WFS1 p.Asp151=
c.453C>T · rs1200601453 · VCV2047407
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00116%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.055 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.9 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 12.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00116%
South Asian · 1/85,984 alleles
Overall
7.02e-05%
1/1,425,168 alleles · very rare
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.Asp151=
- Coding
- c.453C>T
- MANE Select
- NM_006005
- dbSNP
- rs1200601453
- Type
- single nucleotide variant
- Location
- chr4:6289124 (GRCh38)
- Gene constraint
- LOEUF 1.64 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 73.85
- Residue 151
- the 'interaction with atp6v1a' region
Similar variants
- WFS1 p.Asp151Asn Uncertain significance ★★ ⚠ same residue
- WFS1 c.233-1G>C Pathogenic/Likely pathogenic ★★ same type
- WFS1 c.316-2A>G Pathogenic ★★ same type
- WFS1 c.460+1G>A Pathogenic ★★ same type
- WFS1 c.631+1G>A Likely pathogenic ★★ same type
- WFS1 c.861+1G>A Pathogenic/Likely pathogenic ★★ same type
- WFS1 c.861+2T>C Pathogenic ★★ same type
- WFS1 p.Ala126Thr Pathogenic/Likely pathogenic ★★ 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-asp151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown