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.868G>C (p.Asp290His)

CA345145962

521371 (ClinVar)

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: da8a4820-72dd-4373-bc1d-ec60f9fde1e8
Approved on: 2024-08-27
Published on: 2024-12-12

HGVS expressions

NM_001100.4:c.868G>C
NM_001100.4(ACTA1):c.868G>C (p.Asp290His)
NC_000001.11:g.229431843C>G
CM000663.2:g.229431843C>G
NC_000001.10:g.229567590C>G
CM000663.1:g.229567590C>G
NC_000001.9:g.227634213C>G
NG_006672.1:g.7254G>C
ENST00000366683.4:c.868G>C
ENST00000684723.1:c.733G>C
ENST00000366683.3:c.499G>C
ENST00000366684.7:c.868G>C
NM_001100.3:c.868G>C
More

Pathogenic

Met criteria codes 7
PS2 PP3 PP2 PS4_Supporting PM5 PM2_Supporting PP4_Moderate

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.868G>C variant in ACTA1 is a missense variant predicted to cause substitution of aspartic acid by histidine at amino acid 290 (legacy nomenclature: p.Asp288His). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.985, 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 , including one with a muscle biopsy containing nemaline rods (PS4_Supporting, PP4_Moderate; PMIDs: 29565416, 28516742). In both individuals, the variant has been identified as a de novo occurrence with confirmed parental relationships (PS2). Another missense variant c.868G>A, p.Asp290Asn (PMIDs: 19562689, 27242277) in the same codon has been classified as pathogenic for AD nemaline myopathy by the ClinGen Congenital Myopathies VCEP (PM5). 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: PS2, PM5, PP4_Moderate, PS4_Supporting, PM2_Supporting, PP2, PP3 (Congenital Myopathies VCEP specifications version 1; 08/27/2024).
Met criteria codes
PS2
The p.Asp290His variant was identified as a de novo observation in two individuals, both with parental relationships confirmed by WES (PMID: 29565416, 28516742). One did not have specific phenotypes detailed and the other had Nemaline rods present in biopsy, which is highly specific for ACTA1 variants.
PP3
The computational predictor REVEL gives a score of 0.985, which is above the threshold of 0.75, evidence that correlates with impact to ACTA1 function (PP3).
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
PS4_Supporting
The p.Asp290His variant was identified as a de novo observation in one individual without specific phenotypes provided. (PMID:29565416) and a second infant with nemaline rods confirmed on biopsy (PMID: 28516742).
PM5
Another missense variant c.868G>A, p.Asp290Asn (PMIDs: 19562689, 27242277) in the same codon has been classified as pathogenic for AD nemaline myopathy by the ClinGen Congenital Myopathies VCEP (PM5).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
PP4_Moderate
This variant has been reported in 2 probands , including one with a muscle biopsy containing nemaline rods (PS4_Supporting, PP4_Moderate; PMIDs: 29565416, 28516742).
Curation History
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