CHUK p.Cys113=
c.339T>C · rs148215833 · VCV749050
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.15%, 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 5.7 | GERP -2.6, phastCons 1 |
| Overall | ||
| CADD | 11.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.15%
African / African-American · 112/74,804 alleles
Filtering AF
0.127%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.119%
Overall
0.00843%
135/1,600,518 alleles · rare
exomes 57/1,448,218 · genomes 78/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.15% | 668 |
| South Asian | 0.0132% | 7,563 |
| Remaining individualsnot grpmax-eligible | 0.00645% | 15,508 |
| Admixed American | 0.005% | 19,997 |
| European (non-Finnish) | 0.000342% | 292,301 |
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.Cys113=
- Coding
- c.339T>C
- MANE Select
- NM_001278
- dbSNP
- rs148215833
- Type
- single nucleotide variant
- Location
- chr10:100222158 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI 0.39 (gnomAD)
- Structure
- AlphaFold pLDDT 84.41 · 5 PDB
- Residue 113
- the protein kinase domain
Similar variants
- CHUK p.Cys113Gly Uncertain significance ★ ⚠ same residue
- 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
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-cys113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown