Is BAX p.Ser87Thr (c.259T>A) pathogenic?

BAX p.Ser87Thr (c.259T>A) is classified Uncertain significance in BAX (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-12). AlphaMissense: likely benign (0.2059); Very rare (popmax 0.007%, afr).

How common is BAX p.Ser87Thr (c.259T>A) in the general population?

BAX p.Ser87Thr (c.259T>A) is very rare (popmax 0.007%, afr) (gnomAD).

What do computational predictors say about BAX p.Ser87Thr (c.259T>A)?

AlphaMissense predicts likely benign (score 0.2059) — an in-silico prediction, not a clinical call.

BAX p.Ser87Thr

c.259T>A · VCV3821116

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2059 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.007%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2059	likely benign
REVEL	0.215	benign-leaning
SaProt	LLR -6.74	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 6,704 bp · p 0.24 · regional, not allelic
Overall
CADD	23.6	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.007% African / African-American · 5/71,418 alleles

Filtering AF 0.00275% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00178%

Overall 0.00032% 5/1,560,770 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: BAX
Protein: p.Ser87Thr
Coding: c.259T>A
MANE Select: NM_138761
Type: single nucleotide variant
Location: chr19:48956223 (GRCh38)
Gene constraint: LOEUF 1.245 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.71 · 37 PDB
Residue 87: a β-strand

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

Similar variants

BAX p.Ser87Cys Uncertain significance ★ ⚠ same residue
BAX p.Asp102= Benign ★★ same type
BAX c.474+151G>A Uncertain significance ★ same type
BAX c.474+20C>A Uncertain significance ★ same type
BAX c.474+34C>T Uncertain significance ★ same type
BAX c.474+76G>A Uncertain significance ★ same type
BAX c.474+95G>C Uncertain significance ★ same type
BAX p.Ala81Pro 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/bax-p-ser87thr (accessed [today's date]).

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