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.1001C>G (p.Pro334Arg)

CA345144971

1031829 (ClinVar)

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 1348c9f8-dc41-4610-b7d0-919a1b090307
Approved on: 2024-08-27
Published on: 2025-01-03

HGVS expressions

NM_001100.4:c.1001C>G
NM_001100.4(ACTA1):c.1001C>G (p.Pro334Arg)
NC_000001.11:g.229431632G>C
CM000663.2:g.229431632G>C
NC_000001.10:g.229567379G>C
CM000663.1:g.229567379G>C
NC_000001.9:g.227634002G>C
NG_006672.1:g.7465C>G
ENST00000366683.4:c.991-68C>G
ENST00000684723.1:c.866C>G
ENST00000366683.3:c.632C>G
ENST00000366684.7:c.1001C>G
NM_001100.3:c.1001C>G
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Pathogenic

Met criteria codes 6
PM2_Supporting PS2 PP3 PP2 PM5 PS4_Supporting
Not Met criteria codes 1
PS3

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.1001C>G variant in ACTA1 is a missense variant predicted to cause a substitution of proline by arginine at amino acid position 334. This variant is absent from gnomAD v4.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.893, which is above the threshold of 0.7 set by the CM VCEP (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 identified as a de novo occurrence with confirmed parental relationships in one individual and as a de novo occurrence with unconfirmed parental relationships in one individual with alpha-actinopathy (PS4_Supporting, PS2; Invitae internal data; PMID: 19562689,). Another missense variant c.1000C>T, p.Pro334Ser (PMID: 15468086) in the same codon has been classified as likely pathogenic for autosomal dominant alpha-actinopathy 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, 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 v 4.1.0 (PM2_Supporting).
PS2
This variant has been identified as a de novo occurrence with confirmed parental relationships in one individual and as a de novo occurrence with unconfirmed parental relationships in one individual with congenital myopathy (PS2; Invitae internal data; PMID: 19562689,).
PP3
The computational predictor REVEL gives a score of 0.893, 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 Z score = 6.09
PM5
Another missense variant c.1000C>T, p.Pro334Ser (PMID: 15468086) in the same codon has been classified as likely pathogenic for autosomal dominant alpha-actinopathy by the ClinGen Congenital Myopathies VCEP (PM5).
PS4_Supporting
The p.Pro334Arg variant was identified as a de novo observation in one individual with nemaline myopathy requested (NMR) (PMID: 19562689). This variant was also reported in an individual with congenital myopathy, severe hypotonia, and stridor/respiratory distress (Invitae internal data; PS4_Supporting).
Not Met criteria codes
PS3
To our knowledge, functional assays have not been reported for this variant.
Curation History
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