FDFT1 p.Ser278=
c.834G>A · VCV4899559
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.117%, afr)
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 -0.89 | GERP -3.5 |
| Overall | ||
| CADD | 3.661 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.117%
African / African-American · 88/74,982 alleles
Filtering AF
0.0975%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0902%
Overall
0.00675%
109/1,613,816 alleles · rare
exomes 58/1,461,630 · genomes 51/152,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.117% | 852 |
| East Asian | 0.0223% | 4,488 |
| Admixed American | 0.01% | 10,000 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,241 |
| South Asian | 0.0022% | 45,533 |
| European (non-Finnish) | 8.48e-05% | 1,179,848 |
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.Ser278=
- Coding
- c.834G>A
- MANE Select
- NM_004462
- Type
- single nucleotide variant
- Location
- chr8:11830375 (GRCh38)
- Gene constraint
- LOEUF 1.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.14 · 32 PDB
- Residue 278
- 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-ser278 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown