Is BAZ2B p.Arg210Ter (c.628C>T) pathogenic?

BAZ2B p.Arg210Ter (c.628C>T) is classified Pathogenic in BAZ2B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2017-09-12). Very rare (popmax 0.00134%, afr); Associated with neurodevelopmental disorder.

What condition is associated with BAZ2B p.Arg210Ter (c.628C>T)?

BAZ2B p.Arg210Ter (c.628C>T) is associated with neurodevelopmental disorder (ClinVar).

How common is BAZ2B p.Arg210Ter (c.628C>T) in the general population?

BAZ2B p.Arg210Ter (c.628C>T) is very rare (popmax 0.00134%, afr) (gnomAD).

BAZ2B p.Arg210Ter

c.628C>T · rs780189423 · VCV800361

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00134%, afr)

Conditions

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 6 of 37
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.8	GERP 0.25, phastCons 1
Overall
CADD	35.0	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 0.00134% African / African-American · 1/74,808 alleles

Overall 0.000658% 1/151,968 alleles · very rare

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.Arg210Ter
Coding: c.628C>T
MANE Select: NM_013450
dbSNP: rs780189423
Type: single nucleotide variant
Location: chr2:159446850 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 210: the 'disordered' region

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

Disease context

neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BAZ2B p.Arg210Leu Uncertain significance ★ ⚠ same residue
BAZ2B c.4213+1G>A Uncertain significance ★ same condition
BAZ2B c.5454+3A>G Uncertain significance ★ same condition
BAZ2B c.6210-3T>C Uncertain significance ★ same condition
BAZ2B p.Asp1867Asn Uncertain significance ★ ⚠ same condition
BAZ2B p.Ser81Ter Uncertain significance ★ same condition
BAZ2B p.Val1140Leu Conflicting classifications of pathogenicity ★ ⚠ same condition
BAZ2B p.Cys709Tyr Pathogenic ⚠ 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-arg210ter (accessed [today's date]).

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