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.4280A>G (p.Tyr1427Cys)

CA392317779

449440 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 963e761f-325b-48ce-a0df-5227b788a759
Approved on: 2023-12-29
Published on: 2023-12-29

HGVS expressions

NM_000138.5:c.4280A>G
NM_000138.5(FBN1):c.4280A>G (p.Tyr1427Cys)
NC_000015.10:g.48472607T>C
CM000677.2:g.48472607T>C
NC_000015.9:g.48764804T>C
CM000677.1:g.48764804T>C
NC_000015.8:g.46552096T>C
NG_008805.2:g.178182A>G
ENST00000683268.1:n.247A>G
ENST00000684448.1:n.2954A>G
ENST00000316623.10:c.4280A>G
ENST00000316623.9:c.4280A>G
ENST00000537463.6:c.*43A>G
NM_000138.4:c.4280A>G
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Likely Pathogenic

Met criteria codes 7
PM2_Supporting PS4_Supporting PP4 PP3 PP2 PM5 PM1
Not Met criteria codes 19
BS2 BS4 BS3 BS1 BP3 BP2 BP4 BP1 BP5 BP7 PS2 PS3 PS1 BA1 PP1 PM4 PM3 PM6 PVS1

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 c.4280A>G is a missense variant in FBN1 predicted to cause a substitution of a tyrosine by cysteine at amino acid 1427 (p.Tyr1427Cys). This variant has been identified in the literature in an individual with either a suspicion or diagnosis of Marfan syndrome, and by a commercial laboratory in two unrelated individuals with thoracic aortic aneurysm and dissection (TAAD), segregating with TAAD in one similarly affected family member (PS4_supporting; PMID: 21907952, Invitae internal data). It was also identified by a commercial laboratory in an individual with Marfan syndrome including ectopia lentis and a systemic score of 8 (PP4; GeneDx internal data). It is absent from gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/ v2.1.1 & 3.1.2). This variant introduces a novel cysteine residue which may impede the normal formation of essential disulfide bridges and occurs at a residue in a critical calcium-binding site within a calcium-binding EGF-like domain (PM1). Computational prediction tools and conservation analysis support that this variant is likely to impact the protein (PP3; REVEL = 0.939). Another variant affecting the same residue (p.Tyr1427Asp) is classified as likely pathogenic, further supporting the functional importance of this amino acid position (PM5; PMID: 17657824). 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, PM5, PS4_supporting, PP2, PP3, PP4, PM2_supporting.
Met criteria codes
PM2_Supporting
absent from v2.1.1 and v3.1.2
PS4_Supporting
3 probands worth 1.5 PS4 points (GeneDx proband accounted for by application of PP4 criterion)
PP4
GeneDx proband meeting revised Ghent criteria
PP3
REVEL = 0.939; > 0.750 threshold
PP2
no benign criteria
PM5
p.Tyr1427Asp is Likely Pathogenic - 2 probands in Comeglio et al. (1.5 PS4 points; PS4_supporting) - REVEL = 0.960 (PP3) - absent from gnomAD (PM2_supporting) - missense (PP2) - p.Tyr1427 part of consensus calcium-binding sequence in cbEGF20 (PM1)
PM1
cysteine-creating variant, also at a tyrosine in the consensus calcium-binding sequencing in cbEGF20
Not Met criteria codes
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
v4.0.0: 1/15786 (0.0064%) A/AA; > 0.005% threshold for BS1, but filtering allele frequency is zero
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
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
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
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
1 segregation with clinical features (Invitae)
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
PM6
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
Curation History
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