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.1708T>C (p.Cys570Arg)

CA269554328

956400 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 38d36d10-5c7c-455c-9338-0706c4a6f7f9
Approved on: 2023-11-16
Published on: 2023-11-16

HGVS expressions

NM_000138.5:c.1708T>C
NM_000138.5(FBN1):c.1708T>C (p.Cys570Arg)
NC_000015.10:g.48510050A>G
CM000677.2:g.48510050A>G
NC_000015.9:g.48802247A>G
CM000677.1:g.48802247A>G
NC_000015.8:g.46589539A>G
NG_008805.2:g.140739T>C
ENST00000684448.1:n.382T>C
ENST00000316623.10:c.1708T>C
ENST00000316623.9:c.1708T>C
ENST00000537463.6:c.636+27661T>C
NM_000138.4:c.1708T>C

Pathogenic

Met criteria codes 7
PM1_Strong PM2_Supporting PP3 PP2 PP4 PS3_Supporting PS4_Moderate
Not Met criteria codes 17
BP5 BP2 BP3 BP4 PS2 PS1 PP1 PM6 PM3 PM4 PM5 PVS1 BA1 BS4 BS3 BS1 BS2

Evidence Links 1

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_00138 c.1708T>C is a missense variant in FBN1 predicted to cause a substitution of a cysteine by arginine at amino acid 570 (p.Cys570Arg). This variant has been found in two probands with ectopia lentis (EL), one of whom was also reported to have numerous systemic features of Marfan syndrome without thoracic aortic aneurysm and dissection (TAAD), as well as a proband with isolated TAAD (PS4_moderate; PMID: 10486319; 3billion & Invitae internal data, ClinVar Variation ID: 956400). An additional proband with a severe Marfan syndrome phenotype including EL, TAAD, and major skeletal involvement (PP4; Bichat internal data). Functional studies performed on patient fibroblasts with this variant demonstrated reduced fibrillin synthesis and secretion (50% and 28% of controls, respectively) (PS3_supporting; PMID: 10486319). This variant is not present in gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/). This variant affects a cysteine residue in a calcium binding EGF domain; cysteine residues are believed to be involved in the formation of disulfide bridges which are essential for the protein structure (PM1_strong). Several other variants affecting this codon have been reported in association with Marfan syndrome (p.Cys570Gly, p.Cys570SerSer, p.Cys570Trp, p.Cys570Tyr). Computational prediction tools and conservation analysis support that this variant may impact the protein’s structure or function (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: PM1_strong, PS4_moderate, PS3_supporting, PM2_supporting, PP2, PP3, PP4.
Met criteria codes
PM1_Strong
Cysteine in cbEGF4
PM2_Supporting
Absent from gnomAD
PP3
REVEL = 0.983
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
1 internal proband meeting revised Ghent criteria (Bichat)
PS3_Supporting
acceptable functional assay per FBN1 VCEP; per ClinGen SVI the study was lacking sufficient replicates to use at full strength

PS4_Moderate
3 probands worth 2.5 PS4 points
Not Met criteria codes
BP5
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
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
PS1
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
PM6
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
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
p.Cys570Ser, p.Cys570Tyr both LP/P per FBN1 VCEP specifications; PM1_strong applied so PM5 n/a
PVS1
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
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
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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