WDR26 p.Asp596=
c.1788T>C · VCV4941215
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000424%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.362 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -2.4 |
| Overall | ||
| CADD | 6.065 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000424%
European (non-Finnish) · 5/1,179,532 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000342%
5/1,460,498 alleles · very rare
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
- WDR26
- Protein
- p.Asp596=
- Coding
- c.1788T>C
- MANE Select
- NM_001379403
- Type
- single nucleotide variant
- Location
- chr1:224398966 (GRCh38)
- Gene constraint
- LOEUF 0.144 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 81.30 · 4 PDB
- Residue 596
- a UniProt-annotated variant site (in skdeas); a UniProt-annotated variant site (in skdeas; uncertain significance); a β-strand
Similar variants
- WDR26 p.Asp735Gly Pathogenic/Likely pathogenic ★★ same type
- WDR26 p.Ala137Val Uncertain significance ★★ ⚠ same type
- WDR26 p.Ala154Pro Uncertain significance ★★ ⚠ same type
- WDR26 p.Arg639Gln Uncertain significance ★★ same type
- WDR26 p.Glu526Asp Uncertain significance ★★ ⚠ same type
- WDR26 p.Ile481Met Uncertain significance ★★ same type
- WDR26 p.Leu490Val Uncertain significance ★★ ⚠ same type
- WDR26 p.Leu655Val 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/wdr26-p-asp596 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown