BCAT2 p.Pro51=
c.153C>T · rs775856674 · VCV1986594
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00878%, sas)
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 0.29 | GERP -1.7, phastCons 0.006 |
| Overall | ||
| CADD | 11.26 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00878%
South Asian · 8/91,090 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00312%
Overall
0.00266%
43/1,613,906 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00878% | 11,386 |
| African / African-American | 0.00801% | 12,484 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| Finnishnot grpmax-eligible | 0.00313% | 31,944 |
| European (non-Finnish) | 0.00212% | 47,202 |
| Admixed American | 0.00167% | 59,990 |
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.Pro51=
- Coding
- c.153C>T
- MANE Select
- NM_001190
- dbSNP
- rs775856674
- Type
- single nucleotide variant
- Location
- chr19:48806664 (GRCh38)
- Gene constraint
- LOEUF 1.038 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.47 · 30 PDB
- Residue 51
- a β-strand
Similar variants
- BCAT2 p.Pro51Thr Uncertain significance ★★ ⚠ same residue
- 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
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-pro51 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown