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.109G>T (p.Val37Leu)

CA345151305

464114 (ClinVar)

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 1dbcbf38-ff96-4bff-a816-a36808aeb828
Approved on: 2024-08-27
Published on: 2024-12-12

HGVS expressions

NM_001100.4:c.109G>T
NM_001100.4(ACTA1):c.109G>T (p.Val37Leu)
NC_000001.11:g.229433007C>A
CM000663.2:g.229433007C>A
NC_000001.10:g.229568754C>A
CM000663.1:g.229568754C>A
NC_000001.9:g.227635377C>A
NG_006672.1:g.6090G>T
ENST00000366683.4:c.109G>T
ENST00000684723.1:c.-6-127G>T
ENST00000366683.3:c.109G>T
ENST00000366684.7:c.109G>T
NM_001100.3:c.109G>T
More

Pathogenic

Met criteria codes 5
PM5_Strong PM2_Supporting PS2 PP3 PP2
Not Met criteria codes 5
BS1 BP4 PS4 PS1 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 NM_001100.4(ACTA1):c.109G>T variant in ACTA1 is a missense variant predicted to cause substitution of valine by leucine at amino acid 37 (legacy nomenclature: p.Val35Leu). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). The computational predictor REVEL gives a score of 0.881, 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). Three other variants occur at the same residue (c.110T>C (p.V37A); c.110T>G (p.V37G)) with c.109G>C (p.V37L) occurring at the same nucleotide (PM5_Strong). This variant has occurred de novo in one individual with nemaline myopathy, hypotonia, respiratory distress, and cardiac arrest (PS2; PMID:28973083, Baylor Genetics, SCV000807332.1). 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_Strong, PM2_Supporting, PP2, PP3 (ClinGen Congenital Myopathies VCEP specifications version 2; 08/27/2024).
Met criteria codes
PM5_Strong
Three other variants occur at the same residue (c.110T>C (p.V37A); c.110T>G (p.V37G)) with c.109G>C (p.V37L) occurring at the same nucleotide.
PM2_Supporting
This variant is absent from gnomAD v4.1 (PM2_Supporting).
PS2
This variant has occurred de novo in one individual with nemaline myopathy, hypotonia, respiratory distress, and cardiac arrest (PS2 PMID:28973083, Baylor Genetics, SCV000807332.1).
PP3
The computational predictor REVEL gives a score of 0.881, 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
PS4
This variant has occurred de novo in one individual with nemaline myopathy, hypotonia, respiratory distress, and cardiac arrest (PS2; PMID:28973083, Baylor Genetics, SCV000807332.1).
PS1
Three other variants occur at the same residue (c.110T>C (p.V37A); c.110T>G (p.V37G)) with c.109G>C (p.V37L) occurring at the same nucleotide.
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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