Is ABAT p.Val103= (c.309C>T) pathogenic?

ABAT p.Val103= (c.309C>T) is classified Benign in ABAT (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-02-03). Common (popmax 15.4%, eas) — too common for a highly-penetrant pathogenic allele; Associated with GABA aminotransaminase deficiency.

What condition is associated with ABAT p.Val103= (c.309C>T)?

ABAT p.Val103= (c.309C>T) is associated with GABA aminotransaminase deficiency (ClinVar).

ABAT p.Val103=

Q: How common is ABAT p.Val103= (c.309C>T) in the general population?

ABAT p.Val103= (c.309C>T) is common (popmax 15.4%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

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

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

c.309C>T · rs2229157 · VCV320845

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Common

common (popmax 15.4%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

GABA aminotransaminase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.03	GERP -2.6, phastCons 0.84
Overall
CADD	6.756	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 15.4% East Asian · 6,911/44,866 alleles

Filtering AF 15.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 15%

Overall 11% 177,022/1,612,246 alleles · common

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	16%	6
East Asiangrpmax	15.4%	6
Finnishnot grpmax-eligible	14.9%	7
South Asian	14.4%	7
Remaining individualsnot grpmax-eligible	11.3%	9
Middle Eastern	10.9%	9
European (non-Finnish)	10.7%	9
Admixed American	9.48%	11
Amishnot grpmax-eligible	8.77%	11
African / African-American	4.7%	21

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: ABAT
Protein: p.Val103=
Coding: c.309C>T
MANE Select: NM_020686
dbSNP: rs2229157
Type: single nucleotide variant
Location: chr16:8750532 (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.Val103Phe Uncertain significance ★ same residue
ABAT c.168+1G>A Pathogenic ★★ same condition
ABAT p.Arg92Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
ABAT p.Gln8Ter Pathogenic/Likely pathogenic ★★ same condition
ABAT p.Leu211Phe Pathogenic/Likely pathogenic ★★ same condition
ABAT p.Tyr376Ter Pathogenic/Likely pathogenic ★★ same condition
ABAT c.1381+6G>T Uncertain significance ★★ same condition
ABAT p.Ala162Thr 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-val103 (accessed [today's date]).

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