Is BAAT p.Pro84Ser (c.250C>T) pathogenic?

BAAT p.Pro84Ser (c.250C>T) is classified Uncertain significance in BAAT (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-09-26). AlphaMissense: likely benign (0.2328); Ultra-rare (popmax 0.0187%, afr).

How common is BAAT p.Pro84Ser (c.250C>T) in the general population?

BAAT p.Pro84Ser (c.250C>T) is ultra-rare (popmax 0.0187%, afr) (gnomAD).

What do computational predictors say about BAAT p.Pro84Ser (c.250C>T)?

AlphaMissense predicts likely benign (score 0.2328) — an in-silico prediction, not a clinical call.

BAAT p.Pro84Ser

c.250C>T · rs369808582 · VCV502529

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2328 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0187%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2328	likely benign
REVEL	0.224	benign-leaning
SaProt	LLR -7.70	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 1.5	GERP 1.7, phastCons 0.98
Regional constraint	o/e 0.97	unconstrained · MANE · 8,973 bp · p 0.5 · regional, not allelic
Overall
CADD	22.8	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0187% African / African-American · 14/74,884 alleles

Filtering AF 0.0112% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00905%

Overall 0.00112% 18/1,613,982 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0187%	5,349
European (non-Finnish)	0.000339%	295,004

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.Pro84Ser
Coding: c.250C>T
MANE Select: NM_001701
dbSNP: rs369808582
Type: single nucleotide variant
Location: chr9:101371155 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 84: a UniProt-annotated variant site (in fhca3; uncertain significance); 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

Similar variants

BAAT p.Pro84Thr Pathogenic ⚠ same residue
BAAT c.*1597C>A Uncertain significance ★★ same type
BAAT p.Ala337Thr Uncertain significance ★★ ⚠ same type
BAAT p.Arg130Ser Uncertain significance ★★ ⚠ same type
BAAT p.Asp42Glu Uncertain significance ★★ ⚠ same type
BAAT p.Glu54Lys Uncertain significance ★★ ⚠ same type
BAAT p.Gly41Arg Uncertain significance ★★ ⚠ same type
BAAT p.His74Tyr Uncertain significance ★★ ⚠ same type

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-pro84ser (accessed [today's date]).

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