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.1074G>T (p.Trp358Cys)

CA269775

127188 (ClinVar)

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: e3a83a0f-ca41-4386-a5fc-43e3e9b1f359
Approved on: 2024-08-27
Published on: 2024-12-16

HGVS expressions

NM_001100.4:c.1074G>T
NM_001100.4(ACTA1):c.1074G>T (p.Trp358Cys)
NC_000001.11:g.229431559C>A
CM000663.2:g.229431559C>A
NC_000001.10:g.229567306C>A
CM000663.1:g.229567306C>A
NC_000001.9:g.227633929C>A
NG_006672.1:g.7538G>T
ENST00000366683.4:c.996G>T
ENST00000684723.1:c.939G>T
ENST00000366683.3:c.705G>T
ENST00000366684.7:c.1074G>T
NM_001100.3:c.1074G>T
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP4_Moderate 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.1074G>T (p.Trp358Cys) variant in ACTA1 is a missense variant predicted to cause substitution of tryptophan by cysteine at amino acid 358. This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.957, 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 probands, one with nemaline rods in muscle biopsy (as well as dilated cardiomyopathy) and the other an infant with hypotonia (PS4_Supporting, PP4_Moderate; PMID: 23650303, Invitae SCV001393788.5). 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: PP4_Moderate, PS4_Supporting, PM2_Supporting, PP2, PP3. (Congenital Myopathies VCEP specifications version 2; 08/27/2024)
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PP4_Moderate
This variant has been reported in 1 proband with nemaline rods in muscle biopsy (as well as dilated cardiomyopathy) (PP4_Moderate; PMID: 23650303).
PS4_Supporting
This variant has been reported in 2 probands, one with nemaline rods in muscle biopsy (as well as dilated cardiomyopathy) and the other an infant with hypotonia (PS4_Supporting, PP4_Moderate; PMID: 23650303, Invitae SCV001393788.5).
PP3
The computational predictor REVEL gives a score of 0.957, 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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