Is BAAT p.Phe167Leu (c.501T>A) pathogenic?

BAAT p.Phe167Leu (c.501T>A) is classified Uncertain significance in BAAT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-23). AlphaMissense: likely pathogenic (0.8663); Very rare (popmax 0.000339%, nfe).

How common is BAAT p.Phe167Leu (c.501T>A) in the general population?

BAAT p.Phe167Leu (c.501T>A) is very rare (popmax 0.000339%, nfe) (gnomAD).

What do computational predictors say about BAAT p.Phe167Leu (c.501T>A)?

AlphaMissense predicts likely pathogenic (score 0.8663) — an in-silico prediction, not a clinical call.

BAAT p.Phe167Leu

c.501T>A · VCV3816611

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8663 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8663	likely pathogenic · top 2% in BAAT
REVEL	0.204	benign-leaning
SaProt	LLR -8.32	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.3	GERP 0.65, phastCons 1
Regional constraint	o/e 0.97	unconstrained · MANE · 8,973 bp · p 0.5 · regional, not allelic
Overall
CADD	22.7	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000339% European (non-Finnish) · 4/1,180,008 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000274% 4/1,460,848 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.Phe167Leu
Coding: c.501T>A
MANE Select: NM_001701
Type: single nucleotide variant
Location: chr9:101368288 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 167: 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 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
BAAT p.Leu153Phe 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-phe167leu (accessed [today's date]).

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