Is BAAT p.Val229Ile (c.685G>A) pathogenic?

BAAT p.Val229Ile (c.685G>A) is classified Conflicting classifications of pathogenicity in BAAT (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2025-07-12). AlphaMissense: likely benign (0.0622); Rare (popmax 0.225%, afr); Associated with bile acid conjugation defect 1.

What condition is associated with BAAT p.Val229Ile (c.685G>A)?

BAAT p.Val229Ile (c.685G>A) is associated with bile acid conjugation defect 1 (ClinVar).

How common is BAAT p.Val229Ile (c.685G>A) in the general population?

BAAT p.Val229Ile (c.685G>A) is rare (popmax 0.225%, afr) (gnomAD).

What do computational predictors say about BAAT p.Val229Ile (c.685G>A)?

AlphaMissense predicts likely benign (score 0.0622) — an in-silico prediction, not a clinical call.

BAAT p.Val229Ile

c.685G>A · rs141722672 · VCV593651

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.0622 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.225%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

bile acid conjugation defect 1

Computational evidence

Protein change
AlphaMissense	0.0622	likely benign
REVEL	0.008	strongly benign-leaning
SaProt	LLR -5.36	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.9	GERP -3.7
Regional constraint	o/e 0.97	unconstrained · MANE · 8,973 bp · p 0.5 · regional, not allelic
Overall
CADD	0.127	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.225% African / African-American · 169/75,008 alleles

Filtering AF 0.198% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.187%

Overall 0.0138% 223/1,613,806 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.225%	444
Remaining individualsnot grpmax-eligible	0.0288%	3,472
Admixed American	0.025%	3,999
East Asian	0.0111%	8,973
European (non-Finnish)	0.00127%	78,661
South Asian	0.0011%	91,068

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.Val229Ile
Coding: c.685G>A
MANE Select: NM_001701
dbSNP: rs141722672
Type: single nucleotide variant
Location: chr9:101363000 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 229: a UniProt-annotated variant site (in fhca3; contrary to wild-type, undetectable expression in hepatocytes)

Full BAAT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

bile acid conjugation defect 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BAAT p.Leu284Ter Uncertain significance ★★ same condition
BAAT p.Met1Lys Uncertain significance ★★ same condition
BAAT p.Thr254Met Uncertain significance ★★ ⚠ same condition
BAAT c.*46G>A Benign ★★ same condition
BAAT p.Arg20Gln Benign ★★ same condition
BAAT p.Ser233Pro Uncertain significance ★ ⚠ same condition
BAAT p.Arg20Ter Pathogenic same condition
BAAT p.Asp69Val Pathogenic ⚠ 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-val229ile (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown