10-88948816-G-A
Variant summary
Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_001613.4(ACTA2):c.115C>T(p.Arg39Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000657 in 152,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R39G) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001613.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ACTA2 | NM_001613.4 | c.115C>T | p.Arg39Cys | missense_variant | 2/9 | ENST00000224784.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ACTA2 | ENST00000224784.10 | c.115C>T | p.Arg39Cys | missense_variant | 2/9 | 1 | NM_001613.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74284
ClinVar
Submissions by phenotype
not provided Pathogenic:5
Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Feb 15, 2023 | The ACTA2 c.115C>T; p.Arg39Cys variant (rs112901682) is reported in multiple individuals with thoracic aortic disorders and shown to segregate with disease in affected family members (Campens 2015, Hoffjan 2011, Kaw 2022, Li 2021, Overwater 2018). This variant is also reported in ClinVar (Variation ID: 65449). This variant is only found on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.853). Additionally, other variants at this codon (p.Arg39Gly, p.Arg39His) are reported in individuals with aortic aneurysm and dissection and are considered to be causative (Hoffjan 2011, Overwater 2018, Regalado 2015). Based on available information, the p.Arg39Cys variant is considered to be pathogenic. References: Campens L et al. Gene panel sequencing in heritable thoracic aortic disorders and related entities - results of comprehensive testing in a cohort of 264 patients. Orphanet J Rare Dis. 2015 Feb 3;10:9. PMID: 25644172. Hoffjan S et al. Three novel mutations in the ACTA2 gene in German patients with thoracic aortic aneurysms and dissections. Eur J Hum Genet. 2011 May;19(5):520-4. PMID: 21248741. Kaw A et al. Expanding ACTA2 genotypes with corresponding phenotypes overlapping with smooth muscle dysfunction syndrome. Am J Med Genet A. 2022 Aug;188(8):2389-2396. PMID: 35567597. Li J et al. Genetic testing and clinical relevance of patients with thoracic aortic aneurysm and dissection in northwestern China. Mol Genet Genomic Med. 2021 Oct;9(10):e1800. PMID: 34498425. Overwater E et al. Results of next-generation sequencing gene panel diagnostics including copy-number variation analysis in 810 patients suspected of heritable thoracic aortic disorders. Hum Mutat. 2018 Sep;39(9):1173-1192. PMID: 29907982. Regalado ES et al. Aortic Disease Presentation and Outcome Associated With ACTA2 Mutations. Circ Cardiovasc Genet. 2015 Jun;8(3):457-64. PMID: 25759435. - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | May 23, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 21733706, 25644172, 25759435, 24243736, 21248741, 21937134, 30030203, 29907982, 31536524, 35567597, 36053285, 34498425) - |
Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | ACTA2: PM1, PM2, PM5, PS4:Moderate, PP1, PP3 - |
Pathogenic, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Familial thoracic aortic aneurysm and aortic dissection Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Jul 18, 2019 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 29, 2024 | The p.R39C variant (also known as c.115C>T), located in coding exon 1 of the ACTA2 gene, results from a C to T substitution at nucleotide position 115. The arginine at codon 39 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant has been reported in individuals with thoracic aortic aneurysm and dissection (TAAD), and co-segregation in affected relatives was reported in two unrelated families (Hoffjan S et al. Eur. J. Hum. Genet., 2011 May;19:520-4; Renard M et al. Int. J. Cardiol., 2013 May;165:314-21; Regalado ES et al. Am. J. Med. Genet. A, 2014 Jan;164A:106-12; Overwater E et al. Hum. Mutat., 2018 09;39:1173-1192). Alternate amino acid substitutions at this position, p.R39H and p.R39G, have also been associated with TAAD and vascular disease findings (Guo DC et al. Am J Hum Genet. 2009;84(5):617-27; Regalado ES et al. Circ Cardiovasc Genet. 2015;8(3):457-64). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD) (Lek M et al. Nature, 2016 08;536:285-91). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Pathogenic, no assertion criteria provided | clinical testing | Blueprint Genetics | Jan 30, 2014 | - - |
Aortic aneurysm, familial thoracic 6 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Oct 18, 2023 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 39 of the ACTA2 protein (p.Arg39Cys). This variant is present in population databases (rs112901682, gnomAD 0.03%). This missense change has been observed in individuals with aortopathy (PMID: 21248741, 21733706, 21937134, 24243736, 25644172, 25759435). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 65449). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ACTA2 protein function. For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2011 | - - |
See cases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University Hospital Muenster | Jul 18, 2022 | ACMG categories: PS4,PM1,PM2,PP1,PP3,PP5,BP1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at