Is BAZ2B p.Leu134Pro (c.401T>C) pathogenic?

BAZ2B p.Leu134Pro (c.401T>C) is classified Likely benign in BAZ2B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-30). AlphaMissense: ambiguous (0.4493); Ultra-rare (popmax 0.0318%, amr); Associated with Inborn genetic diseases.

What condition is associated with BAZ2B p.Leu134Pro (c.401T>C)?

BAZ2B p.Leu134Pro (c.401T>C) is associated with Inborn genetic diseases (ClinVar).

How common is BAZ2B p.Leu134Pro (c.401T>C) in the general population?

BAZ2B p.Leu134Pro (c.401T>C) is ultra-rare (popmax 0.0318%, amr) (gnomAD).

What do computational predictors say about BAZ2B p.Leu134Pro (c.401T>C)?

AlphaMissense predicts ambiguous (score 0.4493) — an in-silico prediction, not a clinical call.

BAZ2B p.Leu134Pro

c.401T>C · VCV3260508

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4493 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0318%, amr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.4493	ambiguous
REVEL	0.462	indeterminate
SaProt	LLR -5.59	tolerated
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.74 · evaluated, not missing
Constraint at this position
Conservation	phyloP 11	GERP 2.7, phastCons 1
Regional constraint	o/e 1.02	unconstrained · MANE · 32 kb · p 0.77 · regional, not allelic
Overall
CADD	25.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0318% Admixed American · 19/59,816 alleles

Filtering AF 0.0207% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0172%

Overall 0.0118% 191/1,613,494 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0318%	3,148
Remaining individualsnot grpmax-eligible	0.016%	6,248
European (non-Finnish)	0.0134%	7,467
African / African-American	0.004%	25,000
Finnishnot grpmax-eligible	0.00156%	64,044

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.Leu134Pro
Coding: c.401T>C
MANE Select: NM_013450
Type: single nucleotide variant
Location: chr2:159448343 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB

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.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
BAZ2B p.Ala913Val Likely benign ★★ 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-leu134pro (accessed [today's date]).

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