BCAT1 p.Lys19=
c.57A>G · rs185686698 · VCV750233
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -1.7 | GERP -2.8 |
| Overall | ||
| CADD | 0.849 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.000558%
9/1,613,996 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Admixed American | 0.01% | 10,004 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 8.48e-05% | 1,179,880 |
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
- BCAT1
- Protein
- p.Lys19=
- Coding
- c.57A>G
- MANE Select
- NM_005504
- dbSNP
- rs185686698
- Type
- single nucleotide variant
- Location
- chr12:24901835 (GRCh38)
- Gene constraint
- LOEUF 1.219 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.05 · 17 PDB
Similar variants
- BCAT1 p.Thr13= Benign ★★ same type
- BCAT1 c.7-1070G>A Uncertain significance ★ same type
- BCAT1 c.7-1075C>T Uncertain significance ★ same type
- BCAT1 c.7-1078C>T Uncertain significance ★ same type
- BCAT1 c.7-1082G>T Uncertain significance ★ same type
- BCAT1 c.7-1091C>T Uncertain significance ★ same type
- BCAT1 p.Ala27Thr Uncertain significance ★ ⚠ same type
- BCAT1 p.Ala298Thr 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/bcat1-p-lys19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown