Is BAAT p.Ser233Pro (c.697T>C) pathogenic?

BAAT p.Ser233Pro (c.697T>C) is classified Uncertain significance in BAAT (ClinVar, Single submitter, 1 submitter). AlphaMissense: likely pathogenic (0.7445); Absent from gnomAD v4.1; Associated with bile acid conjugation defect 1.

What condition is associated with BAAT p.Ser233Pro (c.697T>C)?

BAAT p.Ser233Pro (c.697T>C) is associated with bile acid conjugation defect 1 (ClinVar).

How common is BAAT p.Ser233Pro (c.697T>C) in the general population?

BAAT p.Ser233Pro (c.697T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAAT p.Ser233Pro (c.697T>C)?

AlphaMissense predicts likely pathogenic (score 0.7445) — an in-silico prediction, not a clinical call.

BAAT p.Ser233Pro

c.697T>C · rs554810939 · VCV3242081

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.7445 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

bile acid conjugation defect 1

Computational evidence

Protein change
AlphaMissense	0.7445	likely pathogenic · top 8% in BAAT
REVEL	0.244	benign-leaning
SaProt	LLR -11.50	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.8	GERP 0.62, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 8,973 bp · p 0.5 · regional, not allelic
Overall
CADD	22.1	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BAAT
Protein: p.Ser233Pro
Coding: c.697T>C
MANE Select: NM_001701
dbSNP: rs554810939
Type: single nucleotide variant
Location: chr9:101362988 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 233: 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.Val229Ile Conflicting classifications of pathogenicity ★ ⚠ 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-ser233pro (accessed [today's date]).

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