Reassessment of FBN1 variants of uncertain significance using updated ClinGen guidance for PP1/BS4 and PP4 criteria

Abstract

Marfan syndrome (MFS) is a genetic disorder caused by an FBN1 variant and is diagnosed based on the revised Ghent criteria, which incorporate clinical manifestations and genetic testing. Up-to-date FBN1 variant interpretation is crucial for proper diagnosis and management of MFS; however, some FBN1 variants of uncertain significance (VUSs) remain inconclusive despite applying Clinical Genome Resource (ClinGen) FBN1-specific guideline. Recently, the ClinGen guidance for PP1/BS4 co-segregation and PP4 phenotype specificity criteria (new PP1/PP4 criteria) were released. Here, we performed reassessment of FBN1 VUSs using these new PP1/PP4 criteria. FBN1 VUSs collected from December 2015 to April 2024 were reassessed according to the ClinGen FBN1-specific guideline and new PP1/PP4 criteria. Medical records and previous studies were reviewed to evaluate the phenotype-specificity of evidence based on the revised Ghent criteria. Collectively, 927 patients with suspected MFS underwent FBN1 sequencing and 72 VUSs were detected. When applying the FBN1-specific guideline only, of 72 VUSs, 29 (40.3%) were reclassified as pathogenic variants (PVs) or likely PVs (LPVs). When additionally applying the new PP1/PP4 criteria, 16 (37.2%) of the remaining 43 VUSs were reclassified as LPVs. After reassessing FBN1 VUSs according to the new PP1/PP4 criteria, the rate of reclassification from VUS to PV/LPV significantly increased from 40.3% to 62.5%. The new PP1/PP4 criteria provide sufficient evidence for evaluating the pathogenicity of FBN1 variants detected in MFS patients fulfilling the revised Ghent criteria and will be helpful in clinical analysis.

Fig. 1. Schematic flow showing the selection of VUSs and the results of variant reassessment in this study.

*The reassessed VUS category included 15 VUSs (from 15 cases) and 12 LBVs (from 18 cases) when the points-based system was applied. CNV copy number variation, LBV likely benign variant, LPV likely pathogenic variant, MFS Marfan syndrome, PV pathogenic variant, VUS variant of uncertain significance.

Fig. 2. Pedigree of a family with Marfan syndrome and the FBN1 c.47T>C p.(Leu16Pro) variant.

The results of individuals who underwent genetic testing for FBN1 are indicated using either “+” (variant detected) or “−” (variant not detected).

Fig. 3. Reclassification of VUS subclasses according to ClinGen FBN1-specific guideline with new PP1/PP4 criteria.

LBV likely benign variant, LPV likely pathogenic variant, PV pathogenic variant, VUS variant of uncertain significance, VUS-H variant of uncertain significance-high subclass, VUS-L variant of uncertain significance-low subclass, VUS-M variant of uncertain significance-mid subclass, VUS-U variant of uncertain significance-unsubclassified.