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Variant: NM_000138.5(FBN1):c.4330T>A (p.Cys1444Ser)

CA353655

222604 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 3ae64fc8-99d1-4681-b0cf-6ece56643d71
Approved on: 2023-12-29
Published on: 2023-12-29

HGVS expressions

NM_000138.5:c.4330T>A
NM_000138.5(FBN1):c.4330T>A (p.Cys1444Ser)
NC_000015.10:g.48472557A>T
CM000677.2:g.48472557A>T
NC_000015.9:g.48764754A>T
CM000677.1:g.48764754A>T
NC_000015.8:g.46552046A>T
NG_008805.2:g.178232T>A
ENST00000683268.1:n.297T>A
ENST00000684448.1:n.3004T>A
ENST00000316623.10:c.4330T>A
ENST00000316623.9:c.4330T>A
ENST00000537463.6:c.*93T>A
NM_000138.4:c.4330T>A
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Pathogenic

Met criteria codes 6
PM1_Strong PS4_Moderate PM2_Supporting PP4 PP3 PP2
Not Met criteria codes 20
BS2 BS4 BS3 BS1 BP2 BP3 BP4 BP1 BP5 BP7 PS2 PS3 PS1 BA1 PP1 PM5 PM3 PM4 PM6 PVS1

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.4330T>A is a missense variant in FBN1 predicted to cause a substitution of a cysteine by serine at amino acid 1444 (p.Cys1444Ser). This variant has been identified in an adult patient with Marfan syndrome with bilateral ectopia lentis (EL), borderline thoracic aortic aneurysm and dissection (TAAD), and systemic features (PP4; Invitae internal data). A different nucleotide substitution (c.4331G>C) resulting in the same amino acid change has been identified in three individuals with clinical diagnoses of Marfan syndrome, all of whom were noted to have have EL in addition to other features of Marfan syndrome (PS4_moderate; University of Tokyo, Bichat, & Invitae internal data); in one family, c.4331G>C was found to segregate with annuloaortic ectasia and arachnodactyly in an infant child (University of Tokyo internal data). Of note, there is no predicted difference in splicing patterns between the two nucleotide substitutions. The c.4330T>A variant is absent from gnomAD (PM2_supporting; https://gnomad.broadinstitute.org, v2.1.1 & v3.1.2). It 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 further support that this variant is likely to impact the protein (PP3; REVEL = 0.949). The constraint z-score for missense variants affecting FBN1 is 5.06 (PP2). In summary, c.4330T>A (p.Cys1444Ser) 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, PP2, PP3, PP4, PM2_supporting.
Met criteria codes
PM1_Strong
Cysteine-removing variant in cbEGF20
PS4_Moderate
2 (University of Tokyo and Invitae) probands worth 2.0 PS4 points
PM2_Supporting
absent from gnomAD
PP4
Invitae proband with MFS
PP3
REVEL = 0.949; > 0.750 threshold
PP2
no benign criteria
Not Met criteria codes
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
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
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
VCEP decided to include c.4331G>C (p.Cys1444Ser) as equivalent for purposes of curation; no predicted differences in splicing between the two nucleotide substitutions
BA1
PM2_supporting met
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
p.Cys1444Phe, p.Cys1444Trp, p.Cys1444Tyr all P/LP; PM5 N/A because PM1_strong is applied
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
PM6
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
Curation History
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