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Variant: NM_000138.5(FBN1):c.6032G>A (p.Cys2011Tyr)

CA10587803

263898 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: e1d3d3bc-03fb-47ea-bde6-bb6187a53a24
Approved on: 2024-02-22
Published on: 2024-02-22

HGVS expressions

NM_000138.5:c.6032G>A
NM_000138.5(FBN1):c.6032G>A (p.Cys2011Tyr)
NC_000015.10:g.48444546C>T
CM000677.2:g.48444546C>T
NC_000015.9:g.48736743C>T
CM000677.1:g.48736743C>T
NC_000015.8:g.46524035C>T
NG_008805.2:g.206243G>A
ENST00000559133.6:c.6032G>A
ENST00000674301.2:c.6032G>A
ENST00000684448.1:n.4706G>A
ENST00000316623.10:c.6032G>A
ENST00000674301.1:c.1031G>A
ENST00000316623.9:c.6032G>A
ENST00000537463.6:c.*1795G>A
ENST00000559133.5:c.1339G>A
ENST00000560820.1:n.152G>A
NM_000138.4:c.6032G>A

Likely Pathogenic

Met criteria codes 4
PP3 PP2 PM1_Strong PM2_Supporting
Not Met criteria codes 2
PP4 PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_00138 c.6032G>A is a missense variant in FBN1 predicted to cause a substitution of a cysteine by tyrosine at amino acid 2011 (p.Cys2011Tyr). This variant has been reported four times in ClinVar: once as pathogenic, twice as likely pathogenic, and once as uncertain significance (Variation ID: 263898). At least two probands with clinical features of Marfan syndrome carry the same variant (internal lab data, PS4_Sup). This variant is not present in gnomAD (PM2_sup; https://gnomad.broadinstitute.org/v2.1.1). This variant affects a cysteine residue in a calcium binding EGF-like domain. Cysteine residues in these domains are believed to be involved in the formation of disulfide bridges which are essential for the protein structure (PM1_strong). Other missense variants disrupting the Cysteine at this position, (i.e. p.Cys2011Arg and p.Cys2011Ser), have been reported in individuals with features of Marfan syndrome (PMID 29907982, 31163209). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (REVEL: 0.921, PP3). The constraint z-score for missense variants affecting FBN1 is 5.06 (PP2). In summary, this variant meets criteria to be classified as likely pathogenic for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: PM1_Strong, PS4_Sup, PM2_Sup, PP2, PP3
Met criteria codes
PP3
REVEL: 0.921
PP2
The constraint z-score for missense variants affecting FBN1 is 5.06
PM1_Strong
Cys-disrupting variant in cbEGF-like domain
PM2_Supporting
Absent in gnomAD
Not Met criteria codes
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
PM1_Strong Met
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