The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_001100.4:c.1127G>C

CA345144077

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: e4571073-5716-435c-8a48-25ed7fb25a0c
Approved on: 2024-08-27
Published on: 2024-12-16

HGVS expressions

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

Pathogenic

Met criteria codes 6
PS2 PP3 PP2 PS4_Supporting PM2_Supporting PP4_Moderate
Not Met criteria codes 16
PS1 PS3 PVS1 PM5 PM1 PM4 PM3 BA1 BS3 BS1 BS2 BP7 BP3 BP2 BP4 BP1

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>C in ACTA1 is a missense variant predicted to cause substitution of cysteine by serine at amino acid 376 (p.Cys376Ser) in exon 7/7. The variant is absent from gnomAD v2.1.1 with adequate coverage (PM2_Supporting). The REVEL computational prediction analysis tool gives a score of 0.946, 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). The Z-score in gnomAD v2.1.1 is 4.53 which is above the threshold necessary to apply PP2. This variant has been reported in two probands with congenital nemaline myopathy (PS4_Supporting, PP4_Moderate PMID:25890230,19562689), and as a de novo observation with confirmed parental relationships in one of the probands (PS2, PMID:25890230). In summary, the variant meets the criteria to be classified as Pathogenic for autosomal dominant alpha-actinopathy. ACMG/AMP criteria met, as specified by the ClinGen Congenital Myopathies VCEP: PS2, PP4_Moderate, PS4_Supporting, PP2, PP3, PM2_Supporting (ClinGen Congenital Myopathies VCEP specifications version 2; 08/27/2024).
Met criteria codes
PS2
One proband was identified as de novo with confirmed parental relationships (PMID: 25890230)
PP3
The REVEL score is 0.946, which is above the threshold of 0.7 to apply 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 Z-score in gnomAD v4.1.0 is 6.09 which is above the threshold for PP2
PS4_Supporting
There are two probands with nemaline myopthy reported in two publications (PMID:25890230, 19562689)
PM2_Supporting
This variant is absent from gnomAD v.4.1.0 with adequate coverage
PP4_Moderate
This variant has been reported in two probands with congenital nemaline myopathy (PMID:25890230,19562689). One of these probands had a skeletal muscle biopsy that displayed features specific for nemaline myopathy.
Not Met criteria codes
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
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
PM5 applied to c.1127G>T(p.Cys376Phe) curation
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
PM3
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 with adequate coverage
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 with adequate coverage
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
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
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
The REVEL score is 0.946
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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