Is BAZ2B p.Pro849Leu (c.2546C>T) pathogenic?

BAZ2B p.Pro849Leu (c.2546C>T) is classified Uncertain significance in BAZ2B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-27). AlphaMissense: ambiguous (0.374); Absent from gnomAD v4.1.

How common is BAZ2B p.Pro849Leu (c.2546C>T) in the general population?

BAZ2B p.Pro849Leu (c.2546C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BAZ2B p.Pro849Leu (c.2546C>T)?

AlphaMissense predicts ambiguous (score 0.374) — an in-silico prediction, not a clinical call.

BAZ2B p.Pro849Leu

c.2546C>T · rs1244173719 · VCV2849337

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.374 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Computational evidence

Protein change
AlphaMissense	0.374	ambiguous
REVEL	0.479	indeterminate
SaProt	LLR -9.79	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 0.12, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 38 kb · p 1 · regional, not allelic
Overall
CADD	25.9	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

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.Pro849Leu
Coding: c.2546C>T
MANE Select: NM_013450
dbSNP: rs1244173719
Type: single nucleotide variant
Location: chr2:159412466 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 849: the 'disordered' region

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-pro849leu (accessed [today's date]).

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