Is BAZ2B p.Arg1007Gln (c.3020G>A) pathogenic?

BAZ2B p.Arg1007Gln (c.3020G>A) is classified Uncertain significance in BAZ2B (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-17). AlphaMissense: likely pathogenic (0.9654); Very rare (popmax 0.00223%, eas); Associated with Inborn genetic diseases.

What condition is associated with BAZ2B p.Arg1007Gln (c.3020G>A)?

BAZ2B p.Arg1007Gln (c.3020G>A) is associated with Inborn genetic diseases (ClinVar).

How common is BAZ2B p.Arg1007Gln (c.3020G>A) in the general population?

BAZ2B p.Arg1007Gln (c.3020G>A) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about BAZ2B p.Arg1007Gln (c.3020G>A)?

AlphaMissense predicts likely pathogenic (score 0.9654) — an in-silico prediction, not a clinical call.

BAZ2B p.Arg1007Gln

c.3020G>A · VCV4594438

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9654 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.9654	likely pathogenic · top 10% in BAZ2B
REVEL	0.215	benign-leaning
SaProt	LLR -6.78	tolerated
⇒ AlphaMissense calls this damaging; REVEL and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.80	unconstrained · MANE · 18 kb · p 4.8e-05 · regional, not allelic
Overall
CADD	26.0	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

Grpmax group 0.00223% East Asian · 1/44,752 alleles

Filtering AF 0.000616% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000474%

Overall 0.00118% 19/1,610,668 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,752
South Asian	0.00221%	45,291
Admixed American	0.00168%	59,660
Remaining individualsnot grpmax-eligible	0.00161%	62,294
African / African-American	0.00134%	74,788
European (non-Finnish)	0.0011%	90,631

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.Arg1007Gln
Coding: c.3020G>A
MANE Select: NM_013450
Type: single nucleotide variant
Location: chr2:159395824 (GRCh38)
Gene constraint: LOEUF 0.386 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 55.23 · 265 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BAZ2B p.Arg1007Ter Uncertain significance ★ same residue
BAZ2B p.Arg1290Gln Uncertain significance ★★ ⚠ same condition
BAZ2B p.Ile502Val Uncertain significance ★★ ⚠ same condition
BAZ2B p.Leu587Ser Uncertain significance ★★ ⚠ same condition
BAZ2B p.Met1013Ile Uncertain significance ★★ ⚠ same condition
BAZ2B p.Pro1709Ser Uncertain significance ★★ ⚠ same condition
BAZ2B p.Ser1592Cys Uncertain significance ★★ ⚠ same condition
BAZ2B p.Trp826Arg 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-arg1007gln (accessed [today's date]).

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