Is GSTA2 p.Lys89Arg (c.266A>G) pathogenic?

GSTA2 p.Lys89Arg (c.266A>G) is classified Likely benign in GSTA2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-25). AlphaMissense: likely benign (0.0703); Rare (popmax 0.135%, afr).

How common is GSTA2 p.Lys89Arg (c.266A>G) in the general population?

GSTA2 p.Lys89Arg (c.266A>G) is rare (popmax 0.135%, afr) (gnomAD).

What do computational predictors say about GSTA2 p.Lys89Arg (c.266A>G)?

AlphaMissense predicts likely benign (score 0.0703) — an in-silico prediction, not a clinical call.

GSTA2 p.Lys89Arg

c.266A>G · VCV4267579

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0703 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.135%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0703	likely benign
REVEL	0.07	moderately benign-leaning
SaProt	LLR -4.08	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.29	GERP -0.04, phastCons 0.038
Regional constraint	o/e 1.16	unconstrained · MANE · 7,367 bp · p 0.0095 · regional, not allelic
Overall
CADD	13.96	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 0.135% African / African-American · 101/74,978 alleles

Filtering AF 0.113% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.105%

Overall 0.00793% 128/1,613,620 alleles · rare exomes 69/1,461,316 · genomes 59/152,304 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.135%	742
Remaining individualsnot grpmax-eligible	0.00801%	12,491
European (non-Finnish)	0.00178%	56,186
South Asian	0.0011%	91,072

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: GSTA2
Protein: p.Lys89Arg
Coding: c.266A>G
MANE Select: NM_000846
Type: single nucleotide variant
Location: chr6:52754949 (GRCh38)
Gene constraint: LOEUF 1.635 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 97.70 · 4 PDB
Residue 89: the gst c-terminal domain; an α-helix

Full GSTA2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

GSTA2 p.Ala100Val Uncertain significance ★ ⚠ same type
GSTA2 p.Ala156Val Uncertain significance ★ ⚠ same type
GSTA2 p.Asn130Asp Uncertain significance ★ ⚠ same type
GSTA2 p.Asp118Gly Uncertain significance ★ ⚠ same type
GSTA2 p.Glu168Ala Uncertain significance ★ ⚠ same type
GSTA2 p.Gly150Val Uncertain significance ★ ⚠ same type
GSTA2 p.Ile60Asn Uncertain significance ★ ⚠ same type
GSTA2 p.Leu107Pro Uncertain significance ★ ⚠ 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/gsta2-p-lys89arg (accessed [today's date]).

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