Is ACTC1 p.Arg258= (c.774C>G) pathogenic?

ACTC1 p.Arg258= (c.774C>G) is classified Likely benign in ACTC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-02). Very rare (popmax 0.0011%, sas); Associated with cardiomyopathy.

What condition is associated with ACTC1 p.Arg258= (c.774C>G)?

ACTC1 p.Arg258= (c.774C>G) is associated with cardiomyopathy (ClinVar).

How common is ACTC1 p.Arg258= (c.774C>G) in the general population?

ACTC1 p.Arg258= (c.774C>G) is very rare (popmax 0.0011%, sas) (gnomAD).

ACTC1 p.Arg258=

c.774C>G · rs903582519 · VCV920623

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0011%, sas)

Conditions

cardiomyopathy

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 4	GERP 1.4, phastCons 1
Overall
CADD	10.85	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% South Asian · 1/91,082 alleles

Overall 6.84e-05% 1/1,461,890 alleles · very rare

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: ACTC1
Protein: p.Arg258=
Coding: c.774C>G
MANE Select: NM_005159
dbSNP: rs903582519
Type: single nucleotide variant
Location: chr15:34792124 (GRCh38)
Gene constraint: LOEUF 0.511 · pLI 0.97 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 95.47 · 16 PDB
Residue 258: an α-helix

Full ACTC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

ACTC1 p.Glu101Lys Pathogenic ★★★ same condition
ACTC1 p.Val56Ile Uncertain significance ★★★ ⚠ same condition
ACTC1 p.Gly247Asp Pathogenic/Likely pathogenic ★★ same condition
ACTC1 c.455-6G>A Uncertain significance ★★ same condition
ACTC1 c.808+4A>G Uncertain significance ★★ same condition
ACTC1 c.-12A>G Uncertain significance ★★ same condition
ACTC1 c.-1G>A Uncertain significance ★★ same condition
ACTC1 c.*1G>T 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/actc1-p-arg258 (accessed [today's date]).

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