FLI1 p.Pro80=
c.240G>A · rs368251838 · VCV752906
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
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 -4.9 | GERP -3.9 |
| Overall | ||
| CADD | 3.825 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,774 alleles
Filtering AF
0.00545%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00382%
Overall
0.00347%
56/1,612,224 alleles · ultra-rare
exomes 53/1,460,110 · genomes 3/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,539 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,602 |
| South Asian | 0.0044% | 22,705 |
| European (non-Finnish) | 0.00331% | 30,231 |
| East Asian | 0.00223% | 44,834 |
| African / African-American | 0.00134% | 74,890 |
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
- FLI1
- Protein
- p.Pro80=
- Coding
- c.240G>A
- MANE Select
- NM_002017
- dbSNP
- rs368251838
- Type
- single nucleotide variant
- Location
- chr11:128768127 (GRCh38)
- Gene constraint
- LOEUF 0.367 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.32 · 14 PDB
Similar variants
- FLI1 p.Pro80Gln Uncertain significance ★★ ⚠ same residue
- FLI1 p.Pro80Leu Uncertain significance ★★ ⚠ same residue
- FLI1 p.Ala178Thr Uncertain significance ★★ ⚠ same type
- FLI1 p.Ala247Thr Uncertain significance ★★ ⚠ same type
- FLI1 p.Ala295Ser Uncertain significance ★★ ⚠ same type
- FLI1 p.Ala419Thr Uncertain significance ★★ ⚠ same type
- FLI1 p.Arg177His Uncertain significance ★★ ⚠ same type
- FLI1 p.Arg177Pro 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/fli1-p-pro80 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown