The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000138.5(FBN1):c.7409G>T (p.Cys2470Phe)

CA392327764

1098776 (ClinVar)

Gene: FBN1 (HGNC:2200)
Condition: Marfan syndrome (MONDO:0007947)
Inheritance Mode: Autosomal dominant inheritance
UUID: dd443373-9fa6-4d1e-86c4-b882988ecab5
Approved on: 2024-08-22
Published on: 2024-08-22

HGVS expressions

NM_000138.5(FBN1):c.7409G>T (p.Cys2470Phe)
NM_000138.5:c.7409G>T
NC_000015.10:g.48425413C>A
CM000677.2:g.48425413C>A
NC_000015.9:g.48717610C>A
CM000677.1:g.48717610C>A
NC_000015.8:g.46504902C>A
NG_008805.2:g.225376G>T
ENST00000559133.6:c.*217G>T
ENST00000674301.2:c.*922G>T
ENST00000682170.1:n.1590G>T
ENST00000682767.1:n.706G>T
ENST00000316623.10:c.7409G>T
ENST00000674301.1:c.2575G>T
ENST00000316623.9:c.7409G>T
ENST00000559133.5:c.2778G>T
NM_000138.4:c.7409G>T
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PP4 PP3 PP2 PM1_Strong
Not Met criteria codes 21
PVS1 BS2 BS4 BS3 BS1 BP3 BP2 BP4 BP1 BP5 BP7 PS2 PS1 PS4 PS3 BA1 PM5 PM4 PM3 PM6 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

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Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
NM_000138.5 c.7409G>T is a missense variant in FBN1 predicted to cause a substitution of a cysteine by phenylalanine at amino acid 2470 (p.Cys2470Phe). This variant was found in a proband with thoracic aortic aneurysm (TAA) and a systemic score ≥7 which is a specific phenotype that satisfies the revised Ghent criteria for a clinical diagnosis of Marfan syndrome (MFS) (PP4; PMID: 38374194). This variant has been reported 3 times in ClinVar as pathogenic (1) likely pathogenic (1), and of uncertain significance (1) (Variation ID: 1098776 ). It has been identified in a proband who does not meet diagnostic criteria for MFS but has TAA and several systemic features of MFS (Invitae internal data). This variant is not present in gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/). This variant affects a cysteine residue in a calcium-binding EGF-like domain; cysteine residues are involved in the formation of disulfide bridges which are essential for the protein structure (PM1_strong). Computational prediction tools and conservation analysis suggest that this variant may impact the protein (PP3; REVEL = 0.989). The constraint z-score for missense variants affecting FBN1 is 8.2 (PP2; gnomAD v4.1.0). 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, PP2, PP3, PP4, PM2_supporting.
Met criteria codes
PM2_Supporting
absent from all versions of gnomAD
PP4
patient in Abolhassani et al. meets revised Ghent criteria
PP3
REVEL = 0.989, > 0.750 threshold
PP2
no benign evidence
PM1_Strong
cysteine-removing variant in cbEGF38
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
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
PM2_supporting met
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
PP3 met
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
n/a
PS4
1 proband (excluding that used for PP4) worth 0.5 PS4 points
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
PM2_supporting met
PM5
n/a because PM1_strong is met; several other P/LP variants at this position
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
PM6
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
Curation History
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