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Variant: NM_000138.5(FBN1):c.1453C>T (p.Arg485Cys)

CA012160

16466 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 326c25fb-e8bf-44cd-83e0-6f57e005411d
Approved on: 2023-11-16
Published on: 2023-11-16

HGVS expressions

NM_000138.5:c.1453C>T
NM_000138.5(FBN1):c.1453C>T (p.Arg485Cys)
NC_000015.10:g.48515402G>A
CM000677.2:g.48515402G>A
NC_000015.9:g.48807599G>A
CM000677.1:g.48807599G>A
NC_000015.8:g.46594891G>A
NG_008805.2:g.135387C>T
ENST00000684448.1:n.127C>T
ENST00000316623.10:c.1453C>T
ENST00000316623.9:c.1453C>T
ENST00000537463.6:c.636+22309C>T
NM_000138.4:c.1453C>T

Pathogenic

Met criteria codes 6
PP1_Strong PS4 PP2 PS2_Supporting PM1 PM2_Supporting
Not Met criteria codes 19
BS3 BS4 BS1 BS2 BP7 BP3 BP4 BP1 BP2 PVS1 PS1 PS3 BA1 PP4 PP3 PM6 PM5 PM4 PM3

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_00138 c.1453C>T is a missense variant in FBN1 predicted to cause a substitution of an arginine by cysteine at amino acid 485 (p.Arg484Cys). This variant has been identified in the literature in at least seven probands with features consistent with or suggestive of Marfan syndrome including thoracic aortic aneurysm and dissection (TAAD) with or without additional features (PS4; PMIDs: 16342915, 19293843, 24793577, 30485715). It was found in the homozygous state in two cousins with bilateral ectopia lentis (EL) and additional features of Marfan syndrome; of note, in both instances the variant was inherited from mildly affected or apparently unaffected heterozygous parents (PMID: 17568394). It was identified in trans with a different FBN1 pathogenic variant in three siblings with isolated EL (Bichat internal data); clinical information for the heterozygous parents was not available. The variant has also been identified in the heterozygous state in 5 additional internal probands diagnosed with TAAD with or without systemic features (UZG, Johns Hopkins University, Bichat, & University of Tokyo internal data). It has been found to segregate in the heterozygous state with features of Marfan syndrome in at least 19 individuals among five different families (PP1_strong; PMID: 30485715; Johns Hopkins & Bichat internal data). It has been identified as de novo once with confirmed maternity/paternity in an internal proband with a non-specific phenotype (PS2_supporting; PMID: 19293843; UZG internal data). It is not present in gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/). This variant introduces a novel cysteine residue which may impede the normal formation of critical disulfide bridges (PM1). Computational prediction tools and conservation analysis are unclear about the variant’s predicted impact on the protein’s structure or function. The constraint z-score for missense variants affecting FBN1 is 5.06 (PP2). 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, PS2_supporting, PM2_supporting, PP2.
Met criteria codes
PP1_Strong
at least 19 segregations in the heterozygous state; 3 segregations in homozygous/compound heterozygous state
PS4
7 probands (1 homozygous) worth 7.0 PS4 points
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2_Supporting
1 de novo case (UZG) with confirmed maternity and paternity; phenotype is nonspecific with high genetic heterogeneity
PM1
Cysteine-creating variant
PM2_Supporting
Absent from gnomAD
Not Met criteria codes
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
BS2
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
BP4
REVEL = 0.741
BP1
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
PVS1
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
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
Several internal probands, none of whom met revised Ghent criteria
PP3
REVEL = 0.741
PM6
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
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
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