rs863223737
Variant summary
Our verdict is Pathogenic. Variant got 25 ACMG points: 25P and 0B. PS1_Very_StrongPM1PM2PP2PP3_StrongPP5_Very_Strong
The NM_005902.4(SMAD3):c.733G>A(p.Gly245Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G245E) has been classified as Uncertain significance.
Frequency
Consequence
NM_005902.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 25 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMAD3 | NM_005902.4 | c.733G>A | p.Gly245Arg | missense_variant | 6/9 | ENST00000327367.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMAD3 | ENST00000327367.9 | c.733G>A | p.Gly245Arg | missense_variant | 6/9 | 1 | NM_005902.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461778Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727190
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2022 | The p.G245R variant (also known as c.733G>A), located in coding exon 6 of the SMAD3 gene, results from a G to A substitution at nucleotide position 733. The glycine at codon 245 is replaced by arginine, an amino acid with dissimilar properties. This alteration has been detected in multiple individuals with SMAD3-related phenotypes and has been reported to segregate with disease in a small number of affected relatives (Hostetler EM et al. J. Med. Genet., 2019 Apr;56:252-260; Ambry internal data; GeneDx pers. comm.; Invitae pers. comm.). Internal structural analysis indicates that this variant causes a significant decrease in SMAD3 structural stability (Qin BY et al. Genes Dev. 2002 Aug;16(15):1950-63; Ambry internal data). A different alteration located at the same position, resulting in the same protein change, c.733G>C (p.G245R), has been reported in an individual with aortic root dilation (Arroyave J et al. Cardiol Young, 2018;28:765-767). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). 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 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 majority of available evidence to date, this variant is likely to be pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 18, 2023 | This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 245 of the SMAD3 protein (p.Gly245Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of SMAD3-related conditions (PMID: 24804794, 29444731; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 213762). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is expected to disrupt SMAD3 function with a positive predictive value of 95%. This variant disrupts the p.Gly245 amino acid residue in SMAD3. Other variant(s) that disrupt this residue have been observed in individuals with SMAD3-related conditions (Invitae), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. - |
not provided Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Aug 21, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); Reported in association with Loeys-Dietz syndrome (LDS) or thoracic aortic aneurysm and dissection (TAAD) in published literature and in patients referred for genetic testing at GeneDx (Ripoll-Vera et al., 2021; Hostetler et al., 2019; Aubart et al., 2014); 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: 26221609, 28185953, 35830949, 30661052, 29444731, 32917565, 24804794) - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Apr 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at