Is ABAT p.Pro136fs (c.405del) pathogenic?

ABAT p.Pro136fs (c.405del) is classified Pathogenic in ABAT (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-03). Associated with GABA aminotransaminase deficiency.

What condition is associated with ABAT p.Pro136fs (c.405del)?

ABAT p.Pro136fs (c.405del) is associated with GABA aminotransaminase deficiency (ClinVar).

ABAT p.Pro136fs

Q: How is Gamma-aminobutyric acid transaminase deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.405del · VCV4736587

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

GABA aminotransaminase deficiency

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 7 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.5	GERP 2.1, phastCons 1

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

Variant & gene context

Gene: ABAT
Protein: p.Pro136fs
Coding: c.405del
MANE Select: NM_020686
Type: Deletion
Location: chr16:8764107 (GRCh38)
Gene constraint: LOEUF 0.871 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.91

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

Disease context

GABA aminotransaminase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Gamma-aminobutyric acid transaminase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ABAT p.Pro136= Likely benign ★★ same residue
ABAT p.Ter501LysextTer? Uncertain significance ★★ same condition
ABAT c.(168+1_169-1 Likely pathogenic ★ same condition
ABAT c.199-?_316+?del Pathogenic ★ same condition
ABAT p.Arg220fs Pathogenic ★ same condition
ABAT p.Arg432_Val433insTer Likely pathogenic ★ same condition
ABAT p.Leu276_Ile277insTer Pathogenic ★ same condition
ABAT p.Phe442fs 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/abat-p-pro136fs (accessed [today's date]).

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