WDR1 p.Pro448=
c.1344C>T · rs1481467978 · VCV1624818
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 -8.5 | GERP -2.8 |
| Overall | ||
| CADD | 2.327 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/75,014 alleles
Filtering AF
0.000442%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000434%
7/1,612,778 alleles · very rare
exomes 7/1,460,448 · genomes 0/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,507 |
| East Asian | 0.00224% | 44,726 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,426 |
| South Asian | 0.0011% | 90,928 |
| European (non-Finnish) | 0.00017% | 589,644 |
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.Pro448=
- Coding
- c.1344C>T
- MANE Select
- NM_017491
- dbSNP
- rs1481467978
- Type
- single nucleotide variant
- Location
- chr4:10078942 (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-pro448 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown