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 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.1071G>C (p.Met357Ile)

CA345144479

835545 (ClinVar)

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: ed7dfee9-2fe2-4fce-923a-3eb556a93a2a
Approved on: 2024-08-27
Published on: 2024-12-16

HGVS expressions

NM_001100.4:c.1071G>C
NM_001100.4(ACTA1):c.1071G>C (p.Met357Ile)
NC_000001.11:g.229431562C>G
CM000663.2:g.229431562C>G
NC_000001.10:g.229567309C>G
CM000663.1:g.229567309C>G
NC_000001.9:g.227633932C>G
NG_006672.1:g.7535G>C
ENST00000366683.4:c.993G>C
ENST00000684723.1:c.936G>C
ENST00000366683.3:c.702G>C
ENST00000366684.7:c.1071G>C
NM_001100.3:c.1071G>C
More

Uncertain Significance

Met criteria codes 4
PM2_Supporting PS4_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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The c.1071G>C variant in ACTA1 is a missense variant predicted to cause substitution of methionine by isoleucine at amino acid 357 (legacy nomenclature: p.Met355Ile). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.921, 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). This variant has been reported in 2 adult probands with features of muscle weakness (PS4_Supporting; Invitae, SCV001199812.3, GeneDx, SCV001989742.1). In summary, this variant meets the criteria to be classified as uncertain significance for autosomal dominant alpha-actinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: PS4_Supporting, PM2_Supporting, PP2, PP3 (Congenital Myopathies VCEP specifications version 2; 08/27/2024).
Met criteria codes
PM2_Supporting
The variant is absent from gnomAD v4.1.0 with adequate coverage
PS4_Supporting
The p.Met357Ile variant was identified in two individuals (GeneDx SCV001989742.1 and Invitae SCV001199812.3) with features suggestive, but not specific to ACTA1 variants (PS4_Supporting).
PP3
The REVEL score is 0.921 (>0.75 cutoff), residue is well conserved, and not predicted to impact splicing.
PP2
ACTA1, in which the variant was identified, is defined by the ClinGen CM 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). gnomAD 4.1.0 Z score = 6.09
Curation History
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