Is BAAT p.Leu88= (c.264A>G) pathogenic?

BAAT p.Leu88= (c.264A>G) is classified Uncertain significance in BAAT (ClinVar, Single submitter, 1 submitter; last evaluated 2018-01-13). Absent from gnomAD v4.1; Associated with hypercholanemia, familial 1.

What condition is associated with BAAT p.Leu88= (c.264A>G)?

BAAT p.Leu88= (c.264A>G) is associated with hypercholanemia, familial 1 (ClinVar).

How common is BAAT p.Leu88= (c.264A>G) in the general population?

BAAT p.Leu88= (c.264A>G) is absent from gnomAD v4.1 (gnomAD).

How is Familial hypercholanemia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

BAAT p.Leu88=

c.264A>G · rs886063284 · VCV364281

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hypercholanemia, familial 1

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 -3.1	GERP -3.7
Overall
CADD	0.582	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.Leu88=
Coding: c.264A>G
MANE Select: NM_001701
dbSNP: rs886063284
Type: single nucleotide variant
Location: chr9:101371141 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 88: 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

hypercholanemia, familial 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Familial hypercholanemia (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

BAAT c.*1597C>A Uncertain significance ★★ same condition
BAAT p.Arg130Ser Uncertain significance ★★ ⚠ same condition
BAAT p.Asp42Glu Uncertain significance ★★ ⚠ same condition
BAAT p.Leu60= Uncertain significance ★★ same condition
BAAT p.Thr254Met Uncertain significance ★★ ⚠ same condition
BAAT c.*1029A>T Benign ★★ same condition
BAAT c.*1090A>G Benign ★★ same condition
BAAT c.*1458G>A 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-leu88 (accessed [today's date]).

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