dbSNP rs113249837: FBN1:p.Arg1790* (chr15-48456691-G-A) – ACMG Classification: Pathogenic (18 pts)

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_000138.5(FBN1):c.5368C>T(p.Arg1790*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,698 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

FBN1
NM_000138.5 stop_gained

Scores

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:9

Conservation

PhyloP100: -0.372

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]

FBN1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1

Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 15-48456691-G-A is Pathogenic according to our data. Variant chr15-48456691-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 42382.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBN1	NM_000138.5 link	c.5368C>T	p.Arg1790*	stop_gained	Exon 44 of 66	ENST00000316623.10	NP_000129.3	P35555
FBN1	NM_001406716.1 link	c.5368C>T	p.Arg1790*	stop_gained	Exon 43 of 65		NP_001393645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBN1	ENST00000316623.10 link	c.5368C>T	p.Arg1790*	stop_gained	Exon 44 of 66	1	NM_000138.5	ENSP00000325527.5		P35555

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461698

Hom.:

Cov.:

AF XY:

0.00000138

AC XY:

AN XY:

727162

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.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Marfan syndrome

Pathogenic:6

Nov 07, 2017

Center for Medical Genetics Ghent, University of Ghent

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Nov 08, 2023

All of Us Research Program, National Institutes of Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.5368C>T (p.Arg1790*) variant in of the FBN1 gene creates a premature termination codon that is predicted to lead to an absent or truncated protein product. This variant has been identified in numerous individuals (>10) affected with clinical features of Marfan syndrome (PMID:16222657, 19618372, 16835936, 19533785, 19863550, 19293843, 17627385, 26787436). Loss of function variants are known to be pathogenic for FBN1 (PMID: 17701892, 30286810, 21063442, 17657824, 19293843). Truncating variants downstream of this variant are reported in individuals with Marfan syndrome (PMID: 27906200, 31730815, 24793577). This variant is found to be absent in the general population database (gnomAD) and interpreted as pathogenic by several submitters in the ClinVar database (ClinVar ID: 42382). Therefore, the c.5368C>T (p.Arg1790*) variant in the FBN1 gene is classified as pathogenic. -

Oct 05, 2021

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PVS1, PM2, PP5 -

Nov 01, 2016

Center for Human Genetics, Inc, Center for Human Genetics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 01, 2021

Centre of Medical Genetics, University of Antwerp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: research

PM2, PVS1, PP4 -

Jun 05, 2023

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.Arg1790X variant in FBN1 has been reported in 6 individuals with clinically diagnosed Marfan Syndrome (fulfilled Ghent criteria) and 3 individuals with clinical features of Marfan-like phenotypes (Marfan syndrome suspected, but not fulfilling Ghent criteria; Arbustini 2005 PMID: 16222657, Sakai 2006 PMID: 16835936, Chung 2009 PMID: 19533785, Magyar 2009 PMID: 19618372, Yoo 2010 PMID: 19863550, Zhurayev 2016 PMID: 27724990, Stengl 2020 PMID: 33059708, Meester 2022 PMID: 35058154. This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 42382) and was absent from large population studies (gnomAD, v.3.1.2). This nonsense variant leads to a premature termination codon at position 1790, which is predicted to lead to a truncated or absent protein. Heterozygous loss of function of the FBN1 gene is an established disease mechanism of autosomal dominant Marfan syndrome. In summary, this variant meets criterion to be classified as pathogenic for autosomal dominant Marfan Syndrome. ACMG/AMP Criteria applied: PM2_supporting, PSV1, PS4_Moderate. -

Familial thoracic aortic aneurysm and aortic dissection

Pathogenic:1

Jul 25, 2022

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.R1790* pathogenic mutation (also known as c.5368C>T), located in coding exon 43 of the FBN1 gene, results from a C to T substitution at nucleotide position 5368. This alteration changes the amino acid from an arginine to a stop codon within coding exon 43. This mutation has been reported in numerous Marfan syndrome cohorts (e.g., Arbustini E et al. Hum Mutat. 2005;26(5):494; Magyar I et al. Hum. Mutat. 2009;30:1355-64; Stheneur C et al. Eur. J. Hum. Genet. 2009;17:1121-8; Franken R et al. Eur. Heart J, 2016;37:3285-3290). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -

not provided

Pathogenic:1

Mar 01, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Has been reported several times in association with Marfan syndrome or other Marfan-like syndrome in unrelated patients referred for genetic testing at GeneDx and in the published literature (Arbustini et al., 2005; Sakai et al., 2006; Howarth et al., 2007; Chung et al., 2009; Magyar et al., 2009; Yoo et al., 2010; Stengl et al., 2020); Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 16222657, 19533785, 16835936, 17627385, 19293843, 26787436, 19863550, 19618372, 33059708) -

Marfan syndrome;C4707243:Familial thoracic aortic aneurysm and aortic dissection

Pathogenic:1

Jun 06, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Arg1790*) in the FBN1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FBN1 are known to be pathogenic (PMID: 17657824, 19293843). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with Marfan syndrome (PMID: 16222657, 16835936, 19533785, 19618372, 19863550, 26787436). ClinVar contains an entry for this variant (Variation ID: 42382). For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.63

BayesDel_noAF

Pathogenic

0.56

CADD

Pathogenic

DANN

Uncertain

0.99

Eigen

Uncertain

0.22

Eigen_PC

Benign

-0.035

FATHMM_MKL

Benign

0.70

Vest4

1.0

GERP RS

-4.1

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over