The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_001100.4:c.687G>A

CA345147057

Gene: ACTA1 (HGNC:58)
Condition: alpha-actinopathy (MONDO:0100084)
Inheritance Mode: Autosomal dominant inheritance
UUID: 330bea44-2e46-43fd-b1da-2c8f0f3e0275
Approved on: 2026-09-14
Published on: 2026-09-28

HGVS expressions

NM_001100.4:c.687G>A
NC_000001.11:g.229432115C>T
CM000663.2:g.229432115C>T
NC_000001.10:g.229567862C>T
CM000663.1:g.229567862C>T
NC_000001.9:g.227634485C>T
NG_006672.1:g.6982G>A
ENST00000366683.4:c.687G>A
ENST00000684723.1:c.552G>A
ENST00000366683.3:c.480-253G>A
ENST00000366684.7:c.687G>A
NM_001100.3:c.687G>A
More

Pathogenic

Met criteria codes 6
PM5_Strong PS2_Moderate PS4_Supporting PM2_Supporting PP3 PP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Congenital Myopathies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ACTA1 Version 2.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The NM_001100.4(ACTA1):c.687G>A variant in ACTA1 is a missense variant predicted to cause substitution of methionine by isoleucine at amino acid 229 (p.Met229Ile, also known as p.Met227Thr). This variant is absent from gnomAD v4.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.842, which is above the threshold of 0.7, evidence that correlates with impact to ACTA1 function (PP3). ACTA1, in which the variant was identified, is defined by the ClinGen Congenital Myopathies VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). Different missense variants (c.686T>C (p.Met229Thr), c.685A>T (p.Met229Leu) and c.685A>G (p.Met229Val)) in the same codon have been classified as pathogenic/ likely pathogenic for alpha-actinopathy by the ClinGen Congenital Myopathies VCEP (PM5_Strong; SCV007612356.1, SCV007612355.1, SCV007612357.1). This variant has been reported in two probands with clinical features of congenital myopathies, of which one was a de novo case with confirmed parental relationship (PS4_Supporting, PS2_Moderate; PMID: 38544359, 12921789). In summary, this variant meets the criteria to be classified as pathogenic for autosomal dominant alpha-actinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PM2_Supporting, PP3, PP2, PM5_Strong, PS4_Supporting, PS2_Moderate (ClinGen Congenital Myopathies VCEP specifications version 2.0)
Met criteria codes
PM5_Strong
Different missense variants (c.686T>C (p.Met229Thr), c.685A>T (p.Met229Leu) and c.685A>G (p.Met229Val)) in the same codon have been classified as pathogenic/ likely pathogenic for alpha-actinopathy by the ClinGen Congenital Myopathies VCEP (PM5_Strong; SCV007612356.1, SCV007612355.1, SCV007612357.1).
PS2_Moderate
This variant has been identified as a de novo occurrence with confirmed parental relationships in at least one individual with clinical features of congenital myopathy (PS2_Moderate; PMID: 38544359).
PS4_Supporting
This variant has been reported in two probands with clinical features of congenital myopathies (PS4_Supporting; PMID: 12921789, 38544359).
PM2_Supporting
This variant is absent from gnomAD v4.1.1 (PM2_Supporting).
PP3
The computational predictor REVEL gives a score of 0.842, which is above the threshold of 0.7, evidence that correlates with impact to ACTA1 function (PP3).
PP2
ACTA1, in which the variant was identified, is defined by the ClinGen Congenital Myopathies VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2).
Curation History
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