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.1127G>T (p.Cys376Phe)

CA345144073

801630 (ClinVar)

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: b2f5e908-7dc7-4115-af99-78db860db1e1
Approved on: 2024-08-27
Published on: 2025-01-03

HGVS expressions

NM_001100.4:c.1127G>T
NM_001100.4(ACTA1):c.1127G>T (p.Cys376Phe)
NC_000001.11:g.229431506C>A
CM000663.2:g.229431506C>A
NC_000001.10:g.229567253C>A
CM000663.1:g.229567253C>A
NC_000001.9:g.227633876C>A
NG_006672.1:g.7591G>T
ENST00000366683.4:c.1049G>T
ENST00000684723.1:c.992G>T
ENST00000366683.3:c.758G>T
ENST00000366684.7:c.1127G>T
NM_001100.3:c.1127G>T
More

Likely Pathogenic

Met criteria codes 5
PM5 PM2_Supporting PS2 PP3 PP2
Not Met criteria codes 21
PM6 PM3 PM1 PM4 BA1 BS2 PVS1 BS4 BS3 BS1 BP7 BP5 BP2 BP3 BP4 BP1 PS1 PS3 PS4 PP4 PP1

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 variant NM_001100.4:c.1127G>T in ACTA1 is a missense variant predicted to cause substitution of cysteine by phenylalanine at amino acid 376 (p.Cys376Phe) in exon 7/7. The variant is absent from gnomAD v4.1.1 with adequate coverage (PM2_Supporting). The REVEL computational prediction analysis tool gives a score of 0.955, which is above the threshold necessary to apply PP3. In addition, 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 as a de novo observation with confirmed parental relationships in one proband with features associated with congenital myopathy which meets the criteria for PS2 (Invitae, SCV002228646.2). Another missense variant c.1127G>C (p.Cys376Ser) in the same codon is classified as pathogenic for autosomal dominant alpha-actinopathy (PM5, PMIDs:25890230, 19562689). In summary, the variant meets the criteria to be classified as likely pathogenic for autosomal dominant alpha-actinopathy. ACMG/AMP criteria met, as specified by the ClinGen Congenital Myopathies VCEP: PS2, PM5, PP2, PP3, PM2_Supporting (ClinGen Congenital Myopathies VCEP specifications version 2; 08/27/2024).
Met criteria codes
PM5
c.1127G>C(p.Cys376Ser) in the same codon is classified as pathogenic for autosomal dominant alpha-actinopathy
PM2_Supporting
This variant is absent from gnomAD v.4.1.1 with adequate coverage (PM2_Supporting)
PS2
This variant has been identified as a de novo occurrence with confirmed parental relationships in an individual (Invitae, SCV002228646.2).
PP3
The computational predictor REVEL gives a score of 0.955, 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. The missense Z-score in gnomAD v4.1.1 is 6.09 which is above the threshold set by the ClinGen Congenital Myopathies VCEP.
Not Met criteria codes
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
This variant is absent from gnomAD v.2.1.1
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
This variant is absent from gnomAD v.2.1.1
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
The computational predictor REVEL gives a score of 0.955
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
This variant has been reported in one proband, an infant with severely flaccidity, lower leg spasticity, hypotonia, pronounced facial weakness, joint contractures, inability to swallow (fed via gastric tube) (Invitae internal data, SCV000934090.3).
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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