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Variant: NM_000138.5(FBN1):c.1481G>C (p.Cys494Ser)

CA392342805

502478 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 0fd815a5-f810-4595-8659-2d7a98a4c3f9
Approved on: 2023-11-16
Published on: 2023-11-16

HGVS expressions

NM_000138.5:c.1481G>C
NM_000138.5(FBN1):c.1481G>C (p.Cys494Ser)
NC_000015.10:g.48513656C>G
CM000677.2:g.48513656C>G
NC_000015.9:g.48805853C>G
CM000677.1:g.48805853C>G
NC_000015.8:g.46593145C>G
NG_008805.2:g.137133G>C
ENST00000684448.1:n.155G>C
ENST00000316623.10:c.1481G>C
ENST00000316623.9:c.1481G>C
ENST00000537463.6:c.636+24055G>C
NM_000138.4:c.1481G>C
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PM1_Strong PS4_Supporting PP3 PP2
Not Met criteria codes 21
BS2 BS4 BS3 BS1 BP2 BP3 BP4 BP1 BP7 BP5 PS2 PS3 PS1 BA1 PP4 PP1 PM3 PM4 PM5 PM6 PVS1

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
NM_000138.5(FBN1):c.1481G>C (p.Cys494Ser) NM_00138 c.1481G>C is a missense variant in FBN1 predicted to cause a substitution of a cysteine by serine at amino acid 494 (p.Cys494Ser). This variant was found in two probands, one with isolated thoracic aortic aneurysm and dissection (TAAD) and one with TAAD and systemic features of Marfan syndrome (PS4_supporting; PMID: 32209317; UZG internal data). This variant has been reported twice in ClinVar as likely pathogenic and once as of uncertain significance (Variation ID: 502478). This variant is not present in gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/). This variant affects a cysteine residue in a calcium binding EGF domain; cysteine residues are believed to be involved in the formation of disulfide bridges which are essential for the protein structure (PM1_strong). Other variants affecting this codon have been reported in association with Marfan syndrome (p.Cys494Tyr, p.Cys494Trp, p.Cys494Phe). Computational prediction tools and conservation analysis strongly support 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 likely pathogenic for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: PM1_strong, PS4_supporting, PP2, PP3, PM2_supporting.
Met criteria codes
PM2_Supporting
absent from gnomAD
PM1_Strong
Cysteine in cbEGF3
PS4_Supporting
2 probands worth 1.0 PS4 point
PP3
REVEL = 0.991
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
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
BP2
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
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
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
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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
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
PP1
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
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
.Cys494Tyr and p.Cys494Trp, p.Cys494Phe are LP/P; PM1_strong is applied so PM5 is n/a
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
Curation History
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