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.6446A>G (p.Tyr2149Cys)

CA016465

42402 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 4af545ca-cc58-4dda-a435-17262478443f
Approved on: 2024-08-22
Published on: 2024-08-22

HGVS expressions

NM_000138.5:c.6446A>G
NM_000138.5(FBN1):c.6446A>G (p.Tyr2149Cys)
NC_000015.10:g.48437011T>C
CM000677.2:g.48437011T>C
NC_000015.9:g.48729208T>C
CM000677.1:g.48729208T>C
NC_000015.8:g.46516500T>C
NG_008805.2:g.213778A>G
ENST00000559133.6:c.6446A>G
ENST00000674301.2:c.6446A>G
ENST00000682170.1:n.55A>G
ENST00000316623.10:c.6446A>G
ENST00000674301.1:c.1445A>G
ENST00000316623.9:c.6446A>G
ENST00000537463.6:c.*2209A>G
ENST00000559133.5:c.1753A>G
NM_000138.4:c.6446A>G
More

Pathogenic

Met criteria codes 7
PM2_Supporting PM1 PS2 PS4 PP4 PP3 PP2
Not Met criteria codes 19
PM5 PM4 PM3 PM6 BA1 BS2 PVS1 BS4 BS3 BS1 BP5 BP7 BP3 BP2 BP4 BP1 PS1 PS3 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.6446A>G is a missense variant in FBN1 predicted to cause a substitution of a tyrosine by cysteine amino acid 2149 (p.Tyr2149Cys). This variant has been identified in at least 13 individuals with features suggestive of, or consistent with, Marfan syndrome (MFS), including four patients meeting clinical diagnostic criteria for MFS, seven with thoracic aortic aneurysm or dissection (TAAD) with or without additional features of MFS, and two with unspecified clinical suspicion of MFS (PS4, PP4; Johns Hopkins, University of Texas-Houston, LMM, & Invitae internal data; PMIDs: 24793577, 27611364, 37684520, 31098894). The variant was found to be de novo in five of these patients, including three (maternity/paternity assumed) with phenotypes consistent with, but not highly specific to, FBN1, one (maternity/paternity assumed) with TAAD and borderline systemic involvement, and one (maternity/paternity confirmed) with a non-specific and genetically heterogeneous phenotype of TAAD and mitral valve prolapse (PS2; Johns Hopkins & Invitae internal data; PMIDs: 31098894, 37684520). It is absent from gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/, v2.1.1, 3.1.2, 4.0.0). This variant introduces a novel cysteine residue which may impede the normal formation of essential disulfide bridges and occurs at a conserved residue in a critical calcium-binding site within a calcium-binding EGF-like domain (PM1). Computational prediction tools and conservation analysis support that this variant is likely to impact the protein (PP3; REVEL = 0.900). The constraint z-score for missense variants affecting FBN1 is 8.18 (PP2; gnomAD v4.0.0). 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: PS2, PS4, PM1, PP2, PP3, PP4, PM2_supporting.
Met criteria codes
PM2_Supporting
absent from all versions of gnomAD
PM1
cysteine-creating variant in cbEGF32; also at a tyrosine in the consensus calcium-binding sequence
PS2
1 de novo with confirmed mat/pat, phenotype non-specific/high genetic heterogeneity (0.5 ClinGen de novo points) + 3 de novo with assumed mat/pat, phenotype consistent but not highly specific (1.5 ClinGen de novo points) + 1 de novo with assumed mat/pat, phenotype non-specific/high genetic heterogeneity (0.25 ClinGen de novo points) = 2.25 total de novo points = PM6_strong or PS2
PS4
12+ probands worth >4.0 PS4 points
PP4
Johns Hopkins internal proband meets revised Ghent criteria
PP3
REVEL > 0.750
PP2
no benign evidence
Not Met criteria codes
PM5
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
PM6
see PS2
BA1
PM2_supporting met
BS2
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
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
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
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
PS1
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
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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