Is BAAT p.Arg20Ter (c.58C>T) pathogenic?

BAAT p.Arg20Ter (c.58C>T) is classified Pathogenic in BAAT (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-11-25). Very rare (popmax 0.00167%, amr); Associated with bile acid conjugation defect 1.

What condition is associated with BAAT p.Arg20Ter (c.58C>T)?

BAAT p.Arg20Ter (c.58C>T) is associated with bile acid conjugation defect 1 (ClinVar).

How common is BAAT p.Arg20Ter (c.58C>T) in the general population?

BAAT p.Arg20Ter (c.58C>T) is very rare (popmax 0.00167%, amr) (gnomAD).

BAAT p.Arg20Ter

c.58C>T · rs758476278 · VCV1048534

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

bile acid conjugation defect 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 4
Splicing
SpliceAI	Δ0.22	donor loss, 29 bp away · masked 0 · deltas
Constraint at this position
Conservation	phyloP 0.5	GERP 0.03, phastCons 0.043
Overall
CADD	36.0	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 0.00167% Admixed American · 1/59,964 alleles

Overall 0.000186% 3/1,613,562 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,964
African / African-American	0.00134%	74,896
European (non-Finnish)	8.47e-05%	1,179,986

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.Arg20Ter
Coding: c.58C>T
MANE Select: NM_001701
dbSNP: rs758476278
Type: single nucleotide variant
Location: chr9:101371347 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 20: a UniProt-annotated variant site (in fhca3; contrary to wild-type, undetectable expression in hepatocytes); a UniProt-annotated variant site (in)

Full BAAT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

bile acid conjugation defect 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BAAT p.Arg20Gln Benign ★★ same residue
BAAT p.Leu284Ter Uncertain significance ★★ same condition
BAAT p.Met1Lys Uncertain significance ★★ same condition
BAAT p.Thr254Met Uncertain significance ★★ ⚠ same condition
BAAT c.*46G>A Benign ★★ same condition
BAAT p.Arg20Lys Uncertain significance ★ same residue
BAAT p.Ser233Pro Uncertain significance ★ ⚠ same condition
BAAT p.Val229Ile Conflicting classifications of pathogenicity ★ ⚠ 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-arg20ter (accessed [today's date]).

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