FDFT1 p.Pro350=
c.1050C>T · VCV4899567
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.22 | GERP -3.5 |
| Overall | ||
| CADD | 5.214 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,882 alleles
Filtering AF
0.00883%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.0031%
50/1,613,372 alleles · ultra-rare
exomes 42/1,461,238 · genomes 8/152,134 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,610 |
| Middle Eastern | 0.0164% | 6,084 |
| South Asian | 0.00879% | 11,377 |
| African / African-American | 0.00801% | 12,483 |
| Admixed American | 0.005% | 19,982 |
| Finnishnot grpmax-eligible | 0.00469% | 21,339 |
| European (non-Finnish) | 0.0017% | 58,978 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,462 |
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.Pro350=
- Coding
- c.1050C>T
- MANE Select
- NM_004462
- Type
- single nucleotide variant
- Location
- chr8:11838405 (GRCh38)
- Gene constraint
- LOEUF 1.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.14 · 32 PDB
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-pro350 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown