Is BACH2 p.Arg609fs (c.1825_1826del) pathogenic?

BACH2 p.Arg609fs (c.18251826del) is classified Uncertain significance in BACH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-23). Very rare (popmax 0.00133%, afr).

How common is BACH2 p.Arg609fs (c.1825_1826del) in the general population?

BACH2 p.Arg609fs (c.1825_1826del) is very rare (popmax 0.00133%, afr) (gnomAD).

BACH2 p.Arg609fs

c.1825_1826del · VCV4893412

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

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 7 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.4, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,006 alleles

Overall 6.2e-05% 1/1,614,100 alleles · very rare exomes 1/1,461,890 · genomes 0/152,210 · joint denominator

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: BACH2
Protein: p.Arg609fs
Coding: c.1825_1826del
MANE Select: NM_021813
Type: Deletion
Location: chr6:89950280 (GRCh38)
Gene constraint: LOEUF 0.164 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 54.66 · 2 PDB
Residue 609: the 'disordered' region

Full BACH2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BACH2 p.Arg609Gly Uncertain significance ★★ ⚠ same residue
BACH2 p.Gly465_Trp467del Uncertain significance ★ same type
BACH2 p.Leu689fs Uncertain significance ★ same type
BACH2 p.Pro780fs Uncertain significance ★ same type
BACH2 p.Thr406del Uncertain significance ★ same type
BACH2 c.-12-19_-12-4del Likely benign ★ same type

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/bach2-p-arg609fs (accessed [today's date]).

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