Is BAZ2B p.Asn2000= (c.6000T>C) pathogenic?

BAZ2B p.Asn2000= (c.6000T>C) is classified Likely benign in BAZ2B (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-05). Ultra-rare (popmax 0.0165%, mid); Associated with BAZ2B-related disorder.

What condition is associated with BAZ2B p.Asn2000= (c.6000T>C)?

BAZ2B p.Asn2000= (c.6000T>C) is associated with BAZ2B-related disorder (ClinVar).

How common is BAZ2B p.Asn2000= (c.6000T>C) in the general population?

BAZ2B p.Asn2000= (c.6000T>C) is ultra-rare (popmax 0.0165%, mid) (gnomAD).

BAZ2B p.Asn2000=

c.6000T>C · rs376860541 · VCV3052514

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, mid)

Conditions

BAZ2B-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.6	GERP 1.1, phastCons 1
Overall
CADD	6.759	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% Middle Eastern · 1/6,060 alleles

Filtering AF 0.00624% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0058%

Overall 0.00593% 95/1,601,166 alleles · ultra-rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0165%	6,060
European (non-Finnish)	0.00756%	13,224
Admixed American	0.00529%	18,921
Remaining individualsnot grpmax-eligible	0.00323%	31,007

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.Asn2000=
Coding: c.6000T>C
MANE Select: NM_013450
dbSNP: rs376860541
Type: single nucleotide variant
Location: chr2:159325862 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 2000: the 'disordered' region

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-asn2000 (accessed [today's date]).

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