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
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Variant: NM_001100.4(ACTA1):c.283G>A (p.Glu95Lys)

CA345150112

654469 (ClinVar)

Gene: ACTA1 (HGNC:58)
Condition: alpha-actinopathy (MONDO:0100084)
Inheritance Mode: Autosomal dominant inheritance
UUID: 813ff07f-556e-4768-9347-9b93e3c210dd
Approved on: 2024-08-27
Published on: 2025-01-03

HGVS expressions

NM_001100.4:c.283G>A
NM_001100.4(ACTA1):c.283G>A (p.Glu95Lys)
NC_000001.11:g.229432727C>T
CM000663.2:g.229432727C>T
NC_000001.10:g.229568474C>T
CM000663.1:g.229568474C>T
NC_000001.9:g.227635097C>T
NG_006672.1:g.6370G>A
ENST00000366683.4:c.283G>A
ENST00000684723.1:c.148G>A
ENST00000366683.3:c.283G>A
ENST00000366684.7:c.283G>A
NM_001100.3:c.283G>A
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Pathogenic

Met criteria codes 6
PM2_Supporting PS2_Supporting PP3 PP2 PS4_Moderate PP4_Strong
Not Met criteria codes 4
BS1 BP4 BP1 BA1

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.283G>A variant in ACTA1 is a missense variant predicted to cause substitution of glutamic acid by lysine at amino acid 95 (legacy nomenclature: p.Glu93Lys). This variant is absent from gnomAD v4.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.933, 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 4 probands with severe hypotonia and/or congenital myopathy (PS4_Moderate; PMID: 35810298, Invitae, ClinVar SCV:SCV000950636.2). In one of those four individuals, the variant has been identified as a de novo occurrence with confirmed parental relationships (PS2; Invitae, ClinVar SCV:SCV000950636.2). At least one patient with this variant displayed intranuclear rods and type 1 muscle fiber predominance, which is highly specific for alpha-actinopathy and has had exome testing that is negative for all other causes of myopathy (PP4_Strong, PMID: 35810298). 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: PP4_Strong, PS4_Moderate, PS2_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 v4.1.1 (PM2_Supporting).
PS2_Supporting
In one individual, the variant was determined to occur de novo, parents tested and relatedness confirmed (0.5 PS2 Points, PS2_Supporting). Family testing was not performed for the remaining individuals.
PP3
The computational predictor REVEL gives a score of 0.933, 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).
PS4_Moderate
4 individuals, all were infants with severe hypotonia and/or congenital myopathy (0.25 PS4 Points Each, 1 Total; PS4).
PP4_Strong
At least one patient with this variant displayed intranuclear rods and type 1 muscle fiber predominance, which is highly specific for alpha-actinopathy and has had exome testing that is negative for all other causes of myopathy (PP4_Strong, PMID: 35810298).
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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