WDR45B p.Ser249=
c.747C>T · rs145253791 · VCV719114
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.357%, sas)
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 -0.63 | GERP -3.5 |
| Overall | ||
| CADD | 10.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.357%
South Asian · 325/91,078 alleles
Filtering AF
0.325%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.312%
Overall
0.0318%
514/1,614,054 alleles · rare
exomes 457/1,461,796 · genomes 57/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.357% | 280 |
| East Asian | 0.149% | 670 |
| Remaining individualsnot grpmax-eligible | 0.107% | 933 |
| African / African-American | 0.052% | 1,923 |
| Admixed American | 0.00333% | 30,008 |
| European (non-Finnish) | 0.00119% | 84,285 |
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
- WDR45B
- Protein
- p.Ser249=
- Coding
- c.747C>T
- MANE Select
- NM_019613
- dbSNP
- rs145253791
- Type
- single nucleotide variant
- Location
- chr17:82617355 (GRCh38)
- Gene constraint
- LOEUF 0.634 · pLI 0.09 (gnomAD)
- Structure
- AlphaFold pLDDT 94.78 · 5 PDB
- Residue 249
- a β-strand; a UniProt-annotated variant site (in nedsbas; uncertain significance)
Similar variants
- WDR45B c.332+47A>T Benign ★★ same type
- WDR45B c.68-9C>T Benign ★★ same type
- WDR45B c.807-11T>C Benign ★★ same type
- WDR45B p.Ala26= Likely benign ★★ same type
- WDR45B p.Asp314= Benign/Likely benign ★★ same type
- WDR45B p.Cys6Tyr Benign/Likely benign ★★ same type
- WDR45B p.Pro178= Likely benign ★★ same type
- WDR45B p.Arg225Ter Likely 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/wdr45b-p-ser249 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown