chr15-48463227-ACTT-A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2PM4_SupportingPP5_Very_Strong

The NM_000138.5(FBN1):​c.5076_5078delAAG​(p.Arg1692del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,724 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★★).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

FBN1
NM_000138.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Pathogenic reviewed by expert panel P:7U:2

Conservation

PhyloP100: 8.02
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.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_000138.5. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 15-48463227-ACTT-A is Pathogenic according to our data. Variant chr15-48463227-ACTT-A is described in ClinVar as [Pathogenic]. Clinvar id is 520496.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr15-48463227-ACTT-A is described in Lovd as [Likely_pathogenic]. Variant chr15-48463227-ACTT-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FBN1NM_000138.5 linkc.5076_5078delAAG p.Arg1692del disruptive_inframe_deletion Exon 42 of 66 ENST00000316623.10 NP_000129.3 P35555
FBN1NM_001406716.1 linkc.5076_5078delAAG p.Arg1692del disruptive_inframe_deletion Exon 41 of 65 NP_001393645.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FBN1ENST00000316623.10 linkc.5076_5078delAAG p.Arg1692del disruptive_inframe_deletion Exon 42 of 66 1 NM_000138.5 ENSP00000325527.5 P35555

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461724
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
727170
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:7Uncertain:2
Revision: reviewed by expert panel
LINK: link

Submissions by phenotype

not provided Pathogenic:3
Dec 15, 2023
GeneDx
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

In-frame deletion of one arginine amino acid in a non-repeat region; Not observed in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 17657824, 32679894, 33844962, 27146836, 34281902, 34008892) -

Jul 03, 2017
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

May 10, 2024
Mayo Clinic Laboratories, Mayo Clinic
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PP4, PM2, PM4, PM6_supporting, PS4 -

Marfan syndrome Pathogenic:2Uncertain:1
Aug 22, 2024
ClinGen FBN1 Variant Curation Expert Panel, ClinGen
Significance: Pathogenic
Review Status: reviewed by expert panel
Collection Method: curation

NM_000138.5 c.5076_5078del is a deletion of 3 nucleotides in FBN1 predicted to cause the in-frame deletion of arginine at amino acid 1692 (p.Arg1692del) (PM4). This variant has been identified in a patient with thoracic aortic aneurysm and dissection (TAAD), ectopia lentis (EL), and a systemic score ≥ 7, which is a specific phenotype for Marfan syndrome (MFS) (PP4; University of Tokyo internal data). It has been identified in at least 5 other unrelated individuals meeting the revised Ghent criteria for a clinical diagnosis of MFS (PS4; PMIDs: 27146836, 32679894; University of Tokyo & Invitae internal data); in one of these individuals with TAAD, EL, and a systemic score of 10, a phenotype highly specific to FBN1, it was found to be inherited from an apparently mosaic and unaffected parent (PM6; Invitae internal data). This variant has also been identified in at least 4 additional unrelated individuals who do not meet clinical diagnostic criteria but have phenotypes consistent with MFS, including EL or TAAD with or without systemic features (PMIDs: 17657824, 29144511, 33844962; Bichat & Invitae internal data). In two families, the variant was found to segregate with disease in a similarly affected family member (PP1; Bichat & University of Tokyo internal data). It is present in gnomAD in 1 individual of European (non-Finnish) ancestry, with a frequency of 0.00009% (1/1111872 alleles) (PM2_supporting; https://gnomad.broadinstitute.org/, v4.0.0). 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: PS4, PM4, PM6, PP1, PP4, PM2_supporting. -

Oct 01, 2021
Laboratory of Medical Genetics, National & Kapodistrian University of Athens
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

PM1, PM2, PM4, PP3 -

Nov 07, 2017
Center for Medical Genetics Ghent, University of Ghent
Significance: Uncertain significance
Review Status: flagged submission
Collection Method: clinical testing

- -

Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1Uncertain:1
Aug 30, 2019
Ambry Genetics
Significance: Uncertain significance
Review Status: flagged submission
Collection Method: clinical testing

The c.5076_5078delAAG variant (also known as p.R1692del) is located in coding exon 41 of the FBN1 gene. This variant results from an in-frame AAG deletion at nucleotide positions 5076 to 5078. This results in the in-frame deletion of an arginine at codon 1692, and is located in the TGFB#05 domain. This variant (also described as c.5074_5076delAGA) was first reported in a child with ectopia lentis and no other clinical findings of Marfan syndrome (MFS) at the time of evaluation (Comeglio P et al. Hum. Mutat., 2007 Sep;28:928). This variant has also been detected in an individual meeting clinical diagnostic criteria for MFS, as well as in his asymptomatic father (Poninska JK et al. J Transl Med, 2016 05;14:115). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Jul 02, 2021
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario
Significance: Likely pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Marfan syndrome;C4707243:Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1
Sep 17, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant, c.5076_5078del, results in the deletion of 1 amino acid(s) of the FBN1 protein (p.Arg1692del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with Marfan syndrome (PMID: 17657824, 27146836, 32679894; internal data). ClinVar contains an entry for this variant (Variation ID: 520496). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1555396789; hg19: chr15-48755424; API