Is ABAT p.Arg9His (c.26G>A) pathogenic?

ABAT p.Arg9His (c.26G>A) is classified Conflicting classifications of pathogenicity in ABAT (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-03-01). AlphaMissense: likely benign (0.0833); Rare (popmax 0.143%, sas); Associated with Inborn genetic diseases.

What condition is associated with ABAT p.Arg9His (c.26G>A)?

ABAT p.Arg9His (c.26G>A) is associated with Inborn genetic diseases, GABA aminotransaminase deficiency (ClinVar).

How common is ABAT p.Arg9His (c.26G>A) in the general population?

ABAT p.Arg9His (c.26G>A) is rare (popmax 0.143%, sas) (gnomAD).

What do computational predictors say about ABAT p.Arg9His (c.26G>A)?

AlphaMissense predicts likely benign (score 0.0833) — an in-silico prediction, not a clinical call.

ABAT p.Arg9His

c.26G>A · rs531783337 · VCV320839

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0833 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.143%, sas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0833	likely benign
REVEL	0.159	moderately benign-leaning
SaProt	LLR -10.66	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.5	GERP -4.2, phastCons 0.36
Regional constraint	o/e 0.96	unconstrained · MANE · 46 kb · p 0.32 · regional, not allelic
Overall
CADD	13.62	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.143% South Asian · 128/89,476 alleles

Filtering AF 0.123% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.115%

Overall 0.0221% 355/1,607,346 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.143%	699
Remaining individualsnot grpmax-eligible	0.0321%	3,113
European (non-Finnish)	0.0167%	5,976
Middle Eastern	0.0165%	6,056
African / African-American	0.008%	12,501
East Asian	0.00447%	22,389
Finnishnot grpmax-eligible	0.00159%	63,038

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.Arg9His
Coding: c.26G>A
MANE Select: NM_020686
dbSNP: rs531783337
Type: single nucleotide variant
Location: chr16:8735765 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: GABA aminotransaminase deficiency

Similar variants

ABAT p.Arg9Cys 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-arg9his (accessed [today's date]).

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