Is BAZ2B p.Ala1146= (c.3438T>C) pathogenic?

BAZ2B p.Ala1146= (c.3438T>C) is classified Likely benign in BAZ2B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-27). Ultra-rare (popmax 0.0303%, nfe); Associated with BAZ2B-related disorder.

What condition is associated with BAZ2B p.Ala1146= (c.3438T>C)?

BAZ2B p.Ala1146= (c.3438T>C) is associated with BAZ2B-related disorder (ClinVar).

How common is BAZ2B p.Ala1146= (c.3438T>C) in the general population?

BAZ2B p.Ala1146= (c.3438T>C) is ultra-rare (popmax 0.0303%, nfe) (gnomAD).

BAZ2B p.Ala1146=

c.3438T>C · rs367772317 · VCV3053573

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0303%, nfe)

Conditions

BAZ2B-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.053	moderately benign-leaning
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>C here scores Δ0.39 · evaluated, not missing
Constraint at this position
Conservation	phyloP 3.9	GERP 0.6, phastCons 1
Overall
CADD	16.74	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0303% European (non-Finnish) · 357/1,179,616 alleles

Filtering AF 0.0277% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0267%

Overall 0.0229% 370/1,613,232 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0303%	3,304
African / African-American	0.00801%	12,479
Remaining individualsnot grpmax-eligible	0.0064%	15,614
Finnishnot grpmax-eligible	0.00312%	32,003
Admixed American	0.00167%	59,846

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: BAZ2B
Protein: p.Ala1146=
Coding: c.3438T>C
MANE Select: NM_013450
dbSNP: rs367772317
Type: single nucleotide variant
Location: chr2:159386386 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 1146: the ddt domain

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

Disease context

BAZ2B-related disorder

Similar variants

BAZ2B p.Met1Thr Pathogenic/Likely pathogenic ★★ same condition
BAZ2B p.Lys1761Asn Uncertain significance ★★ ⚠ same condition
BAZ2B c.5797-1G>C Likely pathogenic ★ same condition
BAZ2B p.Glu1854Ter Likely pathogenic ★ same condition
BAZ2B p.Leu718Phe Likely pathogenic ★ ⚠ same condition
BAZ2B c.2255+10A>G Uncertain significance ★ same condition
BAZ2B c.2466+2T>G Uncertain significance ★ same condition
BAZ2B p.Arg855Ter 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-ala1146 (accessed [today's date]).

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