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Variant: NM_000138.5(FBN1):c.5743C>T (p.Arg1915Cys)

CA392341191

495629 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 2a7d7c4d-0a6e-4c19-b14a-9928b8c3e8ed
Approved on: 2024-02-22
Published on: 2024-02-22

HGVS expressions

NM_000138.5:c.5743C>T
NM_000138.5(FBN1):c.5743C>T (p.Arg1915Cys)
NC_000015.10:g.48446751G>A
CM000677.2:g.48446751G>A
NC_000015.9:g.48738948G>A
CM000677.1:g.48738948G>A
NC_000015.8:g.46526240G>A
NG_008805.2:g.204038C>T
ENST00000559133.6:c.5743C>T
ENST00000674301.2:c.5743C>T
ENST00000684448.1:n.4417C>T
ENST00000316623.10:c.5743C>T
ENST00000674301.1:c.742C>T
ENST00000316623.9:c.5743C>T
ENST00000537463.6:c.*1506C>T
ENST00000559133.5:c.1050C>T
NM_000138.4:c.5743C>T
More

Pathogenic

Met criteria codes 6
PS4 PP4 PP2 PP1 PM1 PM2_Supporting
Not Met criteria codes 15
PS3 PS1 PS2 BP4 BP1 BP2 BP5 BA1 PP3 PVS1 PM5 PM6 BS3 BS4 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
The NM_00138 c.5743C>T is a missense variant in FBN1 predicted to cause a substitution of an arginine by cysteine at amino acid 1915 (p.Arg1915Cys) within a calcium binding EGF-like domain of the protein (PM1). This variant was found in a proband with classical Marfan syndrome (MFS) (Internal lab data, PP4). This variant has been reported 6 times in ClinVar: once as pathogenic, 4 times as likely pathogenic, and once as uncertain significance (Variation ID: 495629). This variant has also been identified in at least 7 individuals with clinical diagnosis of MFS as well as in individuals with clinical features of MFS (PMID 27234404, 35916808, 33174221, 27906200, internal data; PS4). In two families with MFS, the variant was found to segregate with disease in three affected relatives (Internal lab data, PP1). Different missense variants at this position, c.5744G>A p.(Arg1915His) and c.5743C>A p.(Arg1915Ser), have previously been reported in individuals with MFS and/or MFS-related features (PMID 11700157, 31830381), however these variants have not yet been reviewed by the FBN1 Variant Curation Expert Panel. This variant is not present in gnomAD (PM2_sup; https://gnomad.broadinstitute.org/v2.1.1). Computational prediction tools and conservation analysis are inconclusive with regards to a possible impact on this variant's protein function and structure (REVEL: 0.62). 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, PM1, PP1, PM2_Sup, PP2, PP4.
Met criteria codes
PS4
>4 probands with MFS/ Clinical features of MFS
PP4
1 proband with typical MFS
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
Identified in 5 affected individuals from two families (3 segregations)
PM1
Creation of Cys in CBD 32 (EGF)
PM2_Supporting
Absent in gnomAD
Not Met criteria codes
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
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
REVEL- No, CADD- No, MetaLR-Yes
BP1
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
BP5
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
PP3
REVEL- No- 0.62
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
Arg1915Ser- found in case, but not definitely pathogenic
PM6
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
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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