Is BAX p.Ser4Pro (c.10T>C) pathogenic?

BAX p.Ser4Pro (c.10T>C) is classified Uncertain significance in BAX (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-12). AlphaMissense: likely benign (0.1331); Absent from gnomAD v4.1.

How common is BAX p.Ser4Pro (c.10T>C) in the general population?

BAX p.Ser4Pro (c.10T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAX p.Ser4Pro (c.10T>C)?

AlphaMissense predicts likely benign (score 0.1331) — an in-silico prediction, not a clinical call.

BAX p.Ser4Pro

c.10T>C · rs894774952 · VCV2260655

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1331 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,236,952)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1331	likely benign
REVEL	0.146	moderately benign-leaning
SaProt	LLR -6.26	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	Δ0.26	donor loss · deltas
Constraint at this position
Conservation	phyloP 3.6	phastCons 1
Regional constraint	o/e 0.93	unconstrained · MANE · 6,704 bp · p 0.24 · regional, not allelic
Overall
CADD	25.4	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

No allele count reported in gnomAD v4.1 (AN 1,236,952). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BAX
Protein: p.Ser4Pro
Coding: c.10T>C
MANE Select: NM_138761
dbSNP: rs894774952
Type: single nucleotide variant
Location: chr19:48954938 (GRCh38)
Gene constraint: LOEUF 1.245 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.71 · 37 PDB
Residue 4: a turn

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

Similar variants

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
BAX p.Arg134Gly 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-ser4pro (accessed [today's date]).

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