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Variant: NM_000138.4(FBN1):c.4459G>A (p.Asp1487Asn)

CA269554323

549232 (ClinVar)

Gene: FBN1 (HGNC:2200)
Condition: Marfan syndrome (MONDO:0007947)
Inheritance Mode: Autosomal dominant inheritance
UUID: bcb32b50-f400-4bba-8030-d8f1e31ee6ac
Approved on: 2022-12-01
Published on: 2022-12-01

HGVS expressions

NM_000138.4(FBN1):c.4459G>A (p.Asp1487Asn)
NM_000138.4:c.4459G>A
NC_000015.10:g.48470634C>T
CM000677.2:g.48470634C>T
NC_000015.9:g.48762831C>T
CM000677.1:g.48762831C>T
NC_000015.8:g.46550123C>T
NG_008805.2:g.180155G>A
ENST00000683268.1:n.426G>A
ENST00000684448.1:n.3133G>A
ENST00000316623.10:c.4459G>A
ENST00000316623.9:c.4459G>A
ENST00000537463.6:c.*222G>A
NM_000138.5:c.4459G>A
NM_000138.5(FBN1):c.4459G>A (p.Asp1487Asn)
More

Pathogenic

Met criteria codes 7
PM2_Supporting PP4 PP3 PP2 PM1 PS4 PP1_Strong
Not Met criteria codes 19
BA1 PVS1 PM6 PM4 PM3 PM5 BS2 BS4 BS3 BS1 PS2 PS3 PS1 BP3 BP2 BP4 BP1 BP7 BP5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen FBN1 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines Version 1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_000138 c.4459G>A, is a missense variant in FBN1 predicted to cause a substitution of an Aspartic acid by Asparagine at amino acid 1487 p.(Asp1487Asn). This variant was found in four probands meeting the Ghent criteria (PP4, PS4_strong). The variant segregates with the disease in six affected family members of one proband and three affected family members of another proband (PP1_strong). This variant has been reported three times in ClinVar as likely pathogenic (Variation ID: 549232). It has been reported one time in the literature in a proband with classical Marfan syndrome (PMID: 19293843). This variant is not present in gnomAD v2.1.1 (PM2_sup; https://gnomad.broadinstitute.org/). This variant lies in a critical calcium binding site within a calcium binding EGF domain (PM1). Computational prediction tools and conservation analysis suggest that this variant may impact the protein structure (PP3). The constraint z-score for missense variants affecting FBN1 is 5.06 (PP2). 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: PS4, PP1_strong, PM1, PP2, PP3, PP4, PM2_supporting
Met criteria codes
PM2_Supporting
Not present in gnomad v2.1.1
PP4
Patient has TAD and EL
PP3
REVEL Score of 0.818, MetaLR and CADD predict this variant as pathogenic
PP2
The constraint z-score for missense variants affecting FBN1 is 5.06
PM1
Affects cb-sequence in cb-EGF domain: cbEGF22
PS4
This variant was identified in four probands meeting the Ghent criteria. An additional proband was described in the literature.
PP1_Strong
Co-segregation with disease in 6 affected family members in one center and 2 family members in another center
Not Met criteria codes
BA1
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
PM6
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
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
Cannot apply PM5.
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
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
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
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
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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