BAAT p.Ala48=
c.144C>T · VCV4738019
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.01%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP -0.27, phastCons 0.003 |
| Overall | ||
| CADD | 7.908 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/59,928 alleles
Filtering AF
0.00429%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.000558%
9/1,612,990 alleles · ultra-rare
exomes 7/1,460,876 · genomes 2/152,114 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 9,988 |
| European (non-Finnish) | 0.000254% | 393,085 |
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.Ala48=
- Coding
- c.144C>T
- MANE Select
- NM_001701
- Type
- single nucleotide variant
- Location
- chr9:101371261 (GRCh38)
- Gene constraint
- LOEUF 1.049 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.31
- Residue 48
- a UniProt-annotated variant site (in fhca3; contrary to wild-type, undetectable expression in hepatocytes)
Similar variants
- BAAT c.*1597C>A Uncertain significance ★★ same type
- BAAT p.Ala337Thr Uncertain significance ★★ ⚠ same type
- BAAT p.Arg130Ser Uncertain significance ★★ ⚠ same type
- BAAT p.Asp42Glu Uncertain significance ★★ ⚠ same type
- BAAT p.Glu54Lys Uncertain significance ★★ ⚠ same type
- BAAT p.Gly41Arg Uncertain significance ★★ ⚠ same type
- BAAT p.His74Tyr Uncertain significance ★★ ⚠ same type
- BAAT p.Leu153Phe 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/baat-p-ala48 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown