WFS1 p.Phe331del
c.985TTC[2] · VCV3360183
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.95 | GERP -2.9 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,058 alleles
Overall
6.2e-05%
1/1,613,928 alleles · very rare
exomes 1/1,461,824 · genomes 0/152,104 · joint denominator
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
- WFS1
- Protein
- p.Phe331del
- Coding
- c.985TTC[2]
- MANE Select
- NM_006005
- Type
- Microsatellite
- Location
- chr4:6300778 (GRCh38)
- Gene constraint
- LOEUF 1.64 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.85
Similar variants
- WFS1 p.Phe331Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
- WFS1 p.Phe331= Likely benign ★ same residue
- WFS1 p.565LF[1] Pathogenic/Likely pathogenic ★★ same type
- WFS1 p.Phe414del Pathogenic/Likely pathogenic ★★ same type
- WFS1 p.Phe516del Pathogenic/Likely pathogenic ★★ same type
- WFS1 p.Ser411fs Pathogenic ★★ same type
- WFS1 p.Glu795del Uncertain significance ★★ same type
- WFS1 p.Gly53_Val54insProGly 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/wfs1-p-phe331del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown