rs727503057

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Pathogenic. The variant received 17 ACMG points: 17P and 0B. PM1PM2PP2PP3_StrongPP5_Very_Strong

The NM_000138.5(FBN1):c.1879C>T(p.Arg627Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,614,046 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R627H) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)

Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

FBN1
NM_000138.5 missense

Scores

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:14

Conservation

PhyloP100: 8.15

Publications

17 publications found

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 Gene-Disease associations (from GenCC):

familial thoracic aortic aneurysm and aortic dissection
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet
Marfan syndrome
Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp, ClinGen, G2P, PanelApp Australia, Orphanet, Ambry Genetics
Acromicric dysplasia
Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics
progeroid and marfanoid aspect-lipodystrophy syndrome
Inheritance: AD Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet
stiff skin syndrome
Inheritance: AD Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
Weill-Marchesani syndrome 2, dominant
Inheritance: AD Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
geleophysic dysplasia
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
isolated ectopia lentis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
neonatal Marfan syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Weill-Marchesani syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
ectopia lentis 1, isolated, autosomal dominant
Inheritance: AD Classification: LIMITED Submitted by: G2P
Shprintzen-Goldberg syndrome
Inheritance: AD, Unknown Classification: LIMITED, NO_KNOWN Submitted by: ClinGen, Labcorp Genetics (formerly Invitae)

FBN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 17 ACMG points.

PM1

In a hotspot region, there are 22 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 13 uncertain in NM_000138.5

PM2

Very rare variant in population databases, with high coverage;

PP2

Missense variant in the FBN1 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 1311 curated pathogenic missense variants (we use a threshold of 10). The gene has 112 curated benign missense variants. Gene score misZ: 5.0644 (above the threshold of 3.09). Trascript score misZ: 8.1787 (above the threshold of 3.09). GenCC associations: The gene is linked to Marfan syndrome, Weill-Marchesani syndrome 2, dominant, progeroid and marfanoid aspect-lipodystrophy syndrome, geleophysic dysplasia, Shprintzen-Goldberg syndrome, stiff skin syndrome, familial thoracic aortic aneurysm and aortic dissection, isolated ectopia lentis, ectopia lentis 1, isolated, autosomal dominant, Acromicric dysplasia, neonatal Marfan syndrome, Weill-Marchesani syndrome.

PP3

MetaRNN computational evidence supports a deleterious effect, 0.955

PP5

Variant 15-48505106-G-A is Pathogenic according to our data. Variant chr15-48505106-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 163480.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.1879C>T	p.Arg627Cys	missense_variant	Exon 16 of 66	ENST00000316623.10	NP_000129.3
FBN1	NM_001406716.1 link	c.1879C>T	p.Arg627Cys	missense_variant	Exon 15 of 65		NP_001393645.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBN1	ENST00000316623.10 link	c.1879C>T	p.Arg627Cys	missense_variant	Exon 16 of 66	1	NM_000138.5	ENSP00000325527.5

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152190

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

6.84e-7

AC:

AN:

1461856

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

727228

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33480

American (AMR)

AF:

0.00

AC:

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26134

East Asian (EAS)

AF:

0.00

AC:

AN:

39696

South Asian (SAS)

AF:

0.00

AC:

AN:

86258

European-Finnish (FIN)

AF:

0.00

AC:

AN:

53418

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

8.99e-7

AC:

AN:

1111982

Other (OTH)

AF:

0.00

AC:

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152190

Hom.:

Cov.:

AF XY:

0.0000134

AC XY:

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41442

American (AMR)

AF:

0.00

AC:

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5204

South Asian (SAS)

AF:

0.00

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.00

AC:

AN:

316

European-Non Finnish (NFE)

AF:

0.0000147

AC:

AN:

68026

Other (OTH)

AF:

0.00

AC:

AN:

2094

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.00000497

Hom.:

Bravo

AF:

0.00000378

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:14

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Marfan syndrome

Pathogenic:5

Nov 07, 2017

Center for Medical Genetics Ghent, University of Ghent

Significance:Likely pathogenic

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Oct 30, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The p.Arg627Cys variant in FBN1 has been reported in 1 individual with Ectopia L entis (Jin 2007) and 9 individuals with Marfan syndrome, including 1 individual in whom the variant occurred de novo. The variant segregated with Marfan syndrom e in 9 affected relatives from 4 families (Hayward 1994, Halliday 2002, Rommel 2 005, Waldmuller 2007, Miyazawa 2007, Stheneur 2009, Attanasio 2013). In one of t hese families, this variant was also observed in 3 asymptomatic individuals; how ever, they were not clinically evaluated for the study (Miyazawa 2007). The vari ant was absent from large population studies. In vitro functional studies provid e some evidence that this variant may impact protein function (Kirschner 2011). However, these types of assays may not accurately represent biological function. In summary, the p.Arg627Cys variant meets our criteria to be classified as path ogenic for Marfan syndrome in an autosomal dominant manner (http://www.partners. org/personalizedmedicine/LMM) based upon segregation studies, absence from contr ols, and functional evidence. -

Juno Genomics, Hangzhou Juno Genomics, Inc

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

PM2_Supporting+PP2+PS3_Moderate+PS4_Moderate+PP1+PP4+PM6 -

Jul 19, 2023

Illumina Laboratory Services, Illumina

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The FBN1 c.1879C>T (p.Arg627Cys) missense variant has been observed in individuals with a phenotype consistent with Marfan syndrome and has been shown to segregate with disease across multiple families (PMID: 16220557; 17418587; 17503327; 17679947; 25644172; 32431097). A functional study conducted in human cell lines demonstrated that this variant impacts protein function (PMID: 21784848). This variant is not observed at a significant frequency in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. This variant has been classified as pathogenic by at least three submitters in ClinVar. Based on the available evidence, the c.1879C>T (p.Arg627Cys) variant is classified as pathogenic for Marfan syndrome. -

Aug 19, 2019

Petrovsky National Research Centre of Surgery, The Federal Agency for Scientific Organizations

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:curation

The p.Arg627Cys is a well known missense variant reported in various individuals (PMID: 8004112, 16220557, 23684891, 12161601, 17418587, 17679947, 25644172, 20591885; DOI: 10.3760/cma.j.issn.1003-9406.2019.06.008), with a frequency of A=0.00001 (1/125568, TOPMED)(ExAC no frequency). This variant has been reported several times in ClinVar (Variation ID: 163480) with a well-established Pathogenic classification. The p.Arg627Cys substitution occurs in the cbEGF-like domain. In FBN1 gene missense affecting/creating cysteine residues is one of the criteria for pathogenic mutations (PMID: 20591885). -

Familial thoracic aortic aneurysm and aortic dissection

Pathogenic:3

Dec 23, 2019

CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Apr 10, 2018

Ambry Genetics

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

The p.R627C pathogenic mutation (also known as c.1879C>T), located in coding exon 15 of the FBN1 gene, results from a C to T substitution at nucleotide position 1879. The arginine at codon 627 is replaced by cysteine, an amino acid with highly dissimilar properties, and is located in the cb EGF-like #06 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 mutation has been detected in multiple unrelated patients with Marfan syndrome (MFS), MFS-related features, or ectopia lentis and was also reported to occur de novo in one individual with MFS (Hayward C et al. Hum Mol Genet. 1994;3(2):373-5; Halliday DJ et al. J Med Genet. 2002;39(8):589-93; Rommel K et al. Hum Mutat. 2005;26(6):529-39; Jin C et al. Mol Vis. 2007;13:1280-4; Waldmüller S et al. Eur J Cardiothorac Surg. 2007;31(6):970-5; Stheneur C et al. Eur J Hum Genet. 2009;17(9):1121-8; Campens L et al. Orphanet J Rare Dis. 2015;10:9). This alteration segregated with disease in one family with MFS, although some carrier individuals appeared asymptomatic (Miyazawa H et al. Am J Hum Genet. 2007;80(6):1090-102). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Apr 06, 2021

Color Diagnostics, LLC DBA Color Health

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This missense variant replaces arginine with cysteine at codon 627 of the FBN1 protein. This variant creates a cysteine residue in a functionally important calcium-binding EGF-like motif and is expected to disrupt normal disulfide bridge formation and affect protein stability. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Functional studies have shown this variant to increase susceptibility to proteolytic degradation (PMID: 15161917, 21784848). This variant has been reported in individuals affected with Marfan syndrome (PMID: 8004112, 16220557, 17503327, 23684891, 31055806, 32431097), suspected Marfan syndrome (PMID: 17679947), ectopia lentis (PMID: 12161601, 33576469), and thoracic aortic aneurysm and dissection (PMID: 17418587, 25644172). This variant has been shown to segregate with disease in four unrelated families (PMID: 17503327, 8004112, 16220557, 32431097). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. -

not provided

Pathogenic:3

Sep 01, 2021

CeGaT Center for Human Genetics Tuebingen

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 24, 2022

GeneDx

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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).; Published functional studies demonstrate a damaging effect as fibrillin protein harboring p.(R627C) is more susceptible to proteolytic degradation by a variety of proteases (Vollbrandt et al., 2004; Kirschner et al., 2011); This variant is associated with the following publications: (PMID: 23684891, 27647783, 15161917, 32431097, 8004112, 17679947, 25644172, 19293843, 12161601, 17418587, 24941995, 31055806, 32209317, 33083483, 12938084, 33059708, 33576469, 21784848, 17503327, 16220557) -

Jul 13, 2022

Clinical Genetics Laboratory, Skane University Hospital Lund

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Marfan Syndrome/Loeys-Dietz Syndrome/Familial Thoracic Aortic Aneurysms and Dissections

Pathogenic:1

May 31, 2021

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Variant summary: FBN1 c.1879C>T (p.Arg627Cys) results in a non-conservative amino acid change located in the cb EGF-like #06 domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. Missense affecting/creating cysteine residues and affecting the conserved residues of the EGF-consensus sequence are among the criteria considered as causal in making a diagnosis of Marfan syndrome The variant was absent in 251538 control chromosomes. c.1879C>T has been widely reported in the literature in multiple individuals affected with features of Marfan Syndrome and has subsequently been cited by others (example, Hayward_1994, Hayward_1997, Rommel_2005, Miyazawa_2007, Waldmuller_2007, Jin_2007, Halliday_2002). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in enhanced proteolytic susceptibility to a variety of proteases (example, Vollbrandt_2004). Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic (n=3)/likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -

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

Pathogenic:1

Mar 01, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 627 of the FBN1 protein (p.Arg627Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of Marfan syndrome (PMID: 8004112, 12161601, 16220557, 17418587, 17679947, 23684891, 25644172). ClinVar contains an entry for this variant (Variation ID: 163480). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on FBN1 protein function. Experimental studies have shown that this missense change affects FBN1 function (PMID: 15161917, 21784848). 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

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

FBN1 NM_000138.4 exon 15 p.Arg627Cys (c.1879C>T): This variant has been reported in the literature in at least 10 individuals with a diagnosis, clinical suspicion or primary feature of Marfan syndrome, one of whom was reported as a de novo (Hayward 1994 PMID:8004112, Halliday 2002 PMID:12161601, Rommel 2005 PMID:16220557, Jin 2007 PMID:17679947, Miyazawa 2007 PMID:17503327, Waldmuller 2007 PMID:17418587, Stheneur 2009 PMID:19293843, Attanasio 2013 PMID:23684891, Campens 2015 PMID:25644172). This variant segregated with disease in at least 6 affected family members (Rommel 2005 PMID:16220557, Miyazawa 2007 PMID:17503327). This variant is not present in large control databases but is present in Clinvar, with several labs classifying this variant as pathogenic or likely pathogenic (Variation ID:163480). Evolutionary conservation and computational predictive tools suggest that this variant may impact the protein. In vitro functional studies also support that this variant will impact the protein (Vollbrandt 2004 PMID:15161917, Kirschner 2011 PMID:21784848). Of note, this variant is predicted to affect a cysteine residue. Cysteine in the FBN1 gene is reported to have important functional relevance; variants that involve a cysteine residue are reported to be particularly significant (Dietz, PMID: 20301510). In summary, this variant is classified as pathogenic based on the data above (multiple probands, segregation studies, presence of a de novo, absence from controls and impact to protein). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.53

BayesDel_addAF

Pathogenic

0.34

BayesDel_noAF

Pathogenic

0.26

CADD

Pathogenic

(source)

DANN

Pathogenic

1.0

Eigen

Pathogenic

0.83

Eigen_PC

Pathogenic

0.78

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Pathogenic

0.98

M_CAP

Uncertain

0.16

MetaRNN

Pathogenic

0.96

MetaSVM

Uncertain

0.15

PhyloP100

8.2

PrimateAI

Uncertain

0.72

PROVEAN

Uncertain

-3.9

REVEL

Pathogenic

0.68

Sift

Benign

0.045

Sift4G

Benign

0.094

Vest4

0.87

MutPred

0.83

Gain of catalytic residue at V629 (P = 0.1096);

MVP

0.88

MPC

2.1

ClinPred

0.97

GERP RS

5.7

Mutation Taster

=52/48

disease causing (ClinVar)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over