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.6448C>T (p.Arg2150Cys)

CA016472

200084 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 4f4f79a3-6c57-4b99-bd02-ae5be4af216f
Approved on: 2024-08-22
Published on: 2024-08-22

HGVS expressions

NM_000138.5:c.6448C>T
NM_000138.5(FBN1):c.6448C>T (p.Arg2150Cys)
NC_000015.10:g.48437009G>A
CM000677.2:g.48437009G>A
NC_000015.9:g.48729206G>A
CM000677.1:g.48729206G>A
NC_000015.8:g.46516498G>A
NG_008805.2:g.213780C>T
ENST00000559133.6:c.6448C>T
ENST00000674301.2:c.6448C>T
ENST00000682170.1:n.57C>T
ENST00000316623.10:c.6448C>T
ENST00000674301.1:c.1447C>T
ENST00000316623.9:c.6448C>T
ENST00000537463.6:c.*2211C>T
ENST00000559133.5:c.1755C>T
NM_000138.4:c.6448C>T
More

Pathogenic

Met criteria codes 6
PP1_Strong PS4 PM1 PP4 PP3 PP2
Not Met criteria codes 20
BP5 BP7 BP2 BP3 BP4 BP1 PVS1 PM6 PM2 PS2 PS1 PS3 PM5 PM3 PM4 BA1 BS2 BS4 BS3 BS1

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.6448C>T is a missense variant in FBN1 predicted to cause a substitution of an arginine by cysteine at amino acid 2150 (p.Arg2150Cys). This variant has been identified in more than 15 patients with features suggestive of, or consistent with, Marfan syndrome (MFS), including at least three who meet clinical diagnostic criteria for MFS and more than 10 individuals who do not meet MFS diagnostic criteria but have thoracic aortic aneurysm and dissection (TAAD), with or without additional clinical features of MFS (PS4, PP4; Bichat, University of Tokyo, UZA, Invitae, & GeneDx internal data; PMIDs: 37042257, 19161152, 37558401, 33059708, 31730815). The variant was found to segregate with a clinical diagnosis of MFS in one patient’s parent, and with mild features suggestive of MFS or another connective tissue disorder in approximately 11 affected family members between two additional families (PP1_strong; UZA & Invitae internal data); notably, this variant is associated with particularly variable expressivity and incomplete penetrance of the MFS phenotype. It is present in gnomAD with a maximum frequency of 0.0008% (1/113462 alleles European, non-Finnish; https://gnomad.broadinstitute.org/, v2.1.1). This variant introduces a novel cysteine residue which may impede the normal formation of essential disulfide bridges (PM1). Computational prediction tools and conservation analysis support that this variant is likely to impact the protein (PP3; REVEL = 0.923). 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: PS4, PP1_strong, PM1, PP2, PP3, PP4.
Met criteria codes
PP1_Strong
>5 segregations
PS4
15+ probands worth >> 4.0 PS4 points
PM1
cysteine-creating variant in cbEGF32
PP4
proband (Mannucci et al.) meeting revised Ghent criteria
PP3
REVEL > 0.750
PP2
no benign evidence
Not Met criteria codes
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
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
PP3 met
BP1
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
0.0015% (1/67996) in European alleles, gnomAD v4.0.0 MAF > 0.0005% threshold
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
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
BA1
Highest MAF (0.0015%) < 0.1% threshold
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
Highest MAF (0.0015%) < 0.005% threshold
Curation History
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