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.6410G>A (p.Cys2137Tyr)

CA392336648

633211 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: e09bca8b-b5bd-4e00-9b72-769cd05c78d9
Approved on: 2024-08-22
Published on: 2024-08-22

HGVS expressions

NM_000138.5:c.6410G>A
NM_000138.5(FBN1):c.6410G>A (p.Cys2137Tyr)
NC_000015.10:g.48437047C>T
CM000677.2:g.48437047C>T
NC_000015.9:g.48729244C>T
CM000677.1:g.48729244C>T
NC_000015.8:g.46516536C>T
NG_008805.2:g.213742G>A
ENST00000559133.6:c.6410G>A
ENST00000674301.2:c.6410G>A
ENST00000682170.1:n.19G>A
ENST00000316623.10:c.6410G>A
ENST00000674301.1:c.1409G>A
ENST00000316623.9:c.6410G>A
ENST00000537463.6:c.*2173G>A
ENST00000559133.5:c.1717G>A
NM_000138.4:c.6410G>A

Pathogenic

Met criteria codes 7
PM1_Strong PP4 PP1 PP3 PP2 PS4_Moderate PM2_Supporting
Not Met criteria codes 19
PM5 PM4 PM3 PS2 PS1 PS3 PM6 BA1 BP3 BP2 BP4 BP1 PVS1 BP5 BP7 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.6410G>A is a missense variant in FBN1 predicted to cause a substitution of cysteine by a tyrosine at amino acid 2137 (p.Cys2137Tyr). This variant has been identified in at least five patients with thoracic aortic aneurysm and dissection (TAAD), including two meeting clinical diagnostic criteria for Marfan syndrome (MFS), and in a patient with an unspecified clinical suspicion of Marfan syndrome (PS4_moderate, PP4; University of Texas-Houston & Invitae internal data). The variant was also found to segregate with aortic dilation in two individuals across two families (PP1; University of Texas-Houston & Invitae 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 = 0.916). 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_moderate, PP1, PP2, PP3, PP4, PM2_supporting.
Met criteria codes
PM1_Strong
cysteine in cbEGF32
PP4
proband at Invitae meeting revised Ghent criteria
PP1
2 segregations
PP3
REVEL > 0.750
PP2
no benign evidence
PS4_Moderate
5 probands worth 3.0 PS4 points (1 other Invitae proband accounted for by PP4)
PM2_Supporting
absent from all versions of gnomAD
Not Met criteria codes
PM5
other variants at this position LP/P; PM5 n/a due to PM1_strong
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
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
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
PVS1
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
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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