WEE2 p.Lys245=
c.735A>G · VCV4533808
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0225%, 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 1.4 | GERP 2.9 |
| Overall | ||
| CADD | 5.955 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0225%
European (non-Finnish) · 265/1,177,782 alleles
Filtering AF
0.0202%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0193%
Overall
0.0173%
279/1,609,330 alleles · ultra-rare
exomes 266/1,457,104 · genomes 13/152,226 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0225% | 4,444 |
| Remaining individualsnot grpmax-eligible | 0.00963% | 10,381 |
| Admixed American | 0.00672% | 14,871 |
| Finnishnot grpmax-eligible | 0.0047% | 21,271 |
| African / African-American | 0.00134% | 74,786 |
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
- WEE2
- Protein
- p.Lys245=
- Coding
- c.735A>G
- MANE Select
- NM_001105558
- Type
- single nucleotide variant
- Location
- chr7:141719221 (GRCh38)
- Gene constraint
- LOEUF 1.031 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.50 · 1 PDB
- Residue 245
- the protein kinase domain; a β-strand
Similar variants
- WEE2 p.Gly357Arg Uncertain significance ★★ ⚠ same type
- WEE2 p.Ile417Thr Uncertain significance ★★ same type
- WEE2 p.Tyr526Asp Benign/Likely benign ★★ same type
- WEE2 p.Gln288Ter Pathogenic ★ same type
- WEE2 c.585+3A>G Uncertain significance ★ same type
- WEE2 p.Ala194Asp Uncertain significance ★ ⚠ same type
- WEE2 p.Ala300Val Uncertain significance ★ ⚠ same type
- WEE2 p.Ala384Thr 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/wee2-p-lys245 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown