Is ACTN2 p.Met216Val (c.646A>G) pathogenic?

ACTN2 p.Met216Val (c.646A>G) is classified Conflicting classifications of pathogenicity in ACTN2 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2024-12-02). AlphaMissense: likely benign (0.1684); Very rare (popmax 0.00407%, nfe); Associated with dilated cardiomyopathy 1AA.

What condition is associated with ACTN2 p.Met216Val (c.646A>G)?

ACTN2 p.Met216Val (c.646A>G) is associated with dilated cardiomyopathy 1AA, cardiomyopathy, familial hypertrophic cardiomyopathy (ClinVar).

How common is ACTN2 p.Met216Val (c.646A>G) in the general population?

ACTN2 p.Met216Val (c.646A>G) is very rare (popmax 0.00407%, nfe) (gnomAD).

What do computational predictors say about ACTN2 p.Met216Val (c.646A>G)?

AlphaMissense predicts likely benign (score 0.1684) — an in-silico prediction, not a clinical call.

ACTN2 p.Met216Val

c.646A>G · rs749019847 · VCV296499

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

AlphaMissense

likely benign

0.1684 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00407%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

dilated cardiomyopathy 1AA

Computational evidence

Protein change
AlphaMissense	0.1684	likely benign
REVEL	0.236	benign-leaning
SaProt	LLR -9.91	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 7	GERP -1.4, phastCons 1
Regional constraint	o/e 0.65	unconstrained · MANE · 50 kb · p 1.6e-10 · regional, not allelic
Overall
CADD	23.6	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 0.00407% European (non-Finnish) · 48/1,179,790 alleles

Filtering AF 0.00315% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00279%

Overall 0.00356% 52/1,461,580 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00407%	24,579
South Asian	0.0022%	45,542
Admixed American	0.00167%	60,030
Remaining individualsnot grpmax-eligible	0.0016%	62,504

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.Met216Val
Coding: c.646A>G
MANE Select: NM_001103
dbSNP: rs749019847
Type: single nucleotide variant
Location: chr1:236731263 (GRCh38)
Gene constraint: LOEUF 0.432 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.88 · 18 PDB
Residue 216: the calponin-homology (ch) 2 domain; an α-helix; 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: cardiomyopathy familial hypertrophic cardiomyopathy

Similar variants

ACTN2 p.Met216Leu 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
ACTN2 c.126+2T>G Uncertain significance ★★ same condition
ACTN2 c.127-3C>A 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-met216val (accessed [today's date]).

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