Is BAAT p.Arg130fs (c.388dup) pathogenic?

BAAT p.Arg130fs (c.388dup) is classified Likely pathogenic in BAAT (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-08). Very rare (popmax 0.00669%, eas); Associated with BAAT-related disorder.

What condition is associated with BAAT p.Arg130fs (c.388dup)?

BAAT p.Arg130fs (c.388dup) is associated with BAAT-related disorder (ClinVar).

How common is BAAT p.Arg130fs (c.388dup) in the general population?

BAAT p.Arg130fs (c.388dup) is very rare (popmax 0.00669%, eas) (gnomAD).

BAAT p.Arg130fs

c.388dup · VCV4903943

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00669%, eas)

Conditions

BAAT-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.2	GERP 1.7, phastCons 1
Overall
CADD	32.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00669% East Asian · 3/44,864 alleles

Filtering AF 0.00177% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000892%

Overall 0.000186% 3/1,614,132 alleles · very rare

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.Arg130fs
Coding: c.388dup
MANE Select: NM_001701
Type: Duplication
Location: chr9:101371016 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 130: 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.Arg130Ser Uncertain significance ★★ ⚠ same residue
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.Asn195fs Likely pathogenic same condition
BAAT p.Phe152fs Uncertain significance same condition
BAAT p.Ala253= 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-arg130fs (accessed [today's date]).

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