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Variant: NM_000138.5(FBN1):c.5885A>G (p.Tyr1962Cys)

CA392339987

570737 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 3581bb52-68a5-4ba7-baaa-558273d668f0

HGVS expressions

NM_000138.5:c.5885A>G
NM_000138.5(FBN1):c.5885A>G (p.Tyr1962Cys)
NC_000015.10:g.48445408T>C
CM000677.2:g.48445408T>C
NC_000015.9:g.48737605T>C
CM000677.1:g.48737605T>C
NC_000015.8:g.46524897T>C
NG_008805.2:g.205381A>G
ENST00000559133.6:c.5885A>G
ENST00000674301.2:c.5885A>G
ENST00000684448.1:n.4559A>G
ENST00000316623.10:c.5885A>G
ENST00000674301.1:c.884A>G
ENST00000316623.9:c.5885A>G
ENST00000537463.6:c.*1648A>G
ENST00000559133.5:c.1192A>G
ENST00000560820.1:n.5A>G
NM_000138.4:c.5885A>G

Likely Pathogenic

Met criteria codes 6
PP3 PP2 PP4 PS4_Supporting PM1 PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_00138 c.5885A>G is a missense variant in FBN1 predicted to cause a substitution of a tyrosine by cysteine at amino acid 1962 (p.Tyr1962Cys) within a calcium binding EGF-like domain of the protein (PM1). This variant was found in a proband diagnosed who met revised Ghent criteria, which is a highly specific phenotype for Marfan syndrome (MFS) (PMID 27112580, PP4). This variant has been reported four times in ClinVar: once as likely pathogenic and three times as uncertain significance (Variation ID: 570737). At least two other probands with clinical features of MFS carry the same variant (PMID 33483583, Invitae ClinVar, PS4_Sup). This variant is not present in gnomAD (PM2_sup; https://gnomad.broadinstitute.org/v2.1.1). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (REVEL: 0.972, 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, PS4_Sup, PM2_Sup, PP2, PP3, PP4
Met criteria codes
PP3
REVEL: 0.972
PP2
The constraint z-score for missense variants affecting FBN1 is 5.06
PP4
identified in an individual meeting revised Ghent criteria
PS4_Supporting
2 patients with MFS-related features
PM1
Cys-creating residue in a cbEGF-like domain
PM2_Supporting
Absent in gnomAD (v2.1.1- AC0 flag for exomes- not high quality genotypes) V4.0.0- present in 2/1111238 (0.0002%) European (non-Finnish) alleles
Approved on: 2024-02-22
Published on: 2024-02-22
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