Is BAAT p.Lys117Arg (c.350A>G) pathogenic?

BAAT p.Lys117Arg (c.350A>G) is classified Benign in BAAT (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-12). AlphaMissense: likely benign (0.0657); Low-frequency (popmax 3.87%, afr); Associated with hypercholanemia, familial 1.

What condition is associated with BAAT p.Lys117Arg (c.350A>G)?

BAAT p.Lys117Arg (c.350A>G) is associated with hypercholanemia, familial 1 (ClinVar).

How common is BAAT p.Lys117Arg (c.350A>G) in the general population?

BAAT p.Lys117Arg (c.350A>G) is low-frequency (popmax 3.87%, afr) (gnomAD).

How is Familial hypercholanemia inherited?

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

What do computational predictors say about BAAT p.Lys117Arg (c.350A>G)?

AlphaMissense predicts likely benign (score 0.0657) — an in-silico prediction, not a clinical call.

BAAT p.Lys117Arg

c.350A>G · rs115215226 · VCV364280

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.0657 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 3.87%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hypercholanemia, familial 1

Computational evidence

Protein change
AlphaMissense	0.0657	likely benign
REVEL	0.109	moderately benign-leaning
SaProt	LLR -5.86	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 -2.9	GERP -3
Regional constraint	o/e 0.97	unconstrained · MANE · 8,973 bp · p 0.5 · regional, not allelic
Overall
CADD	0.105	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 3.87% African / African-American · 2,899/74,956 alleles

Filtering AF 3.75% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.7%

Overall 0.201% 3,244/1,613,972 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.87%	26
Remaining individualsnot grpmax-eligible	0.28%	357
Admixed American	0.213%	469
Middle Eastern	0.0825%	1,212
South Asian	0.0176%	5,692
European (non-Finnish)	0.00178%	56,190

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.Lys117Arg
Coding: c.350A>G
MANE Select: NM_001701
dbSNP: rs115215226
Type: single nucleotide variant
Location: chr9:101371055 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 117: 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-lys117arg (accessed [today's date]).

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