BCKDK p.Val307=
c.921C>T · VCV3341769
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00212%, nfe)
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 -7.7 | GERP -4.7 |
| Overall | ||
| CADD | 0.455 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00212%
European (non-Finnish) · 25/1,179,982 alleles
Filtering AF
0.00145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00161%
26/1,613,954 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00212% | 47,199 |
| Admixed American | 0.00167% | 59,984 |
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.Val307=
- Coding
- c.921C>T
- MANE Select
- NM_005881
- Type
- single nucleotide variant
- Location
- chr16:31111375 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.03 · 5 PDB
- Residue 307
- the histidine kinase domain; a β-strand
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-val307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown