Is ACTN2 p.Arg89Gln (c.266G>A) pathogenic?

ACTN2 p.Arg89Gln (c.266G>A) is classified Likely benign in ACTN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-10-08). AlphaMissense: likely pathogenic (0.6669); Very rare (popmax 0.00891%, eas); Associated with dilated cardiomyopathy 1AA.

What condition is associated with ACTN2 p.Arg89Gln (c.266G>A)?

ACTN2 p.Arg89Gln (c.266G>A) is associated with dilated cardiomyopathy 1AA, familial hypertrophic cardiomyopathy (ClinVar).

How common is ACTN2 p.Arg89Gln (c.266G>A) in the general population?

ACTN2 p.Arg89Gln (c.266G>A) is very rare (popmax 0.00891%, eas) (gnomAD).

What do computational predictors say about ACTN2 p.Arg89Gln (c.266G>A)?

AlphaMissense predicts likely pathogenic (score 0.6669) — an in-silico prediction, not a clinical call.

ACTN2 p.Arg89Gln

c.266G>A · rs772390012 · VCV657052

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.6669 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00891%, eas)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

dilated cardiomyopathy 1AA

Computational evidence

Protein change
AlphaMissense	0.6669	likely pathogenic
REVEL	0.562	indeterminate
SaProt	LLR -12.84	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.3, phastCons 1
Regional constraint	o/e 0.65	unconstrained · MANE · 50 kb · p 1.6e-10 · regional, not allelic
Overall
CADD	29.0	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 0.00891% East Asian · 4/44,898 alleles

Filtering AF 0.00298% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0018%

Overall 0.000558% 9/1,614,038 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00891%	11,225
Admixed American	0.00167%	59,996
Finnishnot grpmax-eligible	0.00156%	64,028
African / African-American	0.00133%	74,916
European (non-Finnish)	0.000169%	590,016

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: ACTN2
Protein: p.Arg89Gln
Coding: c.266G>A
MANE Select: NM_001103
dbSNP: rs772390012
Type: single nucleotide variant
Location: chr1:236718918 (GRCh38)
Gene constraint: LOEUF 0.432 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.88 · 18 PDB
Residue 89: the calponin-homology (ch) 1 domain; the 'actin-binding' region

Full ACTN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

dilated cardiomyopathy 1AA — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: familial hypertrophic cardiomyopathy

Similar variants

ACTN2 p.Arg89Trp Uncertain significance ★★ ⚠ same residue
ACTN2 p.Arg89= Likely benign ★ same residue
ACTN2 p.Arg89Gly Uncertain significance ★ same residue
ACTN2 p.Ala119Thr Pathogenic/Likely pathogenic ★★ same condition
ACTN2 p.Thr247Met Likely pathogenic ★★ same condition
ACTN2 c.1107+3G>A Uncertain significance ★★ same condition
ACTN2 c.1108-10A>G Uncertain significance ★★ same condition
ACTN2 c.1255+1G>C 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/actn2-p-arg89gln (accessed [today's date]).

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