ClinVar Genomic variation as it relates to human health

This sequence change falls in intron 12 of the FBN1 gene. It does not directly change the encoded amino acid sequence of the FBN1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with Marfan syndrome (PMID: 10464652, 17627385, 17657824, 25101912, 25907466). In at least one individual the variant was observed to be de novo. This variant is also known as IVS11+5G>A. ClinVar contains an entry for this variant (Variation ID: 42284). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in creation of a new donor splice site and introduces a premature termination codon (PMID: 21907952). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.

The c.1468+5G>A variant in FBN1 has been reported in 9 individuals with clinical features of Marfan syndrome (Aalberts 2014, Baetens 2011, Comeglio 2007, Liu 19 97-1998, LMM data). It has not been identified in large population studies. In a ddition, this variant has segregated with disease in 5 affected individuals from one family tested by our laboratory. The c.1468+5G>A variant is located in the 5' splice region and RNA studies have revealed this splice site variant leads to abnormal splicing and exon skipping in FBN1 (Aalberts 2014, Ogawa 2011, Liu 199 7-1998), resulting in an abnormal or absent protein. Heterozygous loss of functi on of the FBN1 gene is an established disease mechanism in Marfan syndrome. In summary, this variant meets criteria to be classified as pathogenic for autosoma l dominant Marfan syndrome based on its recurrence in multiple affected individu als, segregation in families, extremely low allele frequency in the general popu lation, and functional impact on splicing.

Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Published functional studies demonstrate that c.1468+5 G>A destroys the natural splice donor site and results in abnormal splicing (Ogawa et al., 2011); This variant is associated with the following publications: (PMID: 29543232, 31730815, 25525159, 17657824, 19949477, 19339519, 25907466, 24161884, 21542060, 17627385, 11702223, 27085269, 11933199, 33726816, 10464652, 25101912, 21907952, 34498425)

PM2, PS1, PP4

Variant summary: FBN1 c.1468+5G>A alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict abolishing and two predict severe weakening of the 5' splice site. RNA studies found that a cryptic donor site in exon 11 became activated, resulting in loss of critical region (Ogawa_2011). The variant was absent in 251358 control chromosomes. c.1468+5G>A has been reported in the literature in multiple individuals affected with Marfan Syndrome (Example: Baetens_2011, Liu_1997, Hogwarth_2007, Ogawa_2011, Comeglio_2007 etc.). These data indicate that the variant is very likely to be associated with disease. Eleven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic (n=9) and likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as pathogenic.

The c.1468+5G>A intronic pathogenic mutation (also known as c.IVS11+5G>A) results from a G to A substitution 5 nucleotides after coding exon 11 in the FBN1 gene. This mutation has been detected in individuals with classical Marfan syndrome and in individuals with Marfan-related features, including isolated ectopia lentis, thoracic aortic aneurysm and dissections, and/or skeletal findings (Liu WO et al. Genet Test. 1997-1998;1:237-42; Comeglio P et al. Hum Mutat. 2007;28:928; Aalberts JJ et al. Gene, 2014 Jan;534:40-3; Weerakkody R et al. Genet Med, 2018 11;20:1414-1422; Mannucci L et al. Clin Chim Acta, 2020 Feb;501:154-164). RNA studies found that a cryptic splice donor site within exon 11 can become activated in the presence of this alteration, which leads to loss of a critical region of the protein (Ogawa N et al. Am J Cardiol. 2011;108:1801-7). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration may weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.