rs1553303352
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PP3_StrongPP5_Very_Strong
The NM_003238.6(TGFB2):c.958C>T(p.Arg320Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,454,378 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R320H) has been classified as Uncertain significance.
Frequency
Consequence
NM_003238.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TGFB2 | NM_003238.6 | c.958C>T | p.Arg320Cys | missense_variant | 6/7 | ENST00000366930.9 | |
TGFB2 | NM_001135599.4 | c.1042C>T | p.Arg348Cys | missense_variant | 7/8 | ||
TGFB2 | NR_138148.2 | n.2209C>T | non_coding_transcript_exon_variant | 6/7 | |||
TGFB2 | NR_138149.2 | n.2293C>T | non_coding_transcript_exon_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TGFB2 | ENST00000366930.9 | c.958C>T | p.Arg320Cys | missense_variant | 6/7 | 1 | NM_003238.6 | P1 | |
TGFB2 | ENST00000366929.4 | c.1042C>T | p.Arg348Cys | missense_variant | 7/8 | 1 | |||
TGFB2 | ENST00000479322.1 | n.442C>T | non_coding_transcript_exon_variant | 4/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1454378Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 723334
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Loeys-Dietz syndrome 4 Pathogenic:4
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Mar 03, 2023 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 320 of the TGFB2 protein (p.Arg320Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of TGFB2-related conditions (PMID: 25046559, 27782106; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 495213). 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 expected to disrupt TGFB2 protein function. For these reasons, this variant has been classified as Pathogenic. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | May 28, 2019 | The TGFB2 c.958C>T; p.Arg320Cys variant (rs1553303352), also known as p.Arg348Cys using alternative nomenclature, is reported in the literature in multiple individuals affected with aortic aneurysm or dissection (Al Maskari 2016, Gago-Diaz 2014). This variant was observed to cosegregate with disease in multiple affected individuals in at least two families, although its detection in some unaffected relatives suggests it may exhibit incomplete penetrance (Al Maskari 2016, Gago-Diaz 2014). This variant is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism, and it is reported in ClinVar (Variation ID: 495213). The arginine at codon 320 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Additionally, immunoblotting and immunofluorescence of aortic tissue from an affected individual with this variant exhibited substantially increased levels of TGFB1 and TGFB2 protein compared to unaffected controls (Al Maskari 2016). An increase in TGFB2 in affected aortic tissue may be an indirect effect of haploinsufficiency in aortic disease (Boileau 2012). Based on available information, this variant is considered to be likely pathogenic. References: Al Maskari R et al. A missense TGFB2 variant p.(Arg320Cys) causes a paradoxical and striking increase in aortic TGFB1/2 expression. Eur J Hum Genet. 2016 Jan;25(1):157-160. Boileau C et al. TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome. Nat Genet. 2012 Jul 8;44(8):916-21. Gago-Diaz M et al. Whole exome sequencing for the identification of a new mutation in TGFB2 involved in a familial case of non-syndromic aortic disease. Clin Chim Acta. 2014 Nov 1;437:88-92. - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 06, 2018 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | 3billion | - | The variant is not observed in the gnomAD v2.1.1 dataset. Protein truncation variants are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.98; 3Cnet: 0.98). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000495213 / PMID: 25046559). A different missense change at the same codon (p.Arg320His) has been reported to be associated with TGFB2 related disorder (PMID: 33418956). Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline. - |
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 23, 2022 | Reported in two unrelated individuals with non-syndromic aortic disease and Loeys-Dietz syndrome type 4 (LDS4) (also reported as p.(R348C) due to alternate nomenclature), and segregates with disease in affected family members from these two families (Gago-Diaz et al., 2014; Al Maskari et al., 2016); 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: 25046559, 27782106) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at