BAAT p.Thr254=
c.762G>A · rs760488689 · VCV595169
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0505%, 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 -11 | GERP -3.7 |
| Overall | ||
| CADD | 12.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0505%
South Asian · 46/91,072 alleles
Filtering AF
0.0389%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0348%
Overall
0.00533%
86/1,613,836 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0505% | 1,980 |
| Middle Eastern | 0.0164% | 6,082 |
| Admixed American | 0.005% | 19,988 |
| European (non-Finnish) | 0.00271% | 36,872 |
| African / African-American | 0.00267% | 37,444 |
| East Asian | 0.00223% | 44,886 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,482 |
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.Thr254=
- Coding
- c.762G>A
- MANE Select
- NM_001701
- dbSNP
- rs760488689
- Type
- single nucleotide variant
- Location
- chr9:101362923 (GRCh38)
- Gene constraint
- LOEUF 1.049 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.31
- Residue 254
- a UniProt-annotated variant site (in fhca3; contrary to wild-type, undetectable expression in hepatocytes)
Similar variants
- BAAT p.Thr254Met Uncertain significance ★★ ⚠ same residue
- 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
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-thr254 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown