The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_000138.5(FBN1):c.6254G>A (p.Cys2085Tyr)

CA392337017

547338 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: b718fa92-e734-41e4-a076-e12d27ce2739
Approved on: 2024-08-22
Published on: 2024-08-22

HGVS expressions

NM_000138.5:c.6254G>A
NM_000138.5(FBN1):c.6254G>A (p.Cys2085Tyr)
NC_000015.10:g.48437827C>T
CM000677.2:g.48437827C>T
NC_000015.9:g.48730024C>T
CM000677.1:g.48730024C>T
NC_000015.8:g.46517316C>T
NG_008805.2:g.212962G>A
ENST00000559133.6:c.6254G>A
ENST00000674301.2:c.6254G>A
ENST00000316623.10:c.6254G>A
ENST00000674301.1:c.1253G>A
ENST00000316623.9:c.6254G>A
ENST00000537463.6:c.*2017G>A
ENST00000559133.5:c.1561G>A
ENST00000560820.1:n.374G>A
NM_000138.4:c.6254G>A
More

Likely Pathogenic

Met criteria codes 7
PS4_Moderate PP4 PP3 PP2 PM5 PM1 PM2_Supporting
Not Met criteria codes 19
PVS1 BA1 BS2 BS3 BS4 BS1 BP2 BP3 BP4 BP1 BP5 BP7 PS1 PS2 PS3 PP1 PM6 PM3 PM4

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.6254G>A is a missense variant in FBN1 predicted to cause a substitution of a cysteine by tyrosine at amino acid 2085 (p.Cys2085Tyr). This variant was found in a proband with a phenotype that satisfies the revised Ghent criteria for a clinical diagnosis of Marfan syndrome (MFS) (PP4; PMID: 25907466). It has been identified in another individual who meets clinical diagnostic criteria for MFS and one who does not meet diagnostic criteria but has thoracic aortic aneurysm (TAA) and a systemic score of 4 (PS4_moderate; PMID: 29768367; Bichat internal data). It has been reported 2 times in ClinVar as likely pathogenic (1) and of uncertain significance (1) (Variation ID: 547338). It is not present in gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/). This variant alters a cysteine in a TGFβ binding-protein-like (TB) domain, in which cysteine residues are believed to form disulfide bridges important for proper protein folding (PM1). Computational prediction tools and conservation analysis suggest that this variant may impact the protein structure (PP3; REVEL = 0.886). A different variant at the same amino acid position (c.6253T>G:p.Cys2085Gly) has been identified in at least two individuals with TAA and ectopia lentis and is classified as pathogenic or likely pathogenic; this further supports the functional importance of this amino acid position (PM5; Invitae internal data). The constraint z-score for missense variants affecting FBN1 is 8.2 (PP2; gnomAD v4.1.0). 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, PM5, PP2, PP3, PP4, PM2_supporting, PS4_supporting.
Met criteria codes
PS4_Moderate
2 probands (excluding that used for PP4) worth 2.0 PS4 points
PP4
patient meets revised Ghent criteria
PP3
REVEL = 0.886, > 0.750
PP2
no benign evidence
PM5
c.6253T>G (p.Cys2085Gly): likely pathogenic at minimum - PM1 - PM2_supporting (absent all versions) - PP2 - PP3 (REVEL = 0.802) - PP4 (Invitae patient: MFS clinical dx with EL and TAA) - PS4_supporting (Invitae patient: tall stature, mild TAA, and EL)
PM1
cysteine-removing variant in TB6 domain
PM2_Supporting
absent from all versions of gnomAD
Not Met criteria codes
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
PM2_supporting met
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
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
PM2_supporting met
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
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
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
PS3
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
Curation History
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.