Is BAAT p.Phe55= (c.165C>T) pathogenic?

BAAT p.Phe55= (c.165C>T) is classified Conflicting classifications of pathogenicity in BAAT (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2026-02-01). Ultra-rare (popmax 0.0165%, mid).

How common is BAAT p.Phe55= (c.165C>T) in the general population?

BAAT p.Phe55= (c.165C>T) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

BAAT p.Phe55=

c.165C>T · rs377631387 · VCV595901

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

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 0.026	GERP -2.9
Overall
CADD	10.54	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,076 alleles

Filtering AF 0.00703% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00652%

Overall 0.00701% 113/1,612,974 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,076
Remaining individualsnot grpmax-eligible	0.0128%	7,805
European (non-Finnish)	0.0084%	11,911
Admixed American	0.00334%	29,966
East Asian	0.00223%	44,850
South Asian	0.0022%	45,537

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.Phe55=
Coding: c.165C>T
MANE Select: NM_001701
dbSNP: rs377631387
Type: single nucleotide variant
Location: chr9:101371240 (GRCh38)
Gene constraint: LOEUF 1.049 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 95.31
Residue 55: 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 p.Phe55Leu Uncertain significance ★ ⚠ same residue
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

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-phe55 (accessed [today's date]).

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