Is BAZ2B p.Pro748= (c.2244A>G) pathogenic?

BAZ2B p.Pro748= (c.2244A>G) is classified Benign in BAZ2B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-11). Low-frequency (popmax 1.08%, afr); Associated with BAZ2B-related disorder.

What condition is associated with BAZ2B p.Pro748= (c.2244A>G)?

BAZ2B p.Pro748= (c.2244A>G) is associated with BAZ2B-related disorder (ClinVar).

How common is BAZ2B p.Pro748= (c.2244A>G) in the general population?

BAZ2B p.Pro748= (c.2244A>G) is low-frequency (popmax 1.08%, afr) (gnomAD).

BAZ2B p.Pro748=

c.2244A>G · rs34097173 · VCV3050671

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.08%, afr)

Conditions

BAZ2B-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.096	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.9	GERP -1.2, phastCons 1
Overall
CADD	11.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.08% African / African-American · 796/73,574 alleles

Filtering AF 1.02% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.995%

Overall 0.0577% 895/1,551,234 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.08%	92
Remaining individualsnot grpmax-eligible	0.0911%	1,097
Admixed American	0.0543%	1,841
Middle Eastern	0.0518%	1,932
South Asian	0.00128%	77,926
European (non-Finnish)	0.00096%	104,135

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.Pro748=
Coding: c.2244A>G
MANE Select: NM_013450
dbSNP: rs34097173
Type: single nucleotide variant
Location: chr2:159429211 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 748: the mbd domain; an α-helix

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-pro748 (accessed [today's date]).

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