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.1106C>T (p.Pro369Leu)

CA345144203

431989 (ClinVar)

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: bd4a8da3-d9de-4cda-9c13-1804ac87b583
Approved on: 2024-08-27
Published on: 2025-01-03

HGVS expressions

NM_001100.4:c.1106C>T
NM_001100.4(ACTA1):c.1106C>T (p.Pro369Leu)
NC_000001.11:g.229431527G>A
CM000663.2:g.229431527G>A
NC_000001.10:g.229567274G>A
CM000663.1:g.229567274G>A
NC_000001.9:g.227633897G>A
NG_006672.1:g.7570C>T
ENST00000366683.4:c.1028C>T
ENST00000684723.1:c.971C>T
ENST00000366683.3:c.737C>T
ENST00000366684.7:c.1106C>T
NM_001100.3:c.1106C>T
More

Pathogenic

Met criteria codes 6
PP4_Strong PS4_Moderate PM2_Supporting PP1 PP3 PP2
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.1106C>T (p.Pro369Leu) variant in ACTA1 is a missense variant predicted to cause substitution of proline by leucine at amino acid 369. This variant is absent from gnomAD v4.1.1 (PM2_Supporting). The computational predictor REVEL gives a score of 0.922, 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 nemaline myopathy, 1 with nemaline rods (PS4_Moderate; PMIDs: 19562689, 26172852; ClinVar SCVs: SCV000589626.2, SCV002287790.1; Internal lab contributors: GeneDx, Invitae). At least one patient with this variant displayed nemaline rods and type 1 fiber predominance, which is highly specific for alpha-actinopathy (PP4_Moderate, PMID: 26172852). The variant has been reported to segregate with autosomal dominant nemaline myopathy in 3 affected family members from 1 family (PP1; ClinVar SCV: SCV000589626.2, Internal lab contributors: GeneDx). 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, PM2_Supporting, PP1, PP2, PP3. (Congenital Myopathies VCEP specifications version 2; 08/27/2024)
Met criteria codes
PP4_Strong
At least one patient with this variant displayed nemaline rods and type 1 fiber predominance, which is highly specific for alpha-actinopathy. This patient had comprehensive genetic testing; therefore PP4 was upgraded to Strong (PP4_Strong, PMID: 26172852).
PS4_Moderate
This variant has been reported in 4 probands with nemaline myopathy, 1 with nemaline rods (PS4_Moderate; PMIDs: 19562689, 26172852; ClinVar SCVs: SCV000589626.2, SCV002287790.1; Internal lab contributors: GeneDx, Invitae).
PM2_Supporting
This variant is absent from gnomAD v4.1 (PM2_Supporting).
PP1
The variant has been reported to segregate with nemaline myopathy in 3 affected family members from 1 family (PP1; GeneDx).
PP3
The computational predictor REVEL gives a score of 0.922, 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).
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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