Is BACH2 p.Pro780fs (c.2339_2349del) pathogenic?

BACH2 p.Pro780fs (c.23392349del) is classified Uncertain significance in BACH2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-04-10). Absent from gnomAD.

How common is BACH2 p.Pro780fs (c.2339_2349del) in the general population?

BACH2 p.Pro780fs (c.2339_2349del) is absent from gnomAD (gnomAD).

BACH2 p.Pro780fs

c.2339_2349del · rs2533537213 · VCV1964252

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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	escapes	premature termination codon in the last exon (9 of 9) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.062	GERP -0.84, phastCons 0.97

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: BACH2
Protein: p.Pro780fs
Coding: c.2339_2349del
MANE Select: NM_021813
dbSNP: rs2533537213
Type: Deletion
Location: chr6:89932585 (GRCh38)
Gene constraint: LOEUF 0.164 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 54.66 · 2 PDB
Residue 780: the 'disordered' region

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

Similar variants

BACH2 p.Pro780Arg Uncertain significance ★ ⚠ same residue
BACH2 p.Pro780Leu Uncertain significance ★ ⚠ same residue
BACH2 p.Pro780Ser Uncertain significance ★ ⚠ same residue
BACH2 p.Pro780= Likely benign ★ same residue
BACH2 p.Arg609fs Uncertain significance ★ same type
BACH2 p.Gly465_Trp467del Uncertain significance ★ same type
BACH2 p.Leu689fs Uncertain significance ★ same type
BACH2 p.Thr406del Uncertain significance ★ 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-pro780fs (accessed [today's date]).

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