WDR1 p.Ser258=
c.774C>T · VCV4966467
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0828%, eas)
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 -6.1 | GERP -3.4 |
| Overall | ||
| CADD | 0.477 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0828%
East Asian · 35/42,284 alleles
Filtering AF
0.0611%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0536%
Overall
0.00236%
37/1,564,560 alleles · ultra-rare
exomes 35/1,412,298 · genomes 2/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0828% | 1,208 |
| Remaining individualsnot grpmax-eligible | 0.00165% | 60,670 |
| European (non-Finnish) | 8.67e-05% | 1,153,746 |
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.Ser258=
- Coding
- c.774C>T
- MANE Select
- NM_017491
- Type
- single nucleotide variant
- Location
- chr4:10087884 (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-ser258 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown