15-48485436-C-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP2PP3_StrongPP5
The NM_000138.5(FBN1):c.3650G>A(p.Gly1217Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 11/18 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G1217G) has been classified as Likely benign.
Frequency
Consequence
NM_000138.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBN1 | NM_000138.5 | c.3650G>A | p.Gly1217Asp | missense_variant | 30/66 | ENST00000316623.10 | |
FBN1 | NM_001406716.1 | c.3650G>A | p.Gly1217Asp | missense_variant | 29/65 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBN1 | ENST00000316623.10 | c.3650G>A | p.Gly1217Asp | missense_variant | 30/66 | 1 | NM_000138.5 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Marfan syndrome Pathogenic:1Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Center for Medical Genetics Ghent, University of Ghent | Nov 07, 2017 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Petrovsky National Research Centre of Surgery, The Federal Agency for Scientific Organizations | Aug 02, 2019 | The p.Gly1217Asp variant was found in one individual with MFS (PMID: 27112580) and is absent in large population studies (ExAC no frequency). The substitution of 1217 codon occurs in cbEGF-like domain and it participates in domain-domain packing (UMD-FBN1 Record ID: 2293). FBN1 gene is known to be less tolerant to missense variants (ExAC Z score = 5.33). ClinVar has an entry for this variant (Variation ID: 549180). Computational tools like Provean, PolyPhen2, MutationTaster show a deleterious result. Classification was based on ACMG criteria, concluding p.Gly1217Asp variant as Likely Pathogenic (PM1, PM2, PP2, PP3, PP4), although without function study we can't exclude the possibility of benign. - |
Marfan syndrome;C4707243:Familial thoracic aortic aneurysm and aortic dissection Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 18, 2020 | This sequence change replaces glycine with aspartic acid at codon 1217 of the FBN1 protein (p.Gly1217Asp). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and aspartic acid. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has been reported in an individual affected with Marfan syndrome (PMID: 27112580). This variant is not present in population databases (ExAC no frequency). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at