# NM_002880.4(RAF1):c.769T>C (p.Ser257Pro)

https://sugi.bio/variant/raf1-p-ser257pro

## Summary

**RAF1 p.Ser257Pro (c.769T>C)** is classified **Likely pathogenic** in RAF1 (ClinVar, Expert panel, 4 submitters; last evaluated 2017-04-03). AlphaMissense: likely pathogenic (0.9797); Very rare (popmax 8.47e-05%, nfe); Associated with RASopathy.

**At a glance:** Likely pathogenic · review: Expert panel · rsID rs727505017 · 4 submitters · 2 linked conditions · AlphaMissense likely pathogenic · very rare (popmax 8.47e-05%, nfe)

## For patients & families {#patients}

This is a change in the RAF1 gene that is considered likely disease-causing, submitted by 4 submitters, 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.Ser257Pro |
| Coding change (HGVS c.) | c.769T>C |
| MANE Select transcript | [NM_002880](https://www.ncbi.nlm.nih.gov/nuccore/NM_002880) |
| dbSNP | [rs727505017](https://www.ncbi.nlm.nih.gov/snp/rs727505017/) |
| Variant type | single nucleotide variant |
| Location | chr3:12604201-12604201 (GRCh38) |
| ClinVar | [VCV40600](https://www.ncbi.nlm.nih.gov/clinvar/variation/40600/) |

**All HGVS expressions:** `LRG_413:g.64979T>C`, `LRG_413t1:c.769T>C`, `LRG_413t2:c.769T>C`, `NC_000003.11:g.12645700A>G`, `NC_000003.12:g.12604201A>G`, `NG_007467.1:g.64979T>C`, `NM_001354689.3:c.769T>C`, `NM_001354690.3:c.769T>C`, `NM_001354691.3:c.526T>C`, `NM_001354692.3:c.526T>C`, `NM_001354693.3:c.670T>C`, `NM_001354694.3:c.526T>C`, `NM_001354695.3:c.427T>C`, `NM_002880.4:c.769T>C`, `NR_148940.3:n.1100T>C`, `NR_148941.3:n.1100T>C`, `NR_148942.3:n.1100T>C`

## Computational & population evidence {#evidence}

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

- AlphaMissense **likely pathogenic** (0.9797) — concordant with the pathogenic call
- REVEL 0.667 (pathogenic-leaning) — agrees with AlphaMissense
- SaProt LLR -7.778 (tolerated) — differs from AlphaMissense
- → **In-silico consensus:** AlphaMissense and REVEL call this damaging; SaProt does not
- Conservation: phyloP 11.288, GERP 2.77, phastCons 1 — highly conserved (agrees)
- CADD: **PHRED 29.3**. 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 (gnomAD v4.1): grpmax **8.47e-05%** (nfe) · 1/1,179,980 in the highest group · 1/1,461,888 alleles overall — very rare (popmax 8.47e-05%, nfe).

*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 **257** lies in the 'disordered' region; a UniProt-annotated variant site (in ns5 and lprd2; shows in vitro greater kinase activity and enhanced erk 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.Ser257Pro 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}

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

**Submitter consensus:** conflicting (3 Likely pathogenic, 1 Pathogenic).

**Submission history:** 4 submissions (2016–2023); classifications have differed over time.

**ClinGen expert panel:** Likely Pathogenic — RASopathy VCEP (RASopathy). *Expert-panel curated (ACMG); the highest ClinVar review tier.*
**Applied ACMG criteria (met):** `PM6`, `PM2`, `PS4_Moderate`, `PP2`.
*Considered but not met:* `PM5`.
Inheritance: Autosomal dominant inheritance.

> **Curation rationale (ClinGen, verbatim):** The c.769T>C (p.Ser257Pro) variant in RAF1 was absent from large population studies (PM2; gnomAD.broadinstitute.org). It has been identified in 3 patients with clinical features of a RASopathy (PS4_Moderate, SCV000206160.5; SCV000209015.10; PMID 23321623). In one proband the variant occurred de novo without parental confirmation (PM6). A different pathogenic missense variant has been previously identified at this codon which may indicate that this residue is critical to the function of the protein (PM5; ClinVar 13957) Furthermore, the p.Ser257Pro variant is located in RAF1, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic variants are common (PP2; PMID: 29493581). In summary, this variant meets criteria to be classified as likely pathogenic for RASopathies in an autosomal dominant manner. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4_Moderate, PM1, PM2, PM6, PP2.
*Source: https://cspec.clinicalgenome.org/cspec/ui/svi/affiliation/50021 · approved 2020-07-23 · [ClinGen Evidence Repository](https://erepo.genome.network/evrepo/ui/classification/a0bdf58d-d601-4924-95a5-27039f763685).*
*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 |
| --- | --- | --- | --- | --- |
| Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Pathogenic | criteria provided, single submitter | clinical testing | 2016-07-12 |
| GeneDx | Likely pathogenic | criteria provided, single submitter | clinical testing | 2019-03-19 |
| ClinGen RASopathy Variant Curation Expert Panel | Likely pathogenic | reviewed by expert panel | curation | 2017-04-03 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely pathogenic | criteria provided, single submitter | clinical testing | 2023-12-12 |

## Associated conditions {#conditions}

[RASopathy](https://sugi.bio/atlas/disease/rasopathy/), [Noonan syndrome](https://sugi.bio/atlas/disease/noonan-syndrome/).

**Reported phenotype names (ClinVar):** RASopathy, Noonan syndrome, not provided, none provided, Noonan spectrum disorder, rasopathies, Noonan's syndrome.

## Same-residue context {#hotspot}

Residue **257** carries **2 other pathogenic ClinVar variants** — a recurrently-mutated position: [RAF1 p.Ser257Leu](/variant/raf1-p-ser257leu), [RAF1 p.Ser257Thr](/variant/raf1-p-ser257thr). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related RAF1 variant pages (same residue, condition, or type): [RAF1 p.Ser257Leu](/variant/raf1-p-ser257leu), [RAF1 p.Ser257Thr](/variant/raf1-p-ser257thr), [RAF1 p.Ser257=](/variant/raf1-p-ser257), [RAF1 p.Ser257Trp](/variant/raf1-p-ser257trp), [RAF1 p.Arg256Ser](/variant/raf1-p-arg256ser), [RAF1 p.Gly361Ala](/variant/raf1-p-gly361ala), [RAF1 p.Leu613Val](/variant/raf1-p-leu613val), [RAF1 p.Pro261Ser](/variant/raf1-p-pro261ser).

### 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 40600). 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.*