The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000138.5(FBN1):c.6541T>C (p.Cys2181Arg)

CA392335055

429425 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 8a79b62f-2272-45f5-852c-32bba97da645
Approved on: 2024-08-22
Published on: 2024-08-22

HGVS expressions

NM_000138.5:c.6541T>C
NM_000138.5(FBN1):c.6541T>C (p.Cys2181Arg)
NC_000015.10:g.48434669A>G
CM000677.2:g.48434669A>G
NC_000015.9:g.48726866A>G
CM000677.1:g.48726866A>G
NC_000015.8:g.46514158A>G
NG_008805.2:g.216120T>C
ENST00000559133.6:c.6541T>C
ENST00000674301.2:c.6541T>C
ENST00000682170.1:n.150T>C
ENST00000316623.10:c.6541T>C
ENST00000674301.1:c.1540T>C
ENST00000316623.9:c.6541T>C
ENST00000537463.6:c.*2304T>C
ENST00000559133.5:c.1848T>C
NM_000138.4:c.6541T>C

Likely Pathogenic

Met criteria codes 6
PM1_Strong PM2_Supporting PP4 PP3 PP2 PS4_Supporting
Not Met criteria codes 20
PVS1 BS2 BS4 BS3 BS1 BP2 BP3 BP4 BP1 BP5 BP7 PM5 PM3 PM4 PS2 PS1 PS3 PM6 BA1 PP1

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.6541T>C is a missense variant in FBN1 predicted to cause a substitution of cysteine by an arginine at amino acid 2181 (p.Cys2182Arg). It has been identified in one patient meeting clinical diagnostic criteria for Marfan syndrome, including thoracic aortic aneurysm and dissection (TAAD) and systemic involvement, and was found to segregate with TAAD and systemic features in the patient’s sibling (PP4; University of Tokyo). This variant has also been reported in two patients with TAAD, without additional phenotypes noted (PS4_supporting; PMID: 37042257, GeneDx 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 = 0.993). 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 likely pathogenic for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: PM1_strong, PP2, PP3, PP4, PS4_supporting, PM2_supporting.
Met criteria codes
PM1_Strong
cysteine in cbEGF33
PM2_Supporting
absent from all versions of gnomAD
PP4
University of Tokyo proband meets revised Ghent criteria, with suspected family history of MFS
PP3
REVEL > 0.750
PP2
no benign evidence
PS4_Supporting
2 probands worth 1.0 PS4 point
Not Met criteria codes
PVS1
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
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
PM5
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
PS2
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
PM2_supporting met
PP1
1 segregation (University of Tokyo)
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