CHUK p.Pro239=
c.717A>G · VCV3719378
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
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 0.24 | GERP -0.76, phastCons 0.99 |
| Overall | ||
| CADD | 8.764 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,930 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00228%
Overall
0.00093%
15/1,613,756 alleles · very rare
exomes 11/1,461,526 · genomes 4/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,488 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,470 |
| European (non-Finnish) | 0.000678% | 147,480 |
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
- CHUK
- Protein
- p.Pro239=
- Coding
- c.717A>G
- MANE Select
- NM_001278
- Type
- single nucleotide variant
- Location
- chr10:100218798 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI 0.39 (gnomAD)
- Structure
- AlphaFold pLDDT 84.41 · 5 PDB
- Residue 239
- the protein kinase domain
Similar variants
- CHUK p.Arg365Gln Uncertain significance ★★ ⚠ same type
- CHUK p.Arg424Cys Uncertain significance ★★ ⚠ same type
- CHUK p.Arg563Cys Uncertain significance ★★ ⚠ same type
- CHUK p.Arg563His Uncertain significance ★★ ⚠ same type
- CHUK p.Gln226Pro Uncertain significance ★★ ⚠ same type
- CHUK p.Gly346Arg Uncertain significance ★★ ⚠ same type
- CHUK p.His520Arg Uncertain significance ★★ ⚠ same type
- CHUK p.Lys512Arg 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/chuk-p-pro239 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown