Is ACTN2 p.Thr495= (c.1485G>C) pathogenic?

ACTN2 p.Thr495= (c.1485G>C) is classified Likely benign in ACTN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-07-19). Very rare (popmax 0.000847%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with ACTN2 p.Thr495= (c.1485G>C)?

ACTN2 p.Thr495= (c.1485G>C) is associated with Cardiovascular phenotype (ClinVar).

How common is ACTN2 p.Thr495= (c.1485G>C) in the general population?

ACTN2 p.Thr495= (c.1485G>C) is very rare (popmax 0.000847%, nfe) (gnomAD).

ACTN2 p.Thr495=

c.1485G>C · rs201179281 · VCV1773657

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000847%, nfe)

Conditions

Cardiovascular phenotype

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 -5.3	GERP -4.8
Overall
CADD	0.722	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000847% European (non-Finnish) · 10/1,179,960 alleles

Filtering AF 0.000429% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000312%

Overall 0.000684% 10/1,461,754 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: ACTN2
Protein: p.Thr495=
Coding: c.1485G>C
MANE Select: NM_001103
dbSNP: rs201179281
Type: single nucleotide variant
Location: chr1:236747745 (GRCh38)
Gene constraint: LOEUF 0.432 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 84.88 · 18 PDB
Residue 495: a UniProt-annotated variant site (in cmh23); an α-helix

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

Disease context

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

Similar variants

ACTN2 p.Thr495Met Conflicting classifications of pathogenicity ★ ⚠ same residue
ACTN2 p.Thr495Lys Uncertain significance ★ ⚠ same residue
ACTN2 c.1255+1G>C Uncertain significance ★★ same condition
ACTN2 c.126+2T>G Uncertain significance ★★ same condition
ACTN2 c.2154+4C>T Uncertain significance ★★ same condition
ACTN2 c.697+1G>A Uncertain significance ★★ same condition
ACTN2 c.783+4C>T Uncertain significance ★★ same condition
ACTN2 c.*10T>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-thr495 (accessed [today's date]).

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