WDR11 p.Pro137=
c.411G>A · rs374824479 · VCV704438
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0258%, nfe)
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 -5.3 | GERP -3.4 |
| Overall | ||
| CADD | 3.335 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0258%
European (non-Finnish) · 304/1,180,020 alleles
Filtering AF
0.0233%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0224%
Overall
0.0204%
330/1,613,932 alleles · ultra-rare
exomes 308/1,461,866 · genomes 22/152,066 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0258% | 3,882 |
| South Asian | 0.0154% | 6,506 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,927 |
| African / African-American | 0.00534% | 18,718 |
| Admixed American | 0.00167% | 59,990 |
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
- WDR11
- Protein
- p.Pro137=
- Coding
- c.411G>A
- MANE Select
- NM_018117
- dbSNP
- rs374824479
- Type
- single nucleotide variant
- Location
- chr10:120860167 (GRCh38)
- Gene constraint
- LOEUF 0.617 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.75 · 4 PDB
- Residue 137
- a turn
Similar variants
- WDR11 p.Gln419Ter Pathogenic ★★ same type
- WDR11 p.Ala1076Thr Uncertain significance ★★ ⚠ same type
- WDR11 p.Ala1203Thr Uncertain significance ★★ ⚠ same type
- WDR11 p.Ala26Thr Uncertain significance ★★ ⚠ same type
- WDR11 p.Ala954Val Uncertain significance ★★ ⚠ same type
- WDR11 p.Ala974Val Uncertain significance ★★ ⚠ same type
- WDR11 p.Arg1185Trp Uncertain significance ★★ ⚠ same type
- WDR11 p.Arg471Cys 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/wdr11-p-pro137 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown