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Variant: NM_000138.5(FBN1):c.1850G>A (p.Cys617Tyr)

CA392339186

495563 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 6728ee68-bbe8-4097-a92d-9ce209abb025
Approved on: 2023-11-16
Published on: 2023-11-16

HGVS expressions

NM_000138.5:c.1850G>A
NM_000138.5(FBN1):c.1850G>A (p.Cys617Tyr)
NC_000015.10:g.48505135C>T
CM000677.2:g.48505135C>T
NC_000015.9:g.48797332C>T
CM000677.1:g.48797332C>T
NC_000015.8:g.46584624C>T
NG_008805.2:g.145654G>A
ENST00000684448.1:n.524G>A
ENST00000316623.10:c.1850G>A
ENST00000316623.9:c.1850G>A
ENST00000537463.6:c.637-30485G>A
NM_000138.4:c.1850G>A
More

Pathogenic

Met criteria codes 7
PM1_Strong PS4_Moderate PS2_Supporting PM2_Supporting PP3 PP2 PP4
Not Met criteria codes 3
BP4 PS1 PM5

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_00138 c.1850G>A is a missense variant in FBN1 predicted to cause a substitution of a cysteine by tyrosine at amino acid 617 (p.Cys617Tyr). This variant was found in a proband with ectopia lentis, thoracic aortic aneurysm and dissection, and skeletal features (PP4; Bichat internal data). It has also been reported in the literature in two probands, one meeting revised Ghent criteria for Marfan syndrome and one with EL and a systemic score of 7 (PS4_moderate; PMIDs: 27906200, 33483584). This variant was found to be de novo with confirmation of maternity and paternity in an individual with Marfan syndrome, without specific phenotypic features available (PS2_supporting; deCODE genetics internal data, ClinVar Variation ID: 495563). It 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). Several other variants affecting this codon have been reported in association with Marfan syndrome (p.Cys617Arg, p.Cys617Gly, p.Cys617Ser). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (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: PM1_strong, PS4_moderate, PM2_supporting, PS2_supporting, PP2, PP3, PP4.
Met criteria codes
PM1_Strong
Cysteine in cbEGF6
PS4_Moderate
2 probands worth 2.0 PS4 points
PS2_Supporting
De novo with confirmed maternity and paternity in an individual reportedly with MFS but no clinical details provided
PM2_Supporting
Absent from gnomAD
PP3
REVEL = 0.825
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
1 internal proband meeting revised Ghent criteria (Bichat)
Not Met criteria codes
BP4
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
PM5
p.Cys617Arg, p.Cys617Gly, p.Cys617Ser all LP/P per FBN1 VCEP specifications; PM1_strong applied so PM5 n/a
Curation History
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