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.1007A>C (p.Glu336Ala)

CA128033

18288 (ClinVar)

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 9148486b-0040-49d6-a7d4-c6589b4f51e8
Approved on: 2024-07-08
Published on: 2025-04-02

HGVS expressions

NM_001100.4:c.1007A>C
NM_001100.4(ACTA1):c.1007A>C (p.Glu336Ala)
NC_000001.11:g.229431626T>G
CM000663.2:g.229431626T>G
NC_000001.10:g.229567373T>G
CM000663.1:g.229567373T>G
NC_000001.9:g.227633996T>G
NG_006672.1:g.7471A>C
ENST00000366683.4:c.991-62A>C
ENST00000684723.1:c.872A>C
ENST00000366683.3:c.638A>C
ENST00000366684.7:c.1007A>C
NM_001100.3:c.1007A>C
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Likely Pathogenic

Met criteria codes 5
PP3 PP2 PM2_Supporting PP1_Moderate PP4_Moderate
Not Met criteria codes 1
PS4

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.1007A>C (NM_001100.4(ACTA1):c.1007A>C (p.Glu336Ala)) variant in ACTA1 is a missense variant predicted to cause substitution of glutamate by alanine at amino acid 336 (p.Glu336Ala). 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 0.874, which is above the threshold of 0.7, evidence that correlates with impact to ACTA1 function (PP3). At least one patient with this variant displayed cores and fiber type disproportion on muscle biopsy, which is highly specific for actin accumulation myopathy (PP4_Moderate, PMID: 15520409). This variant has been reported in 5 individuals from one family with muscle weakness (PP1_Moderate; PMID: 15520409). 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, PP4_Moderate, PP1_Moderate (Congenital Myopathies VCEP Specifications Version 2.0; July 8, 2024).
Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.874, 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). Z-score for missense variants in this gene is 6.09.
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting). Coverage of the gene in the region within which the variant is found is adequate.
PP1_Moderate
This variant has been reported in 5 individuals from one family with muscle weakness (PP1_moderate; PMID: 15520409).
PP4_Moderate
At least one patient with this variant displayed cores and fiber type disproportion on muscle biopsy, which is highly specific for actin accumulation myopathy (PP4_moderate, PMID: 15520409).
Not Met criteria codes
PS4
This variant has been reported in 5 probands from one family with muscle weakness (No case codes met; PMID: 15520409).
Curation History
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