The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC related information was provided by the message!
  • No CSPEC computed assertion could be determined for this classification!

  • No Criteria Specification was provided in the publication event for the variant classifaction.
  • The Criteria Specification shown below is a best-estimate based on the VCEP, gene, disease, and publication date.

Variant: NM_000138.5(FBN1):c.1468G>T (p.Asp490Tyr)

CA392343534

549019 (ClinVar)

Gene: FBN1 (HGNC:2200)
Condition: Marfan syndrome (MONDO:0007947)
Inheritance Mode: Autosomal dominant inheritance
UUID: c2666e7c-694f-4748-8c27-3fba06e4f2f6
Approved on: 2024-05-23
Published on: 2024-10-31

HGVS expressions

NM_000138.5(FBN1):c.1468G>T (p.Asp490Tyr)
NM_000138.5:c.1468G>T
NC_000015.10:g.48515387C>A
CM000677.2:g.48515387C>A
NC_000015.9:g.48807584C>A
CM000677.1:g.48807584C>A
NC_000015.8:g.46594876C>A
NG_008805.2:g.135402G>T
ENST00000559133.6:c.1468G>T
ENST00000674301.2:c.1468G>T
ENST00000684448.1:n.142G>T
ENST00000316623.10:c.1468G>T
ENST00000316623.9:c.1468G>T
ENST00000537463.6:c.636+22324G>T
NM_000138.4:c.1468G>T
More

Likely Pathogenic

Met criteria codes 7
PM2_Supporting PS4_Moderate PP3 PP2 PP4 PM5 PM1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_00138 c.1468G>T is a missense variant in FBN1 predicted to cause a substitution of a aspartic acid by tyrosine at amino acid 490 (p.Asp490Tyr). This variant impacts an aspartic acid within a calcium-binding (cb) (D/N)-X-(D/N)-(E/Q)-Xm-(D/N)-Xn-(Y/F) consensus sequence of a cbEGF-like domain (PM1). This variant was found in a proband with a clinical diagnosis of Marfan syndrome (MFS) (PMID 35058154, internal lab data, PP4). This variant has been reported three times in ClinVar: twice as pathogenic and once as uncertain significance (Variation ID: 549019). This variant has also been identified in at least 2 individuals with a clinical diagnosis of MFS as well as in an individual with clinical features of MFS (PMID 11826022, 20886638, Invitae ClinVar entry; PS4_Mod). A different missense variant at this position, c.1468G>C (p.Asp490His), has previously been previously established as (likely) pathogenic and has been found in at least 3 individuals with clinical features of MFS and was found to segregate with disease (PMID 25652356, internal data; PM5), Computational prediction tools and conservation analysis suggest that this variant may impact the protein (REVEL: 0.965, PP3). This variant is located in the last nucleotide of the exon. In silico prediction programs predict that this variant may disrupt RNA splicing (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, PM5, PS4_Moderate, PM2_Sup, PP2, PP3, PP4.
Met criteria codes
PM2_Supporting
Absent in gnomAD
PS4_Moderate
2.5 points
PP3
REVEL score: 0.965; Predicted to weaken/ disrupt canonical donor site: MaxENT: -59.5%, NNSplice: 0.98=> --, GeneSplicer: -67.1%
PP2
Missense variant
PP4
Internal lab data- Lorsartan proband- Met revised Ghent criteria
PM5
c.1468G>C (p.Asp490His)- at least LP: Absent in gnomAD, REVEL: 0.976, Splice: weaken donor site (MaxEnt: -20.6%, NNSPLICE: -40.8%, GeneSplicer: -45.7%) Internal UZG- 2 probands with MFS, classified as LP, applying PP4 and +PP1
PM1
Asp in (D/N)-X-(D/N)-(E/Q)-Xm-(D/N)-Xn-(Y/F) cb consensus sequence
Curation History
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