BCAT2 p.Leu136=
c.408G>A · rs2034627179 · VCV2875205
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00669%, eas)
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 0.32 | GERP 1.7, phastCons 0.99 |
| Overall | ||
| CADD | 8.881 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
East Asian · 3/44,860 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000892%
Overall
0.000205%
3/1,460,970 alleles · very rare
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
- BCAT2
- Protein
- p.Leu136=
- Coding
- c.408G>A
- MANE Select
- NM_001190
- dbSNP
- rs2034627179
- Type
- single nucleotide variant
- Location
- chr19:48800190 (GRCh38)
- Gene constraint
- LOEUF 1.038 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.47 · 30 PDB
- Residue 136
- an α-helix
Similar variants
- BCAT2 p.Ala188Thr Uncertain significance ★★ ⚠ same type
- BCAT2 p.Arg133His Uncertain significance ★★ same type
- BCAT2 p.Arg247Trp Uncertain significance ★★ ⚠ same type
- BCAT2 p.Arg325Trp Uncertain significance ★★ ⚠ same type
- BCAT2 p.Arg333Gly Uncertain significance ★★ ⚠ same type
- BCAT2 p.Arg371His Uncertain significance ★★ ⚠ same type
- BCAT2 p.Asp112Asn Uncertain significance ★★ ⚠ same type
- BCAT2 p.Asp259Asn 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/bcat2-p-leu136 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown