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.4526A>G (p.Tyr1509Cys)

CA015164

180355 (ClinVar)

Gene: FBN1
Condition: Marfan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 013fd5cb-459d-4a9a-9621-16fdafd6d9bc
Approved on: 2023-12-29
Published on: 2023-12-29

HGVS expressions

NM_000138.5:c.4526A>G
NM_000138.5(FBN1):c.4526A>G (p.Tyr1509Cys)
NC_000015.10:g.48468468T>C
CM000677.2:g.48468468T>C
NC_000015.9:g.48760665T>C
CM000677.1:g.48760665T>C
NC_000015.8:g.46547957T>C
NG_008805.2:g.182321A>G
ENST00000684448.1:n.3200A>G
ENST00000316623.10:c.4526A>G
ENST00000316623.9:c.4526A>G
ENST00000537463.6:c.*289A>G
NM_000138.4:c.4526A>G
More

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PM1 PS4_Moderate PP3 PP2
Not Met criteria codes 21
PM5 PM3 PM4 PM6 BA1 BS2 PVS1 BS4 BS3 BS1 BP5 BP7 BP4 BP1 BP2 BP3 PS1 PS3 PS2 PP4 PP1

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.4526A>G is a missense variant in FBN1 predicted to cause a substitution of a tyrosine by cysteine at amino acid 1509 (p.Tyr1509Cys). This variant has been identified in at least four individuals including two probands with clinical diagnoses of Marfan syndrome, an individual with mild thoracic aortic aneurysm and dissection (TAAD) and systemic features without fulfilling Marfan syndrome diagnostic criteria, and an individual of tall stature with TAAD (PS4_moderate; PMID: 26787436; Johns Hopkins & University of Tokyo internal data). It is absent from gnomAD (PM2_supporting; https://gnomad.broadinstitute.org/ v2.1.1 & v3.1.2). This variant introduces a novel cysteine residue which may impede the normal formation of essential disulfide bridges and occurs at a residue in a critical calcium-binding site within a calcium-binding EGF-like domain (PM1). Computational prediction tools and conservation analysis support that this variant is likely to impact the protein (PP3; REVEL = 0.916). 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, PS4_moderate, PP2, PP3, PM2_supporting.
Met criteria codes
PM2_Supporting
absent from gnomAD
PM1
Cysteine-creating variant in cbEGF22; also occurs at tyrosine in consensus calcium-binding sequence
PS4_Moderate
4 probands worth 2.5 - 3.0 PS4 points
PP3
REVEL = 0.916; > 0.750
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
PM5
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
PM6
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
PVS1
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
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
BP4
PP3 met
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
BP3
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
PS3
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
PP4
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
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.