CHEK2 p.Asp203=
c.609T>C · VCV3664224
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,588,446)
Conditions
1
hereditary breast carcinoma
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.29 | acceptor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -0.9, phastCons 0.99 |
| Overall | ||
| CADD | 7.768 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,588,446). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CHEK2
- Protein
- p.Asp203=
- Coding
- c.609T>C
- MANE Select
- NM_007194
- Type
- single nucleotide variant
- Location
- chr22:28719469 (GRCh38)
- Gene constraint
- LOEUF 1.399 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.64 · 38 PDB
- Residue 203
- a β-strand
Disease context
hereditary breast carcinoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hereditary breast cancer (Orphanet):
- Inheritance
- Autosomal dominant, Multigenic/multifactorial
- Onset
- Adult, Elderly
Similar variants
- CHEK2 p.Asp203Asn Uncertain significance ★★ ⚠ same residue
- CHEK2 p.Asp203Gly Uncertain significance ★★ ⚠ same residue
- CHEK2 p.Asp203Val Uncertain significance ★★ ⚠ same residue
- CHEK2 p.Asp203Ala Uncertain significance ★ ⚠ same residue
- CHEK2 p.Asp203Ter Pathogenic/Likely pathogenic ★★ same residue
- CHEK2 p.Asp203fs Pathogenic ★ same residue
- CHEK2 p.Asp203Glu Uncertain significance ★★ ⚠ same residue
- CHEK2 c.1008+1G>A 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-asp203 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown