ClinVar

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Loeys-Dietz syndrome 3 (MIM#613795). Dominant negative is a suggested mechanism of disease in this gene for missense variants in the MH2 domain (PMID: 30661052). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity. Clinical features of Loeys-Dietz syndrome associated with SMAD3 are variable, and the penetrance of aortic events generally increases with age (PMIDs: 20301312, 30661052). (I) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. RT-PCR and Sanger sequencing analysis of an aortic tissue sample from a proband with this variant demonstrated exon 6 skipping. This exon skipping was expected to result in an in-frame deletion and cause protein misfolding (PMID: 32597575). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0703 - Other canonical splice site variants comparable to the one identified in this case have moderate previous evidence for pathogenicity. c.871+1G>T and c.871+2T>C have been reported as likely pathogenic and pathogenic, respectively, by clinical testing laboratories (ClinVar). (SP) 0802 - This variant has moderate previous evidence of pathogenicity in unrelated individuals. It has been reported in two apparently unrelated Cypriot families with nonsyndromic familial thoracic aortic aneurysm and dissection, including two family members with osteoarthritis and skeletal signs but without aortic dilatation or aneurysm reported (PMID: 32597575). It has also been reported in an individual with connective tissue disease findings whose brother also has this variant and required surgery for splenic aneurysm (PMID: 32897753). In addition, this variant has been reported as likely pathogenic by a clinical testing laboratory (ClinVar). A CNV analysis of targeted NGS (exome) data has detected a deletion of exon 6 in an individual with thoracic aortic aneurysm; however, the exact deletion breakpoints are not available (PMIDs: 29907982, 35031499). (SP) 0901 - This variant has strong evidence for segregation with disease. In one of the families with nonsyndromic familial thoracic aortic aneurysm and dissection published in the literature, this variant segregated with disease in a total of eight family members (PMID: 32597575). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign