15-48600217-G-A

Position:

• chr15-48600217-G-A

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM2 PP2 PP3_Moderate PP5_Very_Strong

The NM_000138.5(FBN1):​c.364C>T​(p.Arg122Cys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: FBN1 NM_000138.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:13
• Conservation: PhyloP100: 4.61

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]

ACMG classification

Verdict is Pathogenic. Variant got 15 ACMG points.

• PM1: In a disulfide_bond (size 10) in uniprot entity FBN1_HUMAN there are 5 pathogenic changes around while only 1 benign (83%) in NM_000138.5
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), FBN1. . Gene score misZ 5.0644 (greater than the threshold 3.09). Trascript score misZ 8.1787 (greater than threshold 3.09). GenCC has associacion of gene with MASS syndrome, Weill-Marchesani syndrome, geleophysic dysplasia, Shprintzen-Goldberg syndrome, Acromicric dysplasia, familial thoracic aortic aneurysm and aortic dissection, progeroid and marfanoid aspect-lipodystrophy syndrome, ectopia lentis 1, isolated, autosomal dominant, Marfan syndrome, Weill-Marchesani syndrome 2, dominant, isolated ectopia lentis, neonatal Marfan syndrome, stiff skin syndrome.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.933
• PP5: Variant 15-48600217-G-A is Pathogenic according to our data. Variant chr15-48600217-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 16440.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-48600217-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBN1	NM_000138.5	c.364C>T	p.Arg122Cys	missense_variant	5/66	ENST00000316623.10	NP_000129.3
FBN1	NM_001406716.1	c.364C>T	p.Arg122Cys	missense_variant	4/65		NP_001393645.1
FBN1	NM_001406717.1	c.364C>T	p.Arg122Cys	missense_variant	5/9		NP_001393646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBN1	ENST00000316623.10	c.364C>T	p.Arg122Cys	missense_variant	5/66	1	NM_000138.5	ENSP00000325527	P1
FBN1	ENST00000559133.6	c.364C>T	p.Arg122Cys	missense_variant, NMD_transcript_variant	5/67	1		ENSP00000453958
FBN1	ENST00000674301.2	c.364C>T	p.Arg122Cys	missense_variant, NMD_transcript_variant	5/68			ENSP00000501333
FBN1	ENST00000537463.6	c.364C>T	p.Arg122Cys	missense_variant, NMD_transcript_variant	5/31	5		ENSP00000440294

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:13

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Jul 20, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jan 18, 2022	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Introduces a new cysteine residue within a calcium-binding EGF-like domain of the FBN1 gene, which may affect disulfide bonding and is predicted to alter the structure and function of the protein; cysteine substitutions in the calcium-binding EGF-like domains represent the majority of pathogenic missense changes associated with FBN1-related disorders (Collod-Beroud et al., 2003); Reported in ClinVar by several laboratories as pathogenic (ClinVar Variant ID# 16440); This variant is associated with the following publications: (PMID: 19293843, 25053872, 22772377, 19839986, 12446365, 21932315, 21895641, 11700157, 19089573, 17679947, 9452085, 24161884, 24199744, 32123317, 8040326, 34957211, 12938084, 31730815) -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Jan 16, 2024	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics and Genomics, Karolinska University Hospital	Nov 05, 2014	- -

Marfan syndrome Pathogenic:2

Likely pathogenic, no assertion criteria provided	clinical testing	Center for Medical Genetics Ghent, University of Ghent	Nov 07, 2017	- -
Pathogenic, criteria provided, single submitter	clinical testing;curation	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 18, 2011	- -

Familial thoracic aortic aneurysm and aortic dissection Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 28, 2017	The p.R122C pathogenic mutation (also known as c.364C>T), located in coding exon 4 of the FBN1 gene, results from a C to T substitution at nucleotide position 364. The arginine at codon 122 is replaced by cysteine, an amino acid with highly dissimilar properties, and is located in the EGF-like #02 domain. The majority of FBN1 mutations identified to date have involved the substitution or generation of cysteine residues within cbEGF domains (Vollbrandt T et al. J Biol Chem. 2004;279(31):32924-32931). This particular alteration has been detected in numerous unrelated individuals with ectopia lentis (EL) and/or Marfan syndrome (MFS) (e.g., Loeys B et al. Arch. Intern. Med. 2001;161:2447-54; Comeglio P et al. Br J Ophthalmol. 2002;86:1359-62; Jin C et al. Mol. Vis. 2007;13:1280-4; Hung CC et al. Ann. Hum. Genet. 2009;73:559-67; Li J et al. Mol. Vis. 2014;20:1017-24). In addition, this alteration has been reported to segregate with disease in three families (Ståhl-Hallengren C et al. J. Clin. Invest. 1994;94:709-13; Black C et al. Hum. Mutat. 1998;Suppl 1:S198-200; Zadeh N et al. Am. J. Med. Genet. A. 2011;155A:2661-8). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -
Pathogenic, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	May 17, 2019	- -

not specified Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Aug 13, 2018

The FBN1 c.364C>T; p.Arg122Cys variant (rs137854467) has been reported in multiple families with clinical symptoms suggestive of Marfan syndrome, and is strongly associated with ectopia lentis (Black 1998, Comeglio 2002, Jin 2007, Loeys 2001, Stahl-Hallengran 1994). It is reported in ClinVar as pathogenic (Variation ID: 16440) and is absent from general population databases (1000 Genomes Project, Exome Variant Server, and Genome Aggregation Database), indicating it is not a common polymorphism. The variant changes an arginine in an EGF-like domain into a cysteine residue, which meets the revised Ghent nosology criteria of a causative Marfan syndrome variant (Loeys 2010). Based on available information, this variant is considered to be pathogenic. References: Black C et al. Correlation of a recurrent FBN1 mutation (R122C) with an atypical familial Marfan syndrome phenotype. Hum Mutat. 1998; Suppl 1:S198-200. Comeglio P et al. Identification of FBN1 gene mutations in patients with ectopia lentis and marfanoid habitus. Br J Ophthalmol. 2002; 86(12):1359-62. Jin C et al. Novel FBN1 mutations associated with predominant ectopia lentis and marfanoid habitus in Chinese patients. Mol Vis. 2007; 13:1280-4. Loeys B et al. Genotype and phenotype analysis of 171 patients referred for molecular study of the fibrillin-1 gene FBN1 because of suspected Marfan syndrome. Arch Intern Med. 2001; 2001 Nov 12;161(20):2447-54. Loeys B et al. The revised Ghent nosology for the Marfan syndrome. J Med Genet. 2010; 47(7):476-85. Stahl-Hallengren C et al. An extra cysteine in one of the non-calcium-binding epidermal growth factor-like motifs of the FBN1 polypeptide is connected to a novel variant of Marfan syndrome. J Clin Invest. 1994; 94(2):709-13. -

Marfan syndrome, atypical Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Aug 01, 1994

- -

Arachnodactyly;C0023316:Lens subluxation;C0240635:High palate;C0340643:Aortic dissection Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2017

- -

Marfan syndrome;C4707243:Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Oct 13, 2023

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 122 of the FBN1 protein (p.Arg122Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with ectopia lentis and/or Marfan syndrome (PMID: 8040326, 9452085, 11700157, 12446365, 17679947, 21895641, 21932315, 22772377, 25053872). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 16440). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt FBN1 protein function. For these reasons, this variant has been classified as Pathogenic. -

Marfan syndrome;C0265287:Acromicric dysplasia;C1858556:MASS syndrome;C1861456:Stiff skin syndrome;C1869115:Weill-Marchesani syndrome 2, dominant;C3280054:Geleophysic dysplasia 2;C3541518:Ectopia lentis 1, isolated, autosomal dominant;C4310796:Progeroid and marfanoid aspect-lipodystrophy syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Aug 23, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.88
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.32
CADD	Pathogenic	34
DANN	Pathogenic	1.0
Eigen	Pathogenic	0.84
Eigen_PC	Pathogenic	0.82
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.97	D
M_CAP	Pathogenic	0.32	D
MetaRNN	Pathogenic	0.93	D
MetaSVM	Uncertain	0.44	D
MutationTaster	Benign	1.0	A
PrimateAI	Pathogenic	0.84	D
PROVEAN	Uncertain	-4.2	D
REVEL	Uncertain	0.60
Sift	Benign	0.034	D
Sift4G	Benign	0.10	T
Vest4		0.88
MutPred		0.76		Loss of solvent accessibility (P = 0.4011);
MVP		0.92
MPC		1.7
ClinPred		0.98	D
GERP RS		6.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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

Other links and lift over

dbSNP: rs137854467; hg19: chr15-48892414; COSMIC: COSV57315297;