FGFR4 p.Pro402=
c.1206G>A · rs147603016 · VCV3053826
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.06%, nfe)
Conditions
1
FGFR4-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.267 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.2 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 8.179 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.06%
European (non-Finnish) · 250/416,548 alleles
Filtering AF
0.0539%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0515%
Overall
0.042%
298/709,232 alleles · ultra-rare
exomes 280/566,356 · genomes 18/142,876 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.06% | 1,666 |
| Remaining individualsnot grpmax-eligible | 0.0424% | 2,359 |
| South Asian | 0.0402% | 2,485 |
| Middle Eastern | 0.0281% | 3,556 |
| African / African-American | 0.0075% | 13,341 |
| Admixed American | 0.00386% | 25,881 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- FGFR4
- Protein
- p.Pro402=
- Coding
- c.1206G>A
- MANE Select
- NM_213647
- dbSNP
- rs147603016
- Type
- single nucleotide variant
- Location
- chr5:177093286 (GRCh38)
- Gene constraint
- LOEUF 0.884 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.30 · 52 PDB
Disease context
FGFR4-related disorder
Similar variants
- FGFR4 p.Pro716Leu Uncertain significance ★★ ⚠ same condition
- FGFR4 c.1821+4C>T Benign same condition
- FGFR4 c.2016-8A>G Benign same condition
- FGFR4 p.Ala404Pro Likely benign same condition
- FGFR4 p.Arg234= Benign same condition
- FGFR4 p.Arg54= Benign same condition
- FGFR4 p.Asp297= Likely benign same condition
- FGFR4 p.His706= Likely benign same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/fgfr4-p-pro402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown