Is BAZ2B p.Ser799Ala (c.2395T>G) pathogenic?

BAZ2B p.Ser799Ala (c.2395T>G) is classified Likely benign in BAZ2B (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-01). AlphaMissense: ambiguous (0.4727); Rare (popmax 0.461%, sas).

How common is BAZ2B p.Ser799Ala (c.2395T>G) in the general population?

BAZ2B p.Ser799Ala (c.2395T>G) is rare (popmax 0.461%, sas) (gnomAD).

What do computational predictors say about BAZ2B p.Ser799Ala (c.2395T>G)?

AlphaMissense predicts ambiguous (score 0.4727) — an in-silico prediction, not a clinical call.

BAZ2B p.Ser799Ala

c.2395T>G · VCV4533938

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.4727 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.461%, sas)

Computational evidence

Protein change
AlphaMissense	0.4727	ambiguous
REVEL	0.34	indeterminate
SaProt	LLR -8.66	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.5	GERP 1.8, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 38 kb · p 1 · regional, not allelic
Overall
CADD	22.9	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 0.461% South Asian · 420/91,038 alleles

Filtering AF 0.425% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.411%

Overall 0.027% 435/1,613,426 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.461%	217
Remaining individualsnot grpmax-eligible	0.0176%	5,679
Middle Eastern	0.0165%	6,058
African / African-American	0.00133%	74,988
European (non-Finnish)	0.00017%	589,762

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.Ser799Ala
Coding: c.2395T>G
MANE Select: NM_013450
Type: single nucleotide variant
Location: chr2:159428012 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 799: the mbd domain

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

Similar variants

BAZ2B p.Met1Thr Pathogenic/Likely pathogenic ★★ same type
BAZ2B p.Arg1290Gln Uncertain significance ★★ ⚠ same type
BAZ2B p.Ile502Val Uncertain significance ★★ ⚠ same type
BAZ2B p.Leu1365Pro Uncertain significance ★★ ⚠ same type
BAZ2B p.Leu587Ser Uncertain significance ★★ ⚠ same type
BAZ2B p.Lys1761Asn Uncertain significance ★★ ⚠ same type
BAZ2B p.Met1013Ile Uncertain significance ★★ ⚠ same type
BAZ2B p.Pro1709Ser 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/baz2b-p-ser799ala (accessed [today's date]).

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