WDR45 p.Asp359=
c.1077C>T · VCV3375093
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00217%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.067 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.5 | GERP -0.47, phastCons 1 |
| Overall | ||
| CADD | 9.096 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00217%
Admixed American · 1/46,089 alleles
Overall
8.28e-05%
1/1,207,904 alleles · very rare
exomes 1/1,093,964 · genomes 0/113,940 · joint denominator
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
- WDR45
- Protein
- p.Asp359=
- Coding
- c.1077C>T
- MANE Select
- NM_001029896
- Type
- single nucleotide variant
- Location
- chrX:49074809 (GRCh38)
- Structure
- AlphaFold pLDDT 90.66 · 3 PDB
- Residue 359
- a UniProt-annotated variant site (in nbia5)
Similar variants
- WDR45 p.Asp359Tyr Uncertain significance ★ ⚠ same residue
- WDR45 p.Asp359del Uncertain significance ★ same residue
- WDR45 c.342-2A>G Pathogenic/Likely pathogenic ★★ same type
- WDR45 c.342-3C>G Pathogenic/Likely pathogenic ★★ same type
- WDR45 c.437-1G>A Pathogenic/Likely pathogenic ★★ same type
- WDR45 c.437-2A>G Pathogenic ★★ same type
- WDR45 c.516+1G>A Pathogenic ★★ same type
- WDR45 c.726-1G>A Pathogenic ★★ 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/wdr45-p-asp359 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown