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.4081T>C (p.Cys1361Arg)

CA392320410

626882 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: b2b87aed-71d2-4475-b80a-65a39f73d1ce

HGVS expressions

NM_000138.5:c.4081T>C
NM_000138.5(FBN1):c.4081T>C (p.Cys1361Arg)
NC_000015.10:g.48474534A>G
CM000677.2:g.48474534A>G
NC_000015.9:g.48766731A>G
CM000677.1:g.48766731A>G
NC_000015.8:g.46554023A>G
NG_008805.2:g.176255T>C
ENST00000684448.1:n.2755T>C
ENST00000316623.10:c.4081T>C
ENST00000316623.9:c.4081T>C
ENST00000537463.6:c.753T>C
NM_000138.4:c.4081T>C

Likely Pathogenic

Met criteria codes 6
PM1_Strong PP4 PP3 PP2 PS4_Supporting PM2_Supporting
Not Met criteria codes 20
PS2 PS3 PS1 BP5 BP7 BP2 BP3 BP4 BP1 PP1 BA1 PM3 PM5 PM4 PVS1 PM6 BS2 BS4 BS3 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

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

PDF
Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
FBN1 VCEP
NM_000138.5 c.4081T>C is a missense variant in FBN1 predicted to cause a substitution of a cysteine by arginine at amino acid 1361 (p.Cys1361Arg). This variant has been identified in at least two individuals with clinical diagnoses of Marfan syndrome and in an individual with a clinical suspicion of Marfan syndrome (PP4, PS4_supporting; PMID: 35058154; CHEO internal data). It is absent from gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/). This variant affects a cysteine residue in a calcium-binding EGF-like domain; cysteine residues are involved in the formation of disulfide bridges which are essential for the protein structure (PM1_strong). Computational prediction tools and conservation analysis support that this variant is likely to impact the protein (PP3; REVEL = 0.920). 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_strong, PS4_supporting, PP2, PP3, PP4, PM2_supporting.
Met criteria codes
PM1_Strong
Cysteine-removing variant in cbEGF18
PP4
proband meeting revised Ghent criteria (Meester et al.)
PP3
REVEL = 0.920; > 0.750 threshold
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4_Supporting
2 probands worth 1.5 PS4 points (Meester et al., CHEO internal data) *1 of 2 probands from Meester et al. is accounted for by application of the PP4 criterion
PM2_Supporting
absent from gnomAD
Not Met criteria codes
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
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
BP2
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
BP4
PP3 met
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
PM2_supporting met
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
p.Cys1361Tyr is P/LP; N/A because PM1_strong is applied
PM4
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
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
PM2_supporting met
Approved on: 2023-12-29
Published on: 2023-12-29
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.