CHUK p.Thr499=
c.1497G>A · rs144134728 · VCV1601234
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.276%, 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 0.12 | GERP -3.7, phastCons 0.071 |
| Overall | ||
| CADD | 5.95 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.276%
African / African-American · 207/75,008 alleles
Filtering AF
0.245%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.233%
Overall
0.0204%
329/1,613,274 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.276% | 362 |
| Admixed American | 0.0383% | 2,610 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,675 |
| Middle Eastern | 0.0165% | 6,058 |
| South Asian | 0.00769% | 13,009 |
| European (non-Finnish) | 0.0061% | 16,381 |
| East Asian | 0.00446% | 22,409 |
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.Thr499=
- Coding
- c.1497G>A
- MANE Select
- NM_001278
- dbSNP
- rs144134728
- Type
- single nucleotide variant
- Location
- chr10:100204516 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI 0.39 (gnomAD)
- Structure
- AlphaFold pLDDT 84.41 · 5 PDB
Similar variants
- CHUK p.Thr499Met 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-thr499 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown