FDFT1 p.Val179=
c.537C>T · VCV4899552
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00335%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.042 | GERP -2.6, phastCons 0.47 |
| Overall | ||
| CADD | 5.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00335%
South Asian · 3/89,520 alleles
Filtering AF
0.00089%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000447%
Overall
0.000876%
14/1,597,692 alleles · very rare
exomes 12/1,445,578 · genomes 2/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00335% | 29,840 |
| African / African-American | 0.00134% | 74,606 |
| European (non-Finnish) | 0.000856% | 116,833 |
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.Val179=
- Coding
- c.537C>T
- MANE Select
- NM_004462
- Type
- single nucleotide variant
- Location
- chr8:11826050 (GRCh38)
- Gene constraint
- LOEUF 1.764 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.14 · 32 PDB
- Residue 179
- 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-val179 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown