Is ABAT p.Ala2fs (c.4dup) pathogenic?

ABAT p.Ala2fs (c.4dup) is classified Likely pathogenic in ABAT (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-20). Absent from gnomAD; Associated with GABA aminotransaminase deficiency.

What condition is associated with ABAT p.Ala2fs (c.4dup)?

ABAT p.Ala2fs (c.4dup) is associated with GABA aminotransaminase deficiency (ClinVar).

How common is ABAT p.Ala2fs (c.4dup) in the general population?

ABAT p.Ala2fs (c.4dup) is absent from gnomAD (gnomAD).

ABAT p.Ala2fs

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

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

c.4dup · rs2548959757 · VCV2674703

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 2 of 16
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.5, 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: ABAT
Protein: p.Ala2fs
Coding: c.4dup
MANE Select: NM_020686
dbSNP: rs2548959757
Type: Duplication
Location: chr16:8735741 (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.Asn127fs Pathogenic ★ same condition
ABAT p.Gly289fs Likely pathogenic ★ same condition
ABAT p.Lys367fs Likely pathogenic ★ same condition
ABAT p.Gly289_Ile291dup Uncertain significance ★ same condition
ABAT c.317-18dup Likely benign ★ same condition
ABAT c.540+13_540+14dup Likely benign ★ same condition
ABAT c.667+7_667+8dup Likely benign ★ same condition
ABAT c.70+9dup Benign ★ 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-ala2fs (accessed [today's date]).

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