ClinVar Genomic variation as it relates to human health

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Dominant negative and loss of function are known mechanisms of disease in this gene and are associated with FBN1-related disease. Variants predicted to result in nonsense mediated decay cause loss of function effects and are more commonly associated with severe Marfan syndrome (MIM#154700). Missense variants with both dominant negative and loss of function effects on protein function, are also associated with causing Marfan syndrome and ectopia lentis (MIM#129600) (OMIM, PMID: 29357934). (I) 0107 - This gene is predominantly associated with autosomal dominant disease; however some individuals have been reported with an autosomal recessive form of Marfan syndrome (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity. The genotype-phenotype correlations for this gene are unclear, with the same variant reported in patients with a range of phenotypes (OMIM). (I) 0210 - Splice site variant proven to affect splicing of the transcript with a known effect on protein sequence. RT-PCR analysis of cultured fibroblasts from an affected individual showed that the variant causes in-frame skipping of exon 47 and a small amount of abnormally spliced transcripts utilized a cryptic splice donor or a cryptic splice acceptor (PMID: 7611299). (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v3) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0704 - Another splice variant comparable to the one identified in this case has limited previous evidence for pathogenicity. The c.5788+5G>T variant has been observed in an individual with Marfan syndrome and classified as likely pathogenic (VCGS laboratory). This variant has also been reported twice as a VUS in ClinVar. (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in multiple individuals with Marfan syndrome (ClinVar, PMID: 7611299, PMID: 24161884). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

The c.5788+5G>A intronic pathogenic mutation results from a G to A substitution 5 nucleotides downstream of coding exon 46 in the FBN1 gene. This mutation (also referred to as IVS 46+5G>A) was first described in three unrelated patients (two of whom were reported as de novo) with classic Marfan syndrome (MFS), and was shown to cause exon 46 skipping by mRNA analysis using cultured skin fibroblasts from one patient (Nijbroek G et al, Am. J. Hum. Genet. 1995 Jul; 57(1):8-21). This mutation has also been described in multiple additional patients with MFS with additional reported de novo occurrences (Loeys B et al, Arch. Intern. Med. 2001 Nov; 161(20):2447-54; Rommel K et al, Hum. Mutat. 2002 Nov; 20(5):406-7; Arbustini E et al, Hum. Mutat. 2005 Nov; 26(5):494; Sakai H et al, Am. J. Med. Genet. A 2006 Aug; 140(16):1719-25; Rand-Hendriksen S et al, Am. J. Med. Genet. A 2007 Sep; 143A(17):1968-77; S&ouml;ylen B et al, Clin. Genet. 2009 Mar; 75(3):265-70; Baetens M et al, Hum. Mutat. 2011 Sep; 32(9):1053-62; Li J et al. Sci China Life Sci. 2019;62(12):1630-1637). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

The 5788+5G>A variant has been previously reported in >15 individuals with a cli nical diagnosis or features of Marfan syndrome, and was reported to have occurre d de novo in >10 of these individuals (Nijbroek 1995, Yuan 1999, Loeys 2001, Com eglio 2007, Rommel 2002, Biggin 2004, Arbustini 2005, Sakai 2006, Rand-Hendrikse n 2007, Stheneur 2009, Soylen 2009, Baetens 2011, Aalberts 2014, LMM unpublished data). This variant was absent from large population studies. This variant occu rs in the highly conserved 5' splicing consensus sequence. Nijbroek et al. (1995 ) observed skipping of exon 46 in fibroblasts from an affected individual with t his variant, which is predicted to result in an abnormal protein product. In sum mary, this variant meets our criteria to be classified as pathogenic (http://pcp gm.partners.org/LMM).

ACMG categories: PS2,PM2,PP3,PP5

The c.5788+5G>A intronic variant in the FBN1 gene has been detected in heterozygous status including de novo occurrences in multiple unrelated individuals (>15) with classic Marfan syndrome features (PMID: 7611299, 11700157, 12402346, 8894692, 21542060, 16222657). Functional studies using RT-PCR performed on patient derived fibroblasts harboring this variant demonstrated in-frame skipping of the preceding exon 46 (117bp), resulting in aberrant protein product with deletion of 39 amino acids from the calcium-binding EGF-like domain of the fibrillin-1 protein (PMID: 7611299, 8894692). This variant is absent in the general population database gnomAD and is interpreted as pathogenic by several submitters in ClinVar database (ClinVar ID: 42394). Therefore, the c.5788+5G>A variant in FBN1 is classified as pathogenic.

PM2, PS1, PP1, PP4 and PM2, PS1, PP4

Variant summary: FBN1 c.5788+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: Four predict the variant abolishes the canonical 5' splicing donor site. One predicts the variant weakens the canonical 5' splicing donor site. Two publications report experimental evidence suggesting that this variant causes skipping of exon 46 (Liu_1996; Nijbroek_1995). The variant was absent in 251390 control chromosomes. c.5788+5G>A has been reported in the literature in multiple individuals affected with Marfan Syndrome (example, Baetens_2011, Liu_1996, Nijbroek_1995, Rand-Hendriksen_2007, Stheneur_2009). 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 and all classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Published functional studies showed RT-PCR performed on fibroblasts from individuals harboring this variant revealed c.5788+5 G>A leads to in-frame skipping of the preceding exon (Nijbroek et al., 1995; Lui et al., 1996; Wai et al., 2020).; Reported in ClinVar as pathogenic or likely pathogenic (ClinVar Variant ID# 42394; ClinVar); Intronic +5 splice site variant in a gene for which loss of function is a known mechanism of disease, and splice predictors support a deleterious effect; This variant is associated with the following publications: (PMID: 19293843, 11700157, 21542060, 14695540, 24161884, 8894692, 34818515, 34550612, 34498425, 7611299, 25525159, 17657824, 10533071, 12402346, 16835936, 17663468, 19159394, 33174221, 33083483, 31098894, 31730815, 16220557, 32123317, 16222657, 26582918)

This sequence change falls in intron 47 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 likely results in a shortened 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: 7611299, 11700157, 12402346, 14695540, 17657824, 17663468). In at least one individual the variant was observed to be de novo. This variant is also known as IVS46+5G>A. ClinVar contains an entry for this variant (Variation ID: 42394). 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 skipping of exon 46, but is expected to preserve the integrity of the reading-frame (PMID: 7611299). For these reasons, this variant has been classified as Pathogenic.

The c.5788+5G>A variant occurred de novo in two siblings (shared de novo) with Marfan syndrome, maternity and paternity confirmed, parental mosaicism assumed. Applied ACMG criteria: PS2, PM2, PP2, PP4, PP5_strong

The FBN1 c.5788+5G>A variant is predicted to interfere with splicing. This variant has been reported in many affected individuals in the FBN1 mutation database (http://www.umd.be/FBN1/) and is documented as pathogenic for Marfan syndrome (Liu et al. 1996. PubMed ID: 8894692; Nijbroek et al. 1995. PubMed ID: 7611299; Yuan et al. 1999. PubMed ID: 10533071; Table S1, Li et al. 2019. PubMed ID: 31098894; Mannucci et al. 2020. PubMed ID: 31730815). The c.5788+5G>A has been shown to result in exon skipping in patient-derived skin fibroblasts (Nijbroek et al. 1995. PubMed ID: 7611299; Liu et al. 1996. PubMed ID: 8894692). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic.