CHEK2 p.Gln439=
c.1317G>A · VCV3266942
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.251 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP -0.27, phastCons 1 |
| Overall | ||
| CADD | 8.405 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CHEK2
- Protein
- p.Gln439=
- Coding
- c.1317G>A
- MANE Select
- NM_007194
- Type
- single nucleotide variant
- Location
- chr22:28695185 (GRCh38)
- Gene constraint
- LOEUF 1.399 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.64 · 38 PDB
- Residue 439
- an α-helix; the protein kinase domain
Similar variants
- CHEK2 p.Gln439Ter Pathogenic ★★ same residue
- CHEK2 p.Gln439Arg Uncertain significance ★★ ⚠ same residue
- CHEK2 p.Gln439Glu Uncertain significance ★★ same residue
- CHEK2 p.Gln439His Uncertain significance ★★ ⚠ same residue
- CHEK2 p.Gln439Lys Uncertain significance ★★ ⚠ same residue
- CHEK2 p.Gln439Pro Uncertain significance ★★ ⚠ same residue
- CHEK2 c.1008+1G>A Likely pathogenic ★★ same condition
- CHEK2 c.1008+1G>T Likely pathogenic ★★ same condition
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/chek2-p-gln439 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown