Is BAAT p.Ser188= (c.564C>G) pathogenic?

BAAT p.Ser188= (c.564C>G) is classified Likely benign in BAAT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-08-03). Very rare (popmax 0.0011%, sas); Associated with BAAT-related disorder.

What condition is associated with BAAT p.Ser188= (c.564C>G)?

BAAT p.Ser188= (c.564C>G) is associated with BAAT-related disorder (ClinVar).

How common is BAAT p.Ser188= (c.564C>G) in the general population?

BAAT p.Ser188= (c.564C>G) is very rare (popmax 0.0011%, sas) (gnomAD).

BAAT p.Ser188=

c.564C>G · rs1164013317 · VCV3053191

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

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 -1.2	GERP -3.7
Overall
CADD	4.352	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,084 alleles

Overall 0.000137% 2/1,461,724 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0011%	91,084
European (non-Finnish)	8.47e-05%	1,179,958

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.Ser188=
Coding: c.564C>G
MANE Select: NM_001701
dbSNP: rs1164013317
Type: single nucleotide variant
Location: chr9:101368225 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 188: 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-ser188 (accessed [today's date]).

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