Is BAAT p.Arg201Pro (c.602G>C) pathogenic?

BAAT p.Arg201Pro (c.602G>C) is classified Benign in BAAT (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-24). AlphaMissense: likely benign (0.0865); Common (popmax 21.5%, afr) — too common for a highly-penetrant pathogenic allele; Associated with hypercholanemia, familial 1.

What condition is associated with BAAT p.Arg201Pro (c.602G>C)?

BAAT p.Arg201Pro (c.602G>C) is associated with hypercholanemia, familial 1 (ClinVar).

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.Arg201Pro (c.602G>C)?

AlphaMissense predicts likely benign (score 0.0865) — an in-silico prediction, not a clinical call.

BAAT p.Arg201Pro

Q: How common is BAAT p.Arg201Pro (c.602G>C) in the general population?

BAAT p.Arg201Pro (c.602G>C) is common (popmax 21.5%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.602G>C · rs41281027 · VCV258173

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.0865 · ACMG-weighted

gnomAD v4.1

Common

common (popmax 21.5%, afr) — too common for a highly-penetrant pathogenic allele

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hypercholanemia, familial 1

Computational evidence

Protein change
AlphaMissense	0.0865	likely benign
REVEL	0.031	moderately benign-leaning
SaProt	LLR -4.56	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 -0.71	GERP -3.7
Regional constraint	o/e 0.97	unconstrained · MANE · 8,973 bp · p 0.5 · regional, not allelic
Overall
CADD	1.167	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 21.5% African / African-American · 15,889/73,864 alleles

Filtering AF 21.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 21.1%

Overall 15.5% 244,826/1,584,312 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	21.5%	5
Middle Eastern	19.6%	5
South Asian	18.8%	5
European (non-Finnish)	15.5%	6
Remaining individualsnot grpmax-eligible	15.3%	7
Admixed American	13.8%	7
Ashkenazi Jewishnot grpmax-eligible	12.4%	8
Amishnot grpmax-eligible	10.3%	10
Finnishnot grpmax-eligible	10.2%	10
East Asian	7.6%	13

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.Arg201Pro
Coding: c.602G>C
MANE Select: NM_001701
dbSNP: rs41281027
Type: single nucleotide variant
Location: chr9:101368187 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 201: 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 p.Arg201His Benign/Likely benign ★★ same residue
BAAT p.Arg201Cys Uncertain significance ★ ⚠ same residue
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

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-arg201pro (accessed [today's date]).

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