WEE2 p.Lys134=
c.402G>A · rs781615743 · VCV3043384
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.197%, mid)
Conditions
1
WEE2-related disorder
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 2.9 | GERP 4.4, phastCons 1 |
| Overall | ||
| CADD | 6.921 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.197%
Middle Eastern · 12/6,080 alleles
Filtering AF
0.114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0892%
Overall
0.00167%
27/1,613,738 alleles · rare
exomes 26/1,461,586 · genomes 1/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.197% | 507 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,810 |
| South Asian | 0.0033% | 30,346 |
| Admixed American | 0.00167% | 59,972 |
| European (non-Finnish) | 0.000254% | 393,289 |
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.Lys134=
- Coding
- c.402G>A
- MANE Select
- NM_001105558
- dbSNP
- rs781615743
- Type
- single nucleotide variant
- Location
- chr7:141714268 (GRCh38)
- Gene constraint
- LOEUF 1.031 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.50 · 1 PDB
Disease context
WEE2-related disorder
Similar variants
- WEE2 c.1536-9G>A Likely benign same condition
- WEE2 p.Ala264= Benign same condition
- WEE2 p.Asn62= Likely benign same condition
- WEE2 p.Ser100= Likely benign same condition
- WEE2 p.Glu75fs Pathogenic/Likely pathogenic ★★ same condition
- WEE2 p.Gly357Arg Uncertain significance ★★ ⚠ same type
- WEE2 p.Ile417Thr Uncertain significance ★★ same type
- WEE2 p.Tyr526Asp Benign/Likely benign ★★ 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-lys134 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown