Is BAAT p.Val224= (c.672C>T) pathogenic?

BAAT p.Val224= (c.672C>T) is classified Likely benign in BAAT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-07-12). Ultra-rare (popmax 0.01%, amr); Associated with BAAT-related disorder.

What condition is associated with BAAT p.Val224= (c.672C>T)?

BAAT p.Val224= (c.672C>T) is associated with BAAT-related disorder (ClinVar).

How common is BAAT p.Val224= (c.672C>T) in the general population?

BAAT p.Val224= (c.672C>T) is ultra-rare (popmax 0.01%, amr) (gnomAD).

BAAT p.Val224=

c.672C>T · rs761880919 · VCV3057787

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.01%, amr)

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 0.39	GERP -0.2, phastCons 0.038
Overall
CADD	4.7	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.01% Admixed American · 6/59,952 alleles

Filtering AF 0.00429% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00295%

Overall 0.000753% 11/1,460,468 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.01%	9,992
Remaining individualsnot grpmax-eligible	0.0048%	20,823
European (non-Finnish)	0.00017%	589,602

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.Val224=
Coding: c.672C>T
MANE Select: NM_001701
dbSNP: rs761880919
Type: single nucleotide variant
Location: chr9:101363013 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 224: 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.Pro154= 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-val224 (accessed [today's date]).

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