The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000138.5(FBN1):c.6491G>A (p.Cys2164Tyr)

CA392336264

547340 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 56b0fed5-cc14-4984-881d-92f7643f0f5b
Approved on: 2024-08-22
Published on: 2024-08-22

HGVS expressions

NM_000138.5:c.6491G>A
NM_000138.5(FBN1):c.6491G>A (p.Cys2164Tyr)
NC_000015.10:g.48436966C>T
CM000677.2:g.48436966C>T
NC_000015.9:g.48729163C>T
CM000677.1:g.48729163C>T
NC_000015.8:g.46516455C>T
NG_008805.2:g.213823G>A
ENST00000559133.6:c.6491G>A
ENST00000674301.2:c.6491G>A
ENST00000682170.1:n.100G>A
ENST00000316623.10:c.6491G>A
ENST00000674301.1:c.1490G>A
ENST00000316623.9:c.6491G>A
ENST00000537463.6:c.*2254G>A
ENST00000559133.5:c.1798G>A
NM_000138.4:c.6491G>A

Pathogenic

Met criteria codes 7
PS4 PP1 PP4 PP3 PP2 PM1_Strong PM2_Supporting
Not Met criteria codes 19
BP5 BP7 BP3 BP2 BP4 BP1 PS1 PS2 PS3 PM6 PM5 PM4 PM3 PVS1 BA1 BS2 BS3 BS4 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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
NM_000138.5 c.6419G>A is a missense variant in FBN1 predicted to cause a substitution of a cysteine by tyrosine at amino acid 2164 (p.Cys2164Tyr). This variant has been identified in at least four individuals meeting clinical diagnostic criteria for Marfan syndrome (MFS) and two individuals with non-specific features suggestive of a connective tissue disorder (PS4, PP4; Bichat & UZG internal data; PMIDs: 31730815, 37558401, 29095814). In one of these individuals, it was found to be de novo; however, phenotype details were not provided and therefore the specificity and consistency of the phenotype with FBN1 cannot be assessed (PMID: 29095814). In another of these families, the variant was found to segregate with disease in two affected family members (PP1; Bichat internal data). It is absent from gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/, v2.1.1, 3.1.2, 4.0.0). This variant 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 support that this variant is likely to impact the protein (PP3; REVEL = 0.863). 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: PM1_strong, PS4, PP1, PP2, PP3, PP4, PM2_supporting.
Met criteria codes
PS4
5 probands worth 4.0 PS4 points
PP1
2 segregations with disease (Bichat)
PP4
Mannucci et al. patient meets revised Ghent criteria
PP3
REVEL > 0.750
PP2
no benign evidence
PM1_Strong
cysteine in cbEGF32
PM2_Supporting
absent from all versions of gnomAD
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
BP3
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
BP4
PP3 met
BP1
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
no phenotype data provided for Hu et al. proband, so cannot assess consistency and specificity of their phenotype
PM5
n/a because PM1_strong is applied
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
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
PM2_supporting met
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
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
PM2_supporting met
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