09-11 |
| Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Pathogenic | criteria provided, single submitter | clinical testing | 2019-03-22 |
| Clinical Genomics Laboratory, Washington University in St. Louis | Pathogenic | criteria provided, single submitter | clinical testing | 2026-04-07 |
| ClinGen RASopathy Variant Curation Expert Panel | Pathogenic | reviewed by expert panel | curation | 2017-04-03 |
| GeneDx | Pathogenic | criteria provided, single submitter | clinical testing | 2023-03-14 |
| Molecular Genetics, Centre for Human Genetics | Pathogenic | no assertion criteria provided | clinical testing |  |
| Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Pathogenic | criteria provided, single submitter | clinical testing | 2021-05-06 |
| Clinical Genetics Laboratory, Skane University Hospital Lund | Pathogenic | criteria provided, single submitter | clinical testing | 2022-06-27 |
| Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen | Pathogenic | criteria provided, single submitter | clinical testing | 2020-10-23 |
| Blueprint Genetics | Pathogenic | criteria provided, single submitter | clinical testing | 2024-05-17 |

## Associated conditions {#conditions}

[Noonan syndrome](https://sugi.bio/atlas/disease/noonan-syndrome/), [Noonan syndrome 1](https://sugi.bio/atlas/disease/noonan-syndrome-1/), [Noonan syndrome 5](https://sugi.bio/atlas/disease/noonan-syndrome-5/), [LEOPARD syndrome 2](https://sugi.bio/atlas/disease/leopard-syndrome-2/), [Noonan syndrome and Noonan-related syndrome](https://sugi.bio/atlas/disease/noonan-syndrome-and-noonan-related-syndrome/), [RASopathy](https://sugi.bio/atlas/disease/rasopathy/).

**Reported phenotype names (ClinVar):** Noonan syndrome, Noonan syndrome 5, not provided, RASopathy, Cardiovascular phenotype, Inborn genetic diseases, Noonan syndrome and Noonan-related syndrome, Noonan syndrome 1, LEOPARD syndrome 2, RAF1-related disorder.

## Same-residue context {#hotspot}

Residue **261** carries **5 other pathogenic ClinVar variants** — a recurrently-mutated position: [RAF1 p.Pro261Leu](/variant/raf1-p-pro261leu), [RAF1 p.Pro261His](/variant/raf1-p-pro261his), [RAF1 p.Pro261Thr](/variant/raf1-p-pro261thr), [RAF1 p.Pro261Ala](/variant/raf1-p-pro261ala), [RAF1 p.Pro261Arg](/variant/raf1-p-pro261arg). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related RAF1 variant pages (same residue, condition, or type): [RAF1 p.Pro261Ala](/variant/raf1-p-pro261ala), [RAF1 p.Pro261Arg](/variant/raf1-p-pro261arg), [RAF1 p.Pro261His](/variant/raf1-p-pro261his), [RAF1 p.Pro261Leu](/variant/raf1-p-pro261leu), [RAF1 p.Pro261Thr](/variant/raf1-p-pro261thr), [RAF1 p.Pro261=](/variant/raf1-p-pro261), [RAF1 p.Arg256Ser](/variant/raf1-p-arg256ser), [RAF1 p.Gly361Ala](/variant/raf1-p-gly361ala).

### 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 13958). 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.*