rs363811

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PP4PP1PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The NM_000138 c.7540G>T variant is a nonsense variant in FBN1 that is expected to introduce a premature stop codon at this position, likely resulting in an absent or disrupted protein product (PVS1). This variant was found in a proband with a clinical diagnosis of Marfan syndrome and segregates with disease in three affected family members (PP4, PP1; Bichat), as well as in an individual with features suggestive of or consistent with Marfan syndrome (PMID:17627385). This variant is not present in gnomAD v2.1.1 or v3.1.2 (PM2_supporting; https://gnomad.broadinstitute.org/). 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: PVS1, PM2_supporting, PP1, PP4. LINK:https://erepo.genome.network/evrepo/ui/classification/CA392325892/MONDO:0007947/022

Frequency

Genomes: not found (cov: 33)

Consequence

FBN1
NM_000138.5 stop_gained

Scores

5
1
1

Clinical Significance

Pathogenic reviewed by expert panel P:1

Conservation

PhyloP100: 7.91
Variant links:
Genes affected
FBN1 (HGNC:3603): (fibrillin 1) This gene encodes a member of the fibrillin family of proteins. The encoded preproprotein is proteolytically processed to generate two proteins including the extracellular matrix component fibrillin-1 and the protein hormone asprosin. Fibrillin-1 is an extracellular matrix glycoprotein that serves as a structural component of calcium-binding microfibrils. These microfibrils provide force-bearing structural support in elastic and nonelastic connective tissue throughout the body. Asprosin, secreted by white adipose tissue, has been shown to regulate glucose homeostasis. Mutations in this gene are associated with Marfan syndrome and the related MASS phenotype, as well as ectopia lentis syndrome, Weill-Marchesani syndrome, Shprintzen-Goldberg syndrome and neonatal progeroid syndrome. [provided by RefSeq, Apr 2016]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 11 ACMG points.

PVS1
For more information check the summary or visit ClinGen Evidence Repository.
PM2
For more information check the summary or visit ClinGen Evidence Repository.
PP1
For more information check the summary or visit ClinGen Evidence Repository.
PP4
For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FBN1NM_000138.5 linkc.7540G>T p.Gly2514* stop_gained Exon 61 of 66 ENST00000316623.10 NP_000129.3 P35555
FBN1NM_001406716.1 linkc.7540G>T p.Gly2514* stop_gained Exon 60 of 65 NP_001393645.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FBN1ENST00000316623.10 linkc.7540G>T p.Gly2514* stop_gained Exon 61 of 66 1 NM_000138.5 ENSP00000325527.5 P35555

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

Marfan syndrome Pathogenic:1
Jun 15, 2023
ClinGen FBN1 Variant Curation Expert Panel, ClinGen
Significance: Pathogenic
Review Status: reviewed by expert panel
Collection Method: curation

The NM_000138 c.7540G>T variant is a nonsense variant in FBN1 that is expected to introduce a premature stop codon at this position, likely resulting in an absent or disrupted protein product (PVS1). This variant was found in a proband with a clinical diagnosis of Marfan syndrome and segregates with disease in three affected family members (PP4, PP1; Bichat), as well as in an individual with features suggestive of or consistent with Marfan syndrome (PMID: 17627385). This variant is not present in gnomAD v2.1.1 or v3.1.2 (PM2_supporting; https://gnomad.broadinstitute.org/). 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: PVS1, PM2_supporting, PP1, PP4. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.63
D
BayesDel_noAF
Pathogenic
0.66
CADD
Pathogenic
46
DANN
Uncertain
0.99
Eigen
Pathogenic
1.2
Eigen_PC
Pathogenic
1.1
FATHMM_MKL
Pathogenic
0.99
D
Vest4
0.94
GERP RS
5.9

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-48714179; API