Is ACTC1 p.His103= (c.309C>T) pathogenic?

ACTC1 p.His103= (c.309C>T) is classified Likely benign in ACTC1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-09). Very rare (popmax 0.00801%, afr); Associated with cardiomyopathy.

How common is ACTC1 p.His103= (c.309C>T) in the general population?

ACTC1 p.His103= (c.309C>T) is very rare (popmax 0.00801%, afr) (gnomAD).

ACTC1 p.His103=

Q: What condition is associated with ACTC1 p.His103= (c.309C>T)?

ACTC1 p.His103= (c.309C>T) is associated with cardiomyopathy, hypertrophic cardiomyopathy, hypertrophic cardiomyopathy 11 (ClinVar).

c.309C>T · rs769303249 · VCV416058

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00801%, afr)

Conditions

cardiomyopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 2.6	GERP -1.6, phastCons 1
Overall
CADD	9.585	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00801% African / African-American · 6/74,906 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.000372% 6/1,614,024 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.His103=
Coding: c.309C>T
dbSNP: rs769303249
Type: single nucleotide variant
Location: chr15:34793390 (GRCh38)

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

Also linked: hypertrophic cardiomyopathy hypertrophic cardiomyopathy 11 atrial septal defect 5 dilated cardiomyopathy 1R

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-his103 (accessed [today's date]).

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