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Variant: NM_000138.5(FBN1):c.3689T>C (p.Met1230Thr)

CA051349

263789 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: d616edb5-0f37-43a7-9caf-1bad47d0ce35
Approved on: 2022-12-01
Published on: 2022-12-01

HGVS expressions

NM_000138.5:c.3689T>C
NM_000138.5(FBN1):c.3689T>C (p.Met1230Thr)
NC_000015.10:g.48485397A>G
CM000677.2:g.48485397A>G
NC_000015.9:g.48777594A>G
CM000677.1:g.48777594A>G
NC_000015.8:g.46564886A>G
NG_008805.2:g.165392T>C
ENST00000684448.1:n.2363T>C
ENST00000316623.10:c.3689T>C
ENST00000316623.9:c.3689T>C
ENST00000537463.6:c.637-10747T>C
NM_000138.4:c.3689T>C
More

Likely Benign

Met criteria codes 2
BS4 BP2
Not Met criteria codes 24
PM6 PM2 PM4 PM3 PM1 PM5 BA1 BS2 PVS1 BS3 BS1 BP3 BP4 BP1 BP7 BP5 PS2 PS4 PS3 PS1 PP4 PP1 PP3 PP2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
NM_00138 c.3689T>C is a missense variant in FBN1 predicted to cause a substitution of a Methionine by Threonine at amino acid 1230 p.(Met1230Thr). This variant was identified in an internal proband with ectopia lentis and thoracic aortic aneurysm and dissection, however a pathogenic frameshift variant in FBN1 was also identified in the proband (BP2) and was considered to explain the phenotype. Furthermore this variant does not segregate with disease in an affected family member (BS4). . This variant has been previously reported in ClinVar as of uncertain significance (Variation ID: 263789). This variant has been identified in 0.0018% of individuals of European origin (https://gnomad.broadinstitute.org/). Computational prediction tools and conservation analysis are unclear on the predicted impact on the protein. The constraint z-score for missense variants affecting FBN1 is 5.06 however due to the presence of one benign argument PP2 cannot be used . In summary, this variant meets criteria to be classified as likely benign for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: BS4, BP2
Met criteria codes
BS4
Variant did not segregate with disease in affected father
BP2
Pathogenic frameshift variant in FBN1 identified in this individual
Not Met criteria codes
PM6
No probands with variant reported
PM2
Highest MAF: 0.0018% (2/113756) European alleles (gnomAD v2.1.1) MAF >0.0005%
PM4
N/A for this variant type
PM3
N/A for FBN1
PM1
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
BA1
Highest MAF: 0.0018% (2/113756) European alleles (gnomAD v2.1.1) MAF <0.1%
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
N/A for this variant type
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
MAF: 0.0018% (2/113756) European alleles (gnomAD v2.1.1) MAF <0.005%
BP3
N/A for FBN1
BP4
REVEL = 0.603 (>0.326)
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
N/A for this variant
BP5
Pathogenic frameshift variant in FBN1 also detected - BP2 applied
PS2
No probands with variant reported
PS4
No probands in the literature
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
PP4
Proband meets revised Ghent criteria (EL and aortic dissection), but phenotype and family history likely due to other pathogenic variant identified in the family
PP1
No family study data available
PP3
REVEL = 0.603 (<0.75)
PP2
Not applicable due to presence of evidence supporting benign assertion
Curation History
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