WDR1 p.Ala239=
c.717A>G · rs374592871 · VCV1992300
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0321%, sas)
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 -0.8 | GERP -3.1 |
| Overall | ||
| CADD | 0.499 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0321%
South Asian · 27/84,080 alleles
Filtering AF
0.0226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0194%
Overall
0.00277%
43/1,552,784 alleles · ultra-rare
exomes 38/1,400,448 · genomes 5/152,336 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0321% | 3,114 |
| Admixed American | 0.0117% | 8,551 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,148 |
| African / African-American | 0.00137% | 73,198 |
| European (non-Finnish) | 0.000697% | 143,488 |
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.Ala239=
- Coding
- c.717A>G
- MANE Select
- NM_017491
- dbSNP
- rs374592871
- Type
- single nucleotide variant
- Location
- chr4:10088293 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 96.57 · 2 PDB
Similar variants
- WDR1 p.Ala239Thr Uncertain significance ★ ⚠ same residue
- 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
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-ala239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown