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Variant: NM_000138.5(FBN1):c.1556A>G (p.Tyr519Cys)

CA392342185

549024 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 70862165-bdcf-4d1f-ae67-bae146408176
Approved on: 2023-11-16
Published on: 2023-11-16

HGVS expressions

NM_000138.5:c.1556A>G
NM_000138.5(FBN1):c.1556A>G (p.Tyr519Cys)
NC_000015.10:g.48513581T>C
CM000677.2:g.48513581T>C
NC_000015.9:g.48805778T>C
CM000677.1:g.48805778T>C
NC_000015.8:g.46593070T>C
NG_008805.2:g.137208A>G
ENST00000684448.1:n.230A>G
ENST00000316623.10:c.1556A>G
ENST00000316623.9:c.1556A>G
ENST00000537463.6:c.636+24130A>G
NM_000138.4:c.1556A>G
More

Pathogenic

Met criteria codes 7
PS4 PS2_Supporting PP1 PP3 PP2 PM1 PM2_Supporting
Not Met criteria codes 17
PS3 PS1 BP3 BP2 BP4 BP5 BP7 BA1 PP4 PM4 PM3 PM5 PM6 PVS1 BS3 BS1 BS2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen FBN1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_00138 c.1556A>G, is a missense variant in FBN1 predicted to cause a substitution of a tyrosine by cysteine at amino acid 519 (p.Tyr519Cys). This variant was found in at least 7 probands with features consistent with or suggestive of Marfan syndrome including the following: one proband who met the original Ghent criteria with cardiovascular, skeletal, and skin involvement; one proband with bilateral ectopia lentis (EL) and systemic features; one proband with thoracic aortic aneurysm and dissection (TAAD); one proband with EL and systemic features; one proband with isolated EL; one proband with TAAD and systemic features; and once as de novo with confirmed maternity/paternity with bilateral EL, TAAD, and systemic features, a phenotype highly specific for Marfan syndrome (PS2_supporting, PS4; PMID: 15241795; University of Tokyo, UZG, Invitae, & Ambry internal data; ClinVar Variation ID: 5490254). The variant also segregates with features of Marfan syndrome in at least two affected family members (PP1; Invitae internal data). It is not present in gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/). This variant introduces a novel cysteine residue which may impede the normal formation of critical disulfide bridges (PM1). Computational prediction tools and conservation analysis suggest that this variant may impact the protein’s structure or function (PP3). The constraint z-score for missense variants affecting FBN1 is 5.06 (PP2). In summary, this variant meets criteria to be classified as pathogenic for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: PS4, PM1, PS2_supporting, PM2_supporting, PP1, PP2, PP3.
Met criteria codes
PS4
5 probands worth 4.5 PS4 points
PS2_Supporting
confirmed de novo (Invitae), phenotype is not considered highly specific to FBN1
PP1
at least 2 segregations with features of MFS
PP3
REVEL = 0.933
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
Cysteine-creating variant
PM2_Supporting
absent from gnomAD
Not Met criteria codes
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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