FN1 p.Pro557=
c.1671C>T · rs767104145 · VCV799113
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0379%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -3.1 |
| Overall | ||
| CADD | 7.212 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0379%
East Asian · 17/44,884 alleles
Filtering AF
0.0241%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0197%
Overall
0.00155%
25/1,613,936 alleles · ultra-rare
exomes 20/1,461,820 · genomes 5/152,116 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0379% | 2,640 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,478 |
| South Asian | 0.0011% | 91,078 |
| European (non-Finnish) | 0.000508% | 196,665 |
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
- FN1
- Protein
- p.Pro557=
- Coding
- c.1671C>T
- MANE Select
- NM_212482
- dbSNP
- rs767104145
- Type
- single nucleotide variant
- Location
- chr2:215420677 (GRCh38)
- Gene constraint
- LOEUF 0.404 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.23 · 66 PDB
- Residue 557
- the fibronectin type-i 8 domain; a β-strand; the 'collagen-binding' region
Similar variants
- FN1 p.Pro557Leu Uncertain significance ★ ⚠ same residue
- FN1 p.Cys123Arg Pathogenic/Likely pathogenic ★★ same type
- FN1 p.Cys225Trp Pathogenic/Likely pathogenic ★★ same type
- FN1 p.Cys231Trp Likely pathogenic ★★ same type
- FN1 p.Cys87Trp Pathogenic ★★ same type
- FN1 p.Tyr973Cys Pathogenic ★★ same type
- FN1 c.2122+4T>C Uncertain significance ★★ same type
- FN1 c.2299+3A>T Uncertain significance ★★ same type
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/fn1-p-pro557 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown