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Variant: NM_000138.5(FBN1):c.3422C>T (p.Pro1141Leu)

CA014098

42334 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 33b1c05d-fe29-4995-a9e2-14529a6a0c8f
Approved on: 2022-12-01
Published on: 2022-12-01

HGVS expressions

NM_000138.5:c.3422C>T
NM_000138.5(FBN1):c.3422C>T (p.Pro1141Leu)
NC_000015.10:g.48487353G>A
CM000677.2:g.48487353G>A
NC_000015.9:g.48779550G>A
CM000677.1:g.48779550G>A
NC_000015.8:g.46566842G>A
NG_008805.2:g.163436C>T
ENST00000684448.1:n.2096C>T
ENST00000316623.10:c.3422C>T
ENST00000316623.9:c.3422C>T
ENST00000537463.6:c.637-12703C>T
NM_000138.4:c.3422C>T

Benign

Met criteria codes 2
BS4 BS1
Not Met criteria codes 20
PS2 PS4 PS3 PS1 PP4 PP1 PP3 PP2 PM3 PM1 PM5 PM6 PM2 BA1 BS2 BS3 BP5 BP2 BP4 BP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
NM_00138 c.3422C>T is a missense variant in FBN1 predicted to cause a substitution of a Proline by Leucine at amino acid 1141 (p.Pro1141Leu). This variant has been reported in the literature in at least 3 individuals in association with thoracic aortic aneurysm and dissection (TAAD), MASS syndrome, and features possibly consistent with Marfan syndrome (PMID: 10533071; PMID: 24740214; PMID: 26188975). This variant was also identified in an internal proband with isolated TAAD with a family history highly specific for Marfan syndrome, however it does not segregate with disease in an affected family member (BS4) and therefore PP4 cannot be used. This variant has been previously reported in ClinVar as benign, likely benign, and uncertain significance (Variation ID: 42334). This variant has been identified in 0.026% of individuals of European origin (BS1; https://gnomad.broadinstitute.org/ version 2.1.1). 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 two benign arguments PP2 cannot be used. In summary, this variant meets criteria to be classified as benign for Marfan syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen FBN1 VCEP: BS1, BS4
Met criteria codes
BS4
Variant not present in internal individual's affected son (ectopia lentis, systemic score ≥7, TAD)
BS1
MAF 0.026% (34/129194 alleles) in European sub-population (gnomAD v2.1.1)
Not Met criteria codes
PS2
no evidence for this
PS4
BS1 is met; cannot apply PS4 at any strength (despite multiple probands in the literature without well-described phenotypes which otherwise would meet PS4_supporting)
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
Internal proband meets the Ghent criteria, but this variant does not segregate with the disease in the family, therefore PP4 should not apply
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL = 0.694 (<0.75)
PP2
Due to the use of BS1
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
PM6
no evidence for this
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
MAF 0.026% (34/129194 alleles) in European sub-population (gnomAD v2.1.1)
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
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
no evidence for this
BP4
REVEL = 0.694 (>0.326)
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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