BAAT p.Ala253=
c.759C>A · rs144858457 · VCV3030156
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0534%, afr)
Conditions
1
BAAT-related disorder
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 -0.17 | GERP -0.74 |
| Overall | ||
| CADD | 0.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0534%
African / African-American · 40/74,878 alleles
Filtering AF
0.0402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0357%
Overall
0.00273%
44/1,613,882 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0534% | 1,872 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,827 |
| Admixed American | 0.00167% | 59,978 |
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
- BAAT
- Protein
- p.Ala253=
- Coding
- c.759C>A
- MANE Select
- NM_001701
- dbSNP
- rs144858457
- Type
- single nucleotide variant
- Location
- chr9:101362926 (GRCh38)
- Gene constraint
- LOEUF 1.049 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.31
- Residue 253
- a UniProt-annotated variant site (in fhca3; contrary to wild-type, undetectable expression in hepatocytes)
Disease context
BAAT-related disorder
Similar variants
- BAAT p.Glu54Lys Uncertain significance ★★ ⚠ same condition
- BAAT p.Gly41Arg Uncertain significance ★★ ⚠ same condition
- BAAT p.Tyr108Ter Likely pathogenic ★ same condition
- BAAT p.Arg201Cys Uncertain significance ★ ⚠ same condition
- BAAT p.Gly185= Likely benign same condition
- BAAT p.Leu87= Likely benign same condition
- BAAT p.Pro154= Likely benign same condition
- BAAT p.Ser188= Likely benign same condition
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/baat-p-ala253 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown