The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene label mismatch: ACTA1 vs undefined
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_001100.4(ACTA1):c.304G>A (p.Glu102Lys)

CA16603574

377433 (ClinVar)

Gene: ACTA1 (HGNC:58)
Condition: alpha-actinopathy (MONDO:0100084)
Inheritance Mode: Autosomal dominant inheritance
UUID: 87018d01-b34d-4728-a771-c1f796dfaf59
Approved on: 2024-09-09
Published on: 2025-04-02

HGVS expressions

NM_001100.4:c.304G>A
NM_001100.4(ACTA1):c.304G>A (p.Glu102Lys)
NC_000001.11:g.229432706C>T
CM000663.2:g.229432706C>T
NC_000001.10:g.229568453C>T
CM000663.1:g.229568453C>T
NC_000001.9:g.227635076C>T
NG_006672.1:g.6391G>A
ENST00000366683.4:c.304G>A
ENST00000684723.1:c.169G>A
ENST00000366683.3:c.304G>A
ENST00000366684.7:c.304G>A
NM_001100.3:c.304G>A
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Likely Pathogenic

Met criteria codes 6
PP4_Moderate PS4_Moderate PP1 PP3 PP2 PM2_Supporting

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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The c.304G>A (NM_001100.4(ACTA1):c.304G>A (p.Glu102Lys)) variant in ACTA1 is a missense variant predicted to cause substitution of glutamate by lysine at amino acid 102 (p.Glu102Lys). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). 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). The computational predictor REVEL gives a score of 0.854, which is above the threshold of 0.7, evidence that correlates with impact to ACTA1 function (PP3). This variant has been reported in 4 probands with alpha-actinopathy (PS4_Moderate; SCV000511956, SCV003347757; Invitae & GeneDx Internal Data). At least one patient with this variant displayed muscle biopsy with fiber type disproportion, which is highly specific for alpha-actinopathy (PP4_Moderate; SCV003347757, Invitae internal data). The variant has been reported to segregate with alpha-actinopathy in one affected daughter (PP1; SCV003347757, Invitae internal data). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal dominant alpha-actinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PM2_supporting, PP2, PP3, PS4_Moderate, PP4_Moderate, PP1 (ClinGen Congenital Myopathies VCEP Specifications Version 2.0, 9/9/2024).
Met criteria codes
PP4_Moderate
At least one patient with this variant displayed muscle biopsy with fiber type disproportion, which is highly specific for alpha-actinopathy (PP4_moderate; SCV003347757, Invitae internal data).
PS4_Moderate
This variant has been reported in 5 probands from 4 families with alpha-actinopathy (PS4_moderate).
PP1
The variant has been reported to segregate with alpha-actinopathy in one affected daughter (PP1; SCV003347757, Invitae internal data).
PP3
The computational predictor REVEL gives a score of 0.854, 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). The gnomAD v4.1.0 Z score is 6.09.
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting). Coverage of ACTA1 in the region in which this variant is found is adequate.
Curation History
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