The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000138.5(FBN1):c.1073G>A (p.Cys358Tyr)

CA392347578

549001 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: d8789da1-0fca-41c7-b3af-75a3d4f73d73
Approved on: 2023-11-16
Published on: 2023-11-16

HGVS expressions

NM_000138.5:c.1073G>A
NM_000138.5(FBN1):c.1073G>A (p.Cys358Tyr)
NC_000015.10:g.48520733C>T
CM000677.2:g.48520733C>T
NC_000015.9:g.48812930C>T
CM000677.1:g.48812930C>T
NC_000015.8:g.46600222C>T
NG_008805.2:g.130056G>A
ENST00000316623.10:c.1073G>A
ENST00000316623.9:c.1073G>A
ENST00000537463.6:c.636+16978G>A
NM_000138.4:c.1073G>A

Likely Pathogenic

Met criteria codes 7
PM5 PM1 PM2 PP3 PP2 PP4 PS4_Supporting
Not Met criteria codes 19
PVS1 BS2 BS3 BS4 BS1 BP3 BP2 BP4 BP1 BP5 BP7 PM4 PM3 PS3 PS2 PS1 PM6 BA1 PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
NM_00138 c.1073G>A is a missense variant in FBN1 predicted to cause a substitution of a cysteine by tyrosine at amino acid 358(p.Cys358Tyr). This variant has been found in two probands, one with the clinical diagnosis of Marfan syndrome but without a specified phenotype and one with ectopia lentis, thoracic aortic aneurysm and dissection, and a systemic score of 9 (PP4, PS4_supporting; PMID: 35058154; UZG internal data). This variant has been reported two times in ClinVar, once as likely pathogenic and once as of uncertain significance (Variation ID: 549001). This variant is not present in gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/). This variant affects a cysteine residue in a TGFβ binding-protein-like (TB) domain; cysteine residues are believed to be involved in the formation of disulfide bridges which are essential for the protein structure (PM1). Other variants altering this codon are pathogenic or likely pathogenic (p.Cys358Trp, p.Cys358Arg), supporting the functional importance of this amino acid position (PM5). Computational prediction tools and conservation analysis suggest that this variant may impact protein 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, PM5, PS4_supporting, PM2_supporting, PP2, PP3, PP4.
Met criteria codes
PM5
p.Cys358Trp, p.Cys358Arg are LP/P with FBN1 specifications
PM1
Cysteine in TB1 domain
PM2
absent from gnomAD
PP3
REVEL = 0.939
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
proband meets revised Ghent criteria
PS4_Supporting
1 proband worth 1.0 PS4 point
Not Met criteria codes
PVS1
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
BS3
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
BS1
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
BP1
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
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
PS3
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
PS1
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
BA1
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
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