Is BAX p.Gly39fs (c.115_121del) pathogenic?

BAX p.Gly39fs (c.115121del) is classified Pathogenic in BAX (ClinVar, No assertion criteria, 1 submitter; last evaluated 1998-04-15). Absent from gnomAD; Associated with T-cell acute lymphoblastic leukemia.

What condition is associated with BAX p.Gly39fs (c.115_121del)?

BAX p.Gly39fs (c.115_121del) is associated with T-cell acute lymphoblastic leukemia (ClinVar).

How common is BAX p.Gly39fs (c.115_121del) in the general population?

BAX p.Gly39fs (c.115_121del) is absent from gnomAD (gnomAD).

BAX p.Gly39fs

c.115_121del · rs398122840 · VCV9514

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

T-cell acute lymphoblastic leukemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 6
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	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: BAX
Protein: p.Gly39fs
Coding: c.115_121del
MANE Select: NM_138761
dbSNP: rs398122840
Type: Deletion
Location: chr19:48955714 (GRCh38)
Gene constraint: LOEUF 1.245 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.71 · 37 PDB
Residue 39: a UniProt-annotated variant site (in); a β-strand

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

Disease context

T-cell acute lymphoblastic leukemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

BAX p.Gly67Arg Pathogenic same condition
BAX c.474+50_474+63del Likely pathogenic ★ 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/bax-p-gly39fs (accessed [today's date]).

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