WDR1 p.Pro417=
c.1251C>T · rs570258690 · VCV1176473
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.109%, sas)
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 -5.8 | GERP -3.4 |
| Overall | ||
| CADD | 0.481 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.109%
South Asian · 99/91,076 alleles
Filtering AF
0.0914%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0849%
Overall
0.00812%
131/1,613,854 alleles · rare
exomes 121/1,461,652 · genomes 10/152,202 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.109% | 920 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,620 |
| Admixed American | 0.00333% | 30,005 |
| European (non-Finnish) | 0.00212% | 47,195 |
| African / African-American | 0.00133% | 74,998 |
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
- WDR1
- Protein
- p.Pro417=
- Coding
- c.1251C>T
- MANE Select
- NM_017491
- dbSNP
- rs570258690
- Type
- single nucleotide variant
- Location
- chr4:10081390 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 96.57 · 2 PDB
Similar variants
- WDR1 p.Ala171Thr Uncertain significance ★★ ⚠ same type
- WDR1 p.Ala360Ser Uncertain significance ★★ ⚠ same type
- WDR1 p.Ala502Thr Uncertain significance ★★ ⚠ same type
- WDR1 p.Arg158Gln Uncertain significance ★★ ⚠ same type
- WDR1 p.Arg158Trp Uncertain significance ★★ ⚠ same type
- WDR1 p.Arg161Gln Uncertain significance ★★ ⚠ same type
- WDR1 p.Arg161Trp Uncertain significance ★★ ⚠ same type
- WDR1 p.Arg470His 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/wdr1-p-pro417 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown