BCKDK p.Cys152=
c.456C>T · VCV4929574
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, 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 2.1 | GERP -0.014, phastCons 1 |
| Overall | ||
| CADD | 11.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,014 alleles
Overall
6.2e-05%
1/1,614,076 alleles · very rare
exomes 1/1,461,840 · genomes 0/152,236 · joint denominator
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
- BCKDK
- Protein
- p.Cys152=
- Coding
- c.456C>T
- MANE Select
- NM_005881
- Type
- single nucleotide variant
- Location
- chr16:31110237 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.03 · 5 PDB
- Residue 152
- an α-helix
Similar variants
- BCKDK p.Arg156Ter Pathogenic ★★ same type
- BCKDK c.846-3T>A Uncertain significance ★★ same type
- BCKDK p.Ala283Thr Uncertain significance ★★ ⚠ same type
- BCKDK p.Ala29Val Uncertain significance ★★ ⚠ same type
- BCKDK p.Arg177Trp Uncertain significance ★★ ⚠ same type
- BCKDK p.Arg224Cys Uncertain significance ★★ ⚠ same type
- BCKDK p.Arg406Gly Uncertain significance ★★ ⚠ same type
- BCKDK p.Gln341Lys 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/bckdk-p-cys152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown