WDR5 p.Pro139=
c.417C>A · VCV4872569
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.185%, amr)
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 | GERP -4.8 |
| Overall | ||
| CADD | 9.707 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.185%
Admixed American · 111/60,014 alleles
Filtering AF
0.157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.147%
Overall
0.00756%
122/1,614,184 alleles · rare
exomes 109/1,461,878 · genomes 13/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.185% | 541 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| African / African-American | 0.004% | 25,015 |
| European (non-Finnish) | 0.000169% | 590,016 |
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
- WDR5
- Protein
- p.Pro139=
- Coding
- c.417C>A
- MANE Select
- NM_017588
- Type
- single nucleotide variant
- Location
- chr9:134142395 (GRCh38)
- Gene constraint
- LOEUF 0.053 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 93.66 · 199 PDB
Similar variants
- WDR5 p.Thr208Met Pathogenic ★★ same type
- WDR5 p.Ala36Val Uncertain significance ★★ ⚠ same type
- WDR5 p.Arg196Cys Pathogenic ★ same type
- WDR5 p.Ser171Leu Likely pathogenic ★ same type
- WDR5 p.Trp59Arg Likely pathogenic ★ same type
- WDR5 p.Ala2Val Uncertain significance ★ ⚠ same type
- WDR5 p.Ala74Thr Uncertain significance ★ same type
- WDR5 p.Cys121Trp 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/wdr5-p-pro139 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown