The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000138.5(FBN1):c.7016G>A (p.Cys2339Tyr)

CA392330332

495644 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: ecfd14b5-e2a8-4834-968a-2c45a7922949
Approved on: 2024-08-22
Published on: 2024-08-22

HGVS expressions

NM_000138.5:c.7016G>A
NM_000138.5(FBN1):c.7016G>A (p.Cys2339Tyr)
NC_000015.10:g.48427755C>T
CM000677.2:g.48427755C>T
NC_000015.9:g.48719952C>T
CM000677.1:g.48719952C>T
NC_000015.8:g.46507244C>T
NG_008805.2:g.223034G>A
ENST00000559133.6:c.7078G>A
ENST00000674301.2:c.*529G>A
ENST00000682170.1:n.1197G>A
ENST00000682767.1:n.313G>A
ENST00000316623.10:c.7016G>A
ENST00000674301.1:c.2182G>A
ENST00000316623.9:c.7016G>A
ENST00000559133.5:c.2385G>A
NM_000138.4:c.7016G>A
More

Likely Pathogenic

Met criteria codes 6
PP3 PP2 PM5 PM1 PM2_Supporting PS4_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
NM_00138 c. 7016G>A is a missense variant in FBN1 predicted to cause a substitution of cysteine by tyrosine at amino acid 2339 (p.Cys2339Tyr). This variant has been identified in one individual with clinical features of Marfan syndrome (PS4_Sup). This variant has been reported 1 time in ClinVar as Likely pathogenic and 1 time as uncertain significance (VariationID:495644).This variant is not present in gnomAD (PM2_Sup; https://gnomad.broadinstitute.org/ v4.0.0). This variant affects a cysteine residue in a TB domain. Cysteine residues are believed to be involved in the formation of disulfide bridges which are essential for the protein structure (PM1). The constraint z-score for missense variants affecting FBN1 is 8.18 (PP2; https://gnomad.broadinstitute.org/ v4.0.0). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (REVEL: 0.992, PP3). 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_Sup, PM2_Sup, PP2, PP3.
Met criteria codes
PP3
REVEL score: 0.973
PP2
No benign criteria. The constraint z-score for missense variants affecting FBN1 is 5.06.
PM5
Alternate variants : p.Cys2339Arg, p.Cys2339Gly, p.Cys2339Ser. p.Cys2339Ser: This variant is a likely pathogenic variant (PP3, PS4_Supp (https://doi.org/10.1093/ehjcr/ytac063), PP2, PM2_Supp, PM1_Moderate).
PM1
Cys disrupting residue in a TB7 like domain
PM2_Supporting
Absent in gnomAD
PS4_Supporting
One patient is reported with ocular features such as ectopia lentis, flat corneas and arachnodactyly (PMID 12203992)
Curation History
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