rs121434526

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM2PP2PP3_StrongPP5_Very_Strong

The NM_001613.4(ACTA2):​c.445C>T​(p.Arg149Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,611,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

ACTA2
NM_001613.4 missense

Scores

14
3
1

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:10

Conservation

PhyloP100: 7.93
Variant links:
Genes affected
ACTA2 (HGNC:130): (actin alpha 2, smooth muscle) This gene encodes one of six different actin proteins. Actins are highly conserved proteins that are involved in cell motility, structure, integrity, and intercellular signaling. The encoded protein is a smooth muscle actin that is involved in vascular contractility and blood pressure homeostasis. Mutations in this gene cause a variety of vascular diseases, such as thoracic aortic disease, coronary artery disease, stroke, and Moyamoya disease, as well as multisystemic smooth muscle dysfunction syndrome. [provided by RefSeq, Sep 2017]
STAMBPL1 (HGNC:24105): (STAM binding protein like 1) Predicted to enable Lys63-specific deubiquitinase activity and thiol-dependent deubiquitinase. Predicted to be involved in protein K63-linked deubiquitination. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 15 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in the ACTA2 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 27 curated pathogenic missense variants (we use a threshold of 10). The gene has 0 curated benign missense variants. Trascript score misZ: 4.6117 (above the threshold of 3.09). GenCC associations: The gene is linked to familial thoracic aortic aneurysm and aortic dissection, connective tissue disorder, aortic aneurysm, familial thoracic 6, multisystemic smooth muscle dysfunction syndrome, Moyamoya disease 5.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.978
PP5
Variant 10-88941794-G-A is Pathogenic according to our data. Variant chr10-88941794-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 18276.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-88941794-G-A is described in Lovd as [Likely_pathogenic]. Variant chr10-88941794-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ACTA2NM_001613.4 linkc.445C>T p.Arg149Cys missense_variant Exon 5 of 9 ENST00000224784.10 NP_001604.1 P62736D2JYH4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ACTA2ENST00000224784.10 linkc.445C>T p.Arg149Cys missense_variant Exon 5 of 9 1 NM_001613.4 ENSP00000224784.6 P62736

Frequencies

GnomAD3 genomes
AF:
0.00000657
AC:
1
AN:
152162
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.00000206
AC:
3
AN:
1459660
Hom.:
0
Cov.:
32
AF XY:
0.00000138
AC XY:
1
AN XY:
725868
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000117
Gnomad4 FIN exome
AF:
0.0000188
Gnomad4 NFE exome
AF:
9.00e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000657
AC:
1
AN:
152162
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74330
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:10
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Pathogenic:4
Pathogenic, no assertion criteria providedprovider interpretationStanford Center for Inherited Cardiovascular Disease, Stanford UniversityJan 05, 2017The patient had genetic testing. The test included sequencing of 10 genes associated with aneurysms and dissections and related conditions: ACTA2, CBS, COL3A1, FBN1, FBN2, MYH11, SLC2A10, SMAD3, TGFBR1 and TGFBR2. Results reported on February 21, 2013 show that a variant was found: p.Arg149Cys (c.445C>T) in the ACTA2 gene The lab classifies this variant as pathogenic. Given significant case and segregation data we consider this variant very likely disease causing and we feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). The variant has been seen in at least seven unrelated cases of hereditary thoracic aortic aneurysm and dissection (including this patient's family). There is strong case and segregation data. Guo, et al, 2008 (PMC: 2680995) reported this variant in four pedigrees of patients with aneurysm/dissection, coronary artery disease and livedo reticularis. This is the most common variant in their cohort of patients with ACTA2 variants, 45 out of 134 individuals with ACTA2 variants (33%). Of the 45 individuals from their cohort, 24 had TAAD and 12 had early onset coronary artery disease. Morisaki, et al, 2009 (PMID: 19639654) reported this variant in a proband who had a positive family history of aortic dissection and iris folliculi. She had been an amateur tennis player in her teens. She had an uneventful delivery of a healthy child 4 years prior to referral. At age 31 Y she experienced an acute Stanford type B dissection during spontaneous vaginal delivery of her second child at 40 weeks. She was treated conservatively with antihypertensive therapy and three weeks later she had aggravation of the dissection and underwent and endovascular repair with a tube stent graft. The patient had livedo reticularis on both legs and iris folliculi bilaterally. Her brother had a Stanford type A aortic dissection at 28 Y and iris folliculi but no livedo reticularis. Disabella, et al, 2011 (PMID: 21212136) reported this variant in a family with three affected individuals. One, a 62 Y female with a pre-op AR of 4.8 cm underwent a Tirone-David replacement after having a type A dissection and borderline hypertension. 38 Y female had a pre-op AR of 4.5 cm and A type a dissection during pregnancy at 33 Y and second type b dissection at 35 Y. She had coronary calcification. A 36 Y M had an aortic root of 3.8 cm (z-score: 4.27), a 28 Y male had an aortic root of 4.1 cm (z-score of 4.49 cm). A 7 Y male had an aortic root of 2.04 (z-score: 1.42). Ambry Genetics reports this variant in one of their patients with TAAD. They did not provide phenotypic details. The variant occurs within the hydrophobic cleft between subdomains 1 and 3 and the Cys substitution is expected to impede the actin-ABP interaction as well as actin-actin contacts. of the protein, as does R118 variants which also predispose to early onset CAD. In silico analysis with PolyPhen-2 predicts the variant to be possibly damaging (HumVar: 0.761). The Arg at codon 149 is conserved across species, as are neighboring amino acids, and much of the ACTA2 gene. Another variant has been reported in association with disease at this codon, p.R149L which had multiple affected individuals with aortic disease, premature CAD and premature stroke. There are seven individuals with missense variation at codon 149 listed in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >125,000 unrelated individuals of African, Asian, European, Latino, and Ashkenazi descent. Two individuals have p.R149C and five individuals have p.R149H. -
Pathogenic, criteria provided, single submitterclinical testingGeneDxDec 06, 2024Published functional studies in mice demonstrate a damaging effect through decreased force generation of aortic rings, and increased aortic wall thickness (PMID: 34600884); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 31589614, 36938085, 36053285, 34498425, 29907982, 19639654, 19409525, 19778989, 21212136, 24243736, 25644172, 24020716, 29055370, 31911781, 32154576, 17994018, 34600884) -
Likely pathogenic, no assertion criteria providedclinical testingClinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center-- -
Pathogenic, no assertion criteria providedclinical testingGenome Diagnostics Laboratory, Amsterdam University Medical Center-- -
Familial thoracic aortic aneurysm and aortic dissection Pathogenic:3
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsJul 02, 2024The p.R149C pathogenic mutation (also known as c.445C>T), located in coding exon 4 of the ACTA2 gene, results from a C to T substitution at nucleotide position 445. The arginine at codon 149 is replaced by cysteine, an amino acid with highly dissimilar properties. This missense alteration is located in a region that has a low rate of benign missense variation (Lek M et al. Nature. 2016 Aug 18;536(7616):285-91; DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources. Firth H.V. et al. 2009. Am.J.Hum.Genet. 84, 524-533 (DOI: dx.doi.org/10/1016/j.ajhg.2009.03.010)). This variant has been detected in individuals with features consistent with thoracic aortic aneurysm and dissection (TAAD) or other ACTA2-related vascular phenotypes, and has been reported to segregate with disease features in families (Guo DC et al. Nat Genet. 2007;39(12):1488-1493; Guo DC et al. Am J Hum Genet. 2009;84(5):617-627; Morisaki H et al. Hum Mutat. 2009;30(10):4106-1411). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this variant is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitterclinical testingCenter for Human Genetics, Inc, Center for Human Genetics, IncNov 19, 2012- -
Pathogenic, criteria provided, single submitterclinical testingAll of Us Research Program, National Institutes of HealthNov 07, 2023The c.445C>T (p.Arg149Cys) variant of the ACTA2 gene has been observed in individuals with thoracic aortic aneurysms and dissections, premature coronary artery disease, premature stroke, and livedo reticularis (PMID: 17994018, 19409525, 21212136, 21248741, 24020716, 25644172). It has also been observed to segregate with disease in related individuals (PMID: 17994018, 19409525, 21212136). This variant is rare in the general population according to gnomAD (1/278732). Computational evidence supports a deleterious effect on the gene or gene product. Therefore, the c.445C>T (p.Arg149Cys) variant of the ACTA2 gene is classified as pathogenic. -
Aortic aneurysm, familial thoracic 6 Pathogenic:2
Pathogenic, no assertion criteria providedliterature onlyOMIMMay 01, 2009- -
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpDec 22, 2024This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 149 of the ACTA2 protein (p.Arg149Cys). This variant is present in population databases (rs121434526, gnomAD 0.0008%). This missense change has been observed in individuals with thoracic aortic aneurysms and dissections (PMID: 19409525, 21212136, 21248741, 24020716, 25644172). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 18276). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt ACTA2 protein function with a negative predictive value of 80%. For these reasons, this variant has been classified as Pathogenic. -
Aortic aneurysm, familial thoracic 2 Pathogenic:1
Pathogenic, no assertion criteria providedclinical testingClinical Molecular Genetics Laboratory, Johns Hopkins All Children's HospitalMar 28, 2016- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.59
D
BayesDel_noAF
Pathogenic
0.60
CADD
Pathogenic
33
DANN
Uncertain
1.0
DEOGEN2
Pathogenic
0.85
D;D;D
Eigen
Pathogenic
1.0
Eigen_PC
Pathogenic
0.94
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.89
D;.;D
M_CAP
Pathogenic
0.51
D
MetaRNN
Pathogenic
0.98
D;D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Pathogenic
3.6
H;.;.
PrimateAI
Pathogenic
0.92
D
PROVEAN
Pathogenic
-6.3
D;D;D
REVEL
Pathogenic
0.98
Sift4G
Uncertain
0.0090
D;.;.
Polyphen
1.0
D;.;.
Vest4
0.97
MutPred
0.89
Loss of methylation at R149 (P = 0.0106);Loss of methylation at R149 (P = 0.0106);Loss of methylation at R149 (P = 0.0106);
MVP
0.99
ClinPred
1.0
D
GERP RS
5.5
Varity_R
0.88
gMVP
0.99

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs121434526; hg19: chr10-90701551; API