WDR1 p.Pro455=
c.1365C>T · rs369817887 · VCV1662085
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.085%, 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 -4.9 | GERP -2.5 |
| Overall | ||
| CADD | 7.183 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.085%
East Asian · 38/44,720 alleles
Filtering AF
0.0636%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0562%
Overall
0.00794%
128/1,612,824 alleles · ultra-rare
exomes 113/1,460,498 · genomes 15/152,326 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.085% | 1,177 |
| South Asian | 0.022% | 4,546 |
| Remaining individualsnot grpmax-eligible | 0.0176% | 5,674 |
| African / African-American | 0.00933% | 10,717 |
| Admixed American | 0.00501% | 19,969 |
| European (non-Finnish) | 0.00399% | 25,093 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,546 |
| Finnishnot grpmax-eligible | 0.00156% | 63,972 |
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.Pro455=
- Coding
- c.1365C>T
- MANE Select
- NM_017491
- dbSNP
- rs369817887
- Type
- single nucleotide variant
- Location
- chr4:10078921 (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-pro455 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown