The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000138.5(FBN1):c.1538G>T (p.Cys513Phe)

CA16614674

406288 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: f61e7451-ec4e-4414-9286-7cf6186ab50e
Approved on: 2023-11-16
Published on: 2023-11-16

HGVS expressions

NM_000138.5:c.1538G>T
NM_000138.5(FBN1):c.1538G>T (p.Cys513Phe)
NC_000015.10:g.48513599C>A
CM000677.2:g.48513599C>A
NC_000015.9:g.48805796C>A
CM000677.1:g.48805796C>A
NC_000015.8:g.46593088C>A
NG_008805.2:g.137190G>T
ENST00000684448.1:n.212G>T
ENST00000316623.10:c.1538G>T
ENST00000316623.9:c.1538G>T
ENST00000537463.6:c.636+24112G>T
NM_000138.4:c.1538G>T
More

Likely Pathogenic

Met criteria codes 5
PP3 PP2 PM2_Supporting PS4_Supporting PM1_Strong
Not Met criteria codes 18
PS2 PS3 PS1 BP2 BP3 BP4 BP7 BA1 PP1 PP4 PVS1 PM3 PM4 PM5 PM6 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_00138 c.1538G>T is a missense variant in FBN1 predicted to cause a substitution of a cysteine by phenylalanine at amino acid 513 (p.Cys513Phe). This variant has not been reported in the literature but has been found in at least two probands; this includes one individual with bilateral ectopia lentis and thoracic aortic aneurysm and dissection, and one with unspecified features of a connective tissue disorder (PS4_supporting; Invitae & LabCorp internal data, ClinVar Variation ID: 406288). This variant is not present in gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/). This variant affects a cysteine residue in a calcium binding EGF domain; cysteine residues are believed to be involved in the formation of disulfide bridges which are essential for the protein structure (PM1_strong). Several other variants affecting this codon have been reported in association with Marfan syndrome (p.Cys513Gly, p.Cys513Ser, p.Cys513Tyr, p.Cys513Arg). Computational prediction tools and conservation analysis strongly support that this variant may impact 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 on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: PM1_strong, PM2_supporting, PS4_supporting, PP2, PP3.
Met criteria codes
PP3
REVEL = 0.996
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2_Supporting
absent from gnomAD
PS4_Supporting
2 probands worth 1.5 PS4 points
PM1_Strong
Cysteine in cbEGF3
Not Met criteria codes
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
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
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
BA1
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
PP4
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
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
PM5
p.Cys513Gly, p.Cys513Ser, p.Cys513Tyr, p.Cys513Arg all P/LP; PM5 n/a because PM1_strong is applied
PM6
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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