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Variant: NM_000138.5(FBN1):c.1390C>T (p.Arg464Cys)

CA269559072

549013 (ClinVar)

Gene: FBN1 (HGNC:2200)
Condition: Marfan syndrome (MONDO:0007947)
Inheritance Mode: Autosomal dominant inheritance
UUID: 9177e5b4-a609-4c71-9fd1-aac0638b9f22
Approved on: 2023-11-16
Published on: 2023-11-16

HGVS expressions

NM_000138.5(FBN1):c.1390C>T (p.Arg464Cys)
NM_000138.5:c.1390C>T
NC_000015.10:g.48515465G>A
CM000677.2:g.48515465G>A
NC_000015.9:g.48807662G>A
CM000677.1:g.48807662G>A
NC_000015.8:g.46594954G>A
NG_008805.2:g.135324C>T
ENST00000684448.1:n.64C>T
ENST00000316623.10:c.1390C>T
ENST00000316623.9:c.1390C>T
ENST00000537463.6:c.636+22246C>T
NM_000138.4:c.1390C>T
More

Likely Pathogenic

Met criteria codes 5
PS4_Supporting PP1 PP2 PP4 PM1
Not Met criteria codes 21
PVS1 BA1 BP2 BP3 BP4 BP1 BP7 BP5 BS2 BS3 BS1 BS4 PP3 PM3 PM5 PM4 PM6 PM2 PS3 PS1 PS2

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(FBN1):c.1390C>T (p.Arg464Cys) NM_00138 c.1390C>T is a missense variant in FBN1 predicted to cause a substitution of an arginine by cysteine at amino acid 464 (p.Arg464Cys). This variant has been found in two probands including one with bilateral ectopia lentis (EL) and thoracic aortic aneurysm and dissection (TAAD), and one with isolated EL (PP4, PS4_supporting; Invitae & UZG internal data, ClinVar Variation ID: 549013). The variant segregates with features of Marfan syndrome in at least two affected family members (PP1; Invitae internal data). This variant is present in gnomAD v2.1.1 (1/34578 [0.003%] Latino/Admixed American alleles; 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 predicted impact of this variant on the protein’s structure or function (PP3). The constraint z-score for missense variants affecting FBN1 is 5.06 (PP2). In summary, this variant meets criteria to be classified as likely pathogenic for Marfan syndrome based o the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: PM1, PS4_supporting, PP1, PP2, PP4.
Met criteria codes
PS4_Supporting
1 proband worth 1.0 PS4 point
PP1
2 segregations
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
UZG proband with isolated ectopia lentis
PM1
Cysteine-creating variant
Not Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
highest MAF: 1/34578 alleles (0.003%) in gnomAD v2.1.1
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
REVEL= 0.642
BP1
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
BP5
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
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
highest MAF: 1/34578 alleles (0.003%) in gnomAD v2.1.1
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL= 0.642
PM3
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
highest MAF: 1/34578 alleles (0.003%) in gnomAD v2.1.1
PS3
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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