# NM_000141.5(FGFR2):c.1239G>A (p.Pro413=)

https://sugi.bio/variant/fgfr2-p-pro413

## Summary

**FGFR2 p.Pro413= (c.1239G>A)** is classified **Conflicting classifications of pathogenicity** in FGFR2 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2024-03-18). Ultra-rare (popmax 0.0223%, eas); Associated with Saethre-Chotzen syndrome.

**At a glance:** Conflicting classifications of pathogenicity · review: Conflicting submitters · rsID rs147674677 · 3 submitters · 4 linked conditions · ultra-rare (popmax 0.0223%, eas)

## For patients & families {#patients}

This is a change in the FGFR2 gene that is of uncertain or conflicting significance (submitters disagree on it), submitted by 3 submitters, and is linked to Saethre-Chotzen 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 | 7 registered for this condition — see ClinicalTrials.gov |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0007598/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [FGFR2](https://sugi.bio/atlas/gene/FGFR2/) |
| Protein change (HGVS p.) | p.Pro413= |
| Coding change (HGVS c.) | c.1239G>A |
| MANE Select transcript | [NM_000141](https://www.ncbi.nlm.nih.gov/nuccore/NM_000141) |
| dbSNP | [rs147674677](https://www.ncbi.nlm.nih.gov/snp/rs147674677/) |
| Variant type | single nucleotide variant |
| Location | chr10:121515165-121515165 (GRCh38) |
| ClinVar | [VCV299003](https://www.ncbi.nlm.nih.gov/clinvar/variation/299003/) |

**All HGVS expressions:** `LRG_994:g.88294G>A`, `LRG_994t1:c.1239G>A`, `LRG_994t2:c.1242G>A`, `NC_000010.10:g.123274679C>T`, `NC_000010.11:g.121515165C>T`, `NG_012449.2:g.88294G>A`, `NM_000141.5:c.1239G>A`, `NM_001144913.1:c.1242G>A`, `NM_001144914.1:c.903G>A`, `NM_001144915.2:c.972G>A`, `NM_001144916.2:c.894G>A`, `NM_001144917.2:c.939+4814G>A`, `NM_001144918.2:c.894G>A`, `NM_001144919.2:c.975G>A`, `NM_001320654.2:c.555G>A`, `NM_001320658.2:c.1239G>A`, `NM_022970.4:c.1242G>A`, `NM_023029.3:c.972G>A`, `NR_073009.2:n.1675G>A`

## 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 -5.223, GERP -4.32 — fast-evolving / accelerated position
- CADD: **PHRED 5.198**. 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: **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 FGFR2 (1,395 scored positions, the nearest 13 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 **0.0223%** (eas) · FAF95 0.012% · FAF99 0.00917% · 10/44,876 in the highest group · 61/1,614,150 alleles overall — ultra-rare (popmax 0.0223%, eas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| East Asian (grpmax) | 0.0223% | 4,488 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.00878% | 11,386 |
| African / African-American | 0.00666% | 15,005 |
| European (non-Finnish) | 0.00305% | 32,778 |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,508 |

*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}

**FGFR2** population constraint: LOEUF 0.278, pLI 1, missense-Z 4.4473. *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):

- **Apert syndrome** — Definitive (AD)
- **bent bone dysplasia syndrome 1** — Definitive (AD)
- **Beare-Stevenson cutis gyrata syndrome** — Definitive (AD)
- **Crouzon syndrome** — Definitive (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 74.33, 37% of residues very-high.

**65 experimental structure(s)** (PDB): [10OO](https://www.rcsb.org/structure/10OO), [10OQ](https://www.rcsb.org/structure/10OQ), [10OU](https://www.rcsb.org/structure/10OU), [1DJS](https://www.rcsb.org/structure/1DJS), [1E0O](https://www.rcsb.org/structure/1E0O), [1EV2](https://www.rcsb.org/structure/1EV2) — incl. mutant structure 10OO.

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

*Describes the biological roles of FGFR2 (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:** FGFR2's established molecular role includes fibroblast growth factor receptor activity. In Reactome, FGFR2 is annotated in disease pathway(s) including **Activated point mutants of FGFR2**, **Signaling by FGFR2 amplification mutants**.

**Disease mechanism (Reactome):** FGFR2 loss or alteration is curated in [Activated point mutants of FGFR2](https://reactome.org/content/detail/R-HSA-2033519), [Signaling by FGFR2 amplification mutants](https://reactome.org/content/detail/R-HSA-2023837), [Signaling by FGFR2 fusions](https://reactome.org/content/detail/R-HSA-8853333).

### Pathways affected {#pathways}

FGFR2 participates in **17 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Activated point mutants of FGFR2](https://reactome.org/content/detail/R-HSA-2033519) | curated |
| ⚕ [Signaling by FGFR2 amplification mutants](https://reactome.org/content/detail/R-HSA-2023837) | curated |
| ⚕ [Signaling by FGFR2 fusions](https://reactome.org/content/detail/R-HSA-8853333) | curated |
| ⚕ [Signaling by FGFR2 in disease](https://reactome.org/content/detail/R-HSA-5655253) | curated |
| ⚕ [Constitutive Signaling by Aberrant PI3K in Cancer](https://reactome.org/content/detail/R-HSA-2219530) | other |
| ⚕ [Signaling by FGFR2 IIIa TM](https://reactome.org/content/detail/R-HSA-8851708) | electronic |
| [FGFR2b ligand binding and activation](https://reactome.org/content/detail/R-HSA-190377) | other |
| [FGFR2c ligand binding and activation](https://reactome.org/content/detail/R-HSA-190375) | other |
| [FRS-mediated FGFR2 signaling](https://reactome.org/content/detail/R-HSA-5654700) | other |
| [Negative regulation of FGFR2 signaling](https://reactome.org/content/detail/R-HSA-5654727) | other |
| [PI-3K cascade:FGFR2](https://reactome.org/content/detail/R-HSA-5654695) | other |
| [PI3K Cascade](https://reactome.org/content/detail/R-HSA-109704) | other |
| [PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling](https://reactome.org/content/detail/R-HSA-6811558) | other |
| [PIP3 activates AKT signaling](https://reactome.org/content/detail/R-HSA-1257604) | other |
| [Phospholipase C-mediated cascade; FGFR2](https://reactome.org/content/detail/R-HSA-5654221) | other |
| [RAF/MAP kinase cascade](https://reactome.org/content/detail/R-HSA-5673001) | other |
| [SHC-mediated cascade:FGFR2](https://reactome.org/content/detail/R-HSA-5654699) | other |

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

**Molecular function:** fibroblast growth factor receptor activity, fibroblast growth factor binding, identical protein binding, protein homodimerization activity.

**Biological process:** positive regulation of cell population proliferation, fibroblast growth factor receptor signaling pathway, positive regulation of phospholipase activity, negative regulation of keratinocyte proliferation, peptidyl-tyrosine phosphorylation, positive regulation of MAPK cascade.

## Clinical significance {#significance}

**Conflicting classifications of pathogenicity** — review status Conflicting submitters *(criteria provided, conflicting classifications)*, last evaluated 2024-03-18.

**Submitter consensus:** conflicting (6 Likely benign, 1 Uncertain significance).

**Submission history:** 7 submissions (2018–2024); classifications have differed over time.

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Illumina Laboratory Services, Illumina | Likely benign | criteria provided, single submitter | clinical testing | 2018-01-12 |
| Illumina Laboratory Services, Illumina | Uncertain significance | criteria provided, single submitter | clinical testing | 2018-01-12 |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2024-03-18 |
| PreventionGenetics, part of Exact Sciences | Likely benign | no assertion criteria provided | clinical testing | 2020-01-27 |

## Associated conditions {#conditions}

[Saethre-Chotzen syndrome](https://sugi.bio/atlas/disease/saethre-chotzen-syndrome/), [Crouzon syndrome](https://sugi.bio/atlas/disease/crouzon-syndrome/), [Beare-Stevenson cutis gyrata syndrome](https://sugi.bio/atlas/disease/beare-stevenson-cutis-gyrata-syndrome/), [craniosynostosis](https://sugi.bio/atlas/disease/craniosynostosis/).

**Reported phenotype names (ClinVar):** Saethre-Chotzen syndrome, Isolated Coronal Synostosis, Crouzon syndrome, Beare-Stevenson cutis gyrata syndrome, Craniosynostosis syndrome, FGFR2-related craniosynostosis, FGFR2-related disorder, ACROCEPHALY, SKULL ASYMMETRY, AND MILD SYNDACTYLY, ACS III, CHOTZEN SYNDROME.

## Similar variants {#similar}

Related FGFR2 variant pages (same residue, condition, or type): [FGFR2 p.Pro413Leu](/variant/fgfr2-p-pro413leu), [FGFR2 c.1084+3A>G](/variant/fgfr2-c-1084-plus-3a-g), [FGFR2 p.Ala314Ser](/variant/fgfr2-p-ala314ser), [FGFR2 p.Ala337Pro](/variant/fgfr2-p-ala337pro), [FGFR2 p.Ala344=](/variant/fgfr2-p-ala344), [FGFR2 p.Ala344Gly](/variant/fgfr2-p-ala344gly), [FGFR2 p.Asn549His](/variant/fgfr2-p-asn549his), [FGFR2 p.Asp336Gly](/variant/fgfr2-p-asp336gly).

### 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 299003). 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.*