Is BAAT p.Pro154= (c.462T>A) pathogenic?

BAAT p.Pro154= (c.462T>A) is classified Likely benign in BAAT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-06). Absent from gnomAD v4.1; Associated with BAAT-related disorder.

What condition is associated with BAAT p.Pro154= (c.462T>A)?

BAAT p.Pro154= (c.462T>A) is associated with BAAT-related disorder (ClinVar).

How common is BAAT p.Pro154= (c.462T>A) in the general population?

BAAT p.Pro154= (c.462T>A) is absent from gnomAD v4.1 (gnomAD).

BAAT p.Pro154=

c.462T>A · VCV3346493

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

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 -0.064	GERP -2.5, phastCons 0.073
Overall
CADD	8.69	PHRED · no single calibrated threshold — expert panels disagree

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.Pro154=
Coding: c.462T>A
MANE Select: NM_001701
Type: single nucleotide variant
Location: chr9:101370943 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 154: 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

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.Ala253= Likely benign same condition
BAAT p.Gly185= Likely benign same condition
BAAT p.Leu87= 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-pro154 (accessed [today's date]).

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