Is BAZ2B p.Ser1131Arg (c.3393C>A) pathogenic?

BAZ2B p.Ser1131Arg (c.3393C>A) is classified Uncertain significance in BAZ2B (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-02). AlphaMissense: likely pathogenic (0.9098); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with BAZ2B p.Ser1131Arg (c.3393C>A)?

BAZ2B p.Ser1131Arg (c.3393C>A) is associated with Inborn genetic diseases (ClinVar).

How common is BAZ2B p.Ser1131Arg (c.3393C>A) in the general population?

BAZ2B p.Ser1131Arg (c.3393C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAZ2B p.Ser1131Arg (c.3393C>A)?

AlphaMissense predicts likely pathogenic (score 0.9098) — an in-silico prediction, not a clinical call.

BAZ2B p.Ser1131Arg

c.3393C>A · VCV4198011

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9098 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9098	likely pathogenic
REVEL	0.353	indeterminate
SaProt	LLR -11.11	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 10	GERP 1.1, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 18 kb · p 4.8e-05 · regional, not allelic
Overall
CADD	24.1	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BAZ2B
Protein: p.Ser1131Arg
Coding: c.3393C>A
MANE Select: NM_013450
Type: single nucleotide variant
Location: chr2:159386431 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 1131: the ddt domain

Full BAZ2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BAZ2B p.Ser1131Asn Uncertain significance ★ ⚠ same residue
BAZ2B p.Arg1290Gln Uncertain significance ★★ ⚠ same condition
BAZ2B p.Ile502Val Uncertain significance ★★ ⚠ same condition
BAZ2B p.Leu587Ser Uncertain significance ★★ ⚠ same condition
BAZ2B p.Met1013Ile Uncertain significance ★★ ⚠ same condition
BAZ2B p.Pro1709Ser Uncertain significance ★★ ⚠ same condition
BAZ2B p.Ser1592Cys Uncertain significance ★★ ⚠ same condition
BAZ2B p.Trp826Arg Uncertain significance ★★ ⚠ 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/baz2b-p-ser1131arg (accessed [today's date]).

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