Is BAZ2B p.His479fs (c.1435del) pathogenic?

BAZ2B p.His479fs (c.1435del) is classified Pathogenic in BAZ2B (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-13). Absent from gnomAD; Associated with BAZ2B-related disorder.

What condition is associated with BAZ2B p.His479fs (c.1435del)?

BAZ2B p.His479fs (c.1435del) is associated with BAZ2B-related disorder (ClinVar).

How common is BAZ2B p.His479fs (c.1435del) in the general population?

BAZ2B p.His479fs (c.1435del) is absent from gnomAD (gnomAD).

BAZ2B p.His479fs

c.1435del · rs2546859168 · VCV2505363

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

BAZ2B-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 9 of 37
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.1	GERP 1.5, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BAZ2B
Protein: p.His479fs
Coding: c.1435del
MANE Select: NM_013450
dbSNP: rs2546859168
Type: Deletion
Location: chr2:159433222 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB
Residue 479: 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.Ile938fs Likely pathogenic ★ same condition
BAZ2B p.Val454fs Likely pathogenic ★ same condition
BAZ2B c.2195-5del Likely benign same condition
BAZ2B c.697-10_697-8del Likely benign same condition
BAZ2B p.Met1Thr Pathogenic/Likely pathogenic ★★ same condition
BAZ2B p.Lys1761Asn Uncertain significance ★★ ⚠ same condition
BAZ2B c.3075+3_3075+6del Likely pathogenic ★ same condition
BAZ2B c.5797-1G>C Likely 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-his479fs (accessed [today's date]).

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