FDFT1 p.Ala266=
c.798A>T · VCV4899558
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0446%, 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 -4.3 | GERP -3.8 |
| Overall | ||
| CADD | 0.431 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0446%
East Asian · 20/44,888 alleles
Filtering AF
0.0295%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0246%
Overall
0.0013%
21/1,613,830 alleles · ultra-rare
exomes 18/1,461,574 · genomes 3/152,256 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0446% | 2,244 |
| African / African-American | 0.00133% | 75,006 |
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
- FDFT1
- Protein
- p.Ala266=
- Coding
- c.798A>T
- MANE Select
- NM_004462
- Type
- single nucleotide variant
- Location
- chr8:11830339 (GRCh38)
- Gene constraint
- LOEUF 1.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.14 · 32 PDB
- Residue 266
- an α-helix
Similar variants
- FDFT1 c.100-85G>C Uncertain significance ★★ same type
- FDFT1 p.Ala333Ser Uncertain significance ★★ ⚠ same type
- FDFT1 p.Asn265Ser Uncertain significance ★★ ⚠ same type
- FDFT1 p.Gly151Asp Uncertain significance ★★ ⚠ same type
- FDFT1 p.Ile252Thr Uncertain significance ★★ ⚠ same type
- FDFT1 p.Phe210Leu Uncertain significance ★★ ⚠ same type
- FDFT1 p.Ser102Cys Uncertain significance ★★ ⚠ same type
- FDFT1 c.100-179C>G Likely benign ★★ 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/fdft1-p-ala266 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown