Is BAZ2B p.Arg855Ter (c.2563C>T) pathogenic?

BAZ2B p.Arg855Ter (c.2563C>T) is classified Uncertain significance in BAZ2B (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-26). Very rare (popmax 0.00167%, amr); Associated with BAZ2B-related Neurodevelopmental disorder.

What condition is associated with BAZ2B p.Arg855Ter (c.2563C>T)?

BAZ2B p.Arg855Ter (c.2563C>T) is associated with BAZ2B-related Neurodevelopmental disorder (ClinVar).

How common is BAZ2B p.Arg855Ter (c.2563C>T) in the general population?

BAZ2B p.Arg855Ter (c.2563C>T) is very rare (popmax 0.00167%, amr) (gnomAD).

BAZ2B p.Arg855Ter

c.2563C>T · rs2066971566 · VCV1342425

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

BAZ2B-related Neurodevelopmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 14 of 37
REVEL	0.339	indeterminate
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP -3.7, phastCons 0.95
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,986 alleles

Overall 0.000124% 2/1,613,884 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,986
European (non-Finnish)	8.47e-05%	1,179,994

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.Arg855Ter
Coding: c.2563C>T
MANE Select: NM_013450
dbSNP: rs2066971566
Type: single nucleotide variant
Location: chr2:159412449 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 855: the 'disordered' region

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

Disease context

BAZ2B-related Neurodevelopmental disorder

Similar variants

BAZ2B p.Arg855Gln Uncertain significance ★ ⚠ same residue
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

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-arg855ter (accessed [today's date]).

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