15-48613055-A-T

Position:

• chr15-48613055-A-T

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5_Moderate

The ENST00000316623.10(FBN1):​c.202T>A​(p.Cys68Ser) variant causes a missense change involving the alteration of a conserved nucleotide. 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C68R) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FBN1 ENST00000316623.10 missense
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 8.60

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 13 ACMG points.

• PM1: In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 7 uncertain in ENST00000316623.10
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr15-48613054-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 649153.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• 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, 0.948
• PP5: Variant 15-48613055-A-T is Pathogenic according to our data. Variant chr15-48613055-A-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 520234.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr15-48613055-A-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBN1	NM_000138.5	c.202T>A	p.Cys68Ser	missense_variant	3/66	ENST00000316623.10	NP_000129.3
FBN1	NM_001406716.1	c.202T>A	p.Cys68Ser	missense_variant	2/65		NP_001393645.1
FBN1	NM_001406717.1	c.202T>A	p.Cys68Ser	missense_variant	3/9		NP_001393646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBN1	ENST00000316623.10	c.202T>A	p.Cys68Ser	missense_variant	3/66	1	NM_000138.5	ENSP00000325527	P1
FBN1	ENST00000559133.6	c.202T>A	p.Cys68Ser	missense_variant, NMD_transcript_variant	3/67	1		ENSP00000453958
FBN1	ENST00000674301.2	c.202T>A	p.Cys68Ser	missense_variant, NMD_transcript_variant	3/68			ENSP00000501333
FBN1	ENST00000537463.6	c.202T>A	p.Cys68Ser	missense_variant, NMD_transcript_variant	3/31	5		ENSP00000440294

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 17, 2015

The p.C68S variant (also known as c.202T>A), located in coding exon 2 of the FBN1 gene, results from a T to A substitution at nucleotide position 202. The cysteine at codon 68 is replaced by serine, an amino acid with dissimilar properties. In one study, this variant was detected in an individual with classicalMarfansyndrome, and it was ade novooccurrence (Stheneuret al.Eur J Hum Genet.2009;17(9):1121-1128). In addition, c.203G>C, another variant that results in the same p.C68S substitution in thiscysteine-richregion, was detected in an individual withectopialentis, minor skeletal system involvement and skin involvement (ComeglioP et al.HumMutat.2007;28(9):928). An alteration at the same amino acid position, p.C68F (also known as c.203G>T), was also reported in a Chinese patient presented with ectopia lentis, myopia, atrial septal defect, mild mitral valve regurgitation, pectuscarinatum, arachnodactyly and dental crowding (Jin C et al, Mol. Vis. 2007 ; 13():1280-4).This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6493 samples (12986 alleles) with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.42	D
BayesDel_noAF	Pathogenic	0.36
CADD	Pathogenic	29
DANN	Uncertain	0.99
Eigen	Uncertain	0.63
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.92	D
M_CAP	Pathogenic	0.35	D
MetaRNN	Pathogenic	0.95	D
MetaSVM	Uncertain	0.073	D
MutationTaster	Benign	1.0	D
PrimateAI	Pathogenic	0.87	D
PROVEAN	Pathogenic	-7.1	D
REVEL	Pathogenic	0.82
Sift	Pathogenic	0.0	D
Sift4G	Uncertain	0.0040	D
Vest4		0.94
MutPred		0.80		Gain of ubiquitination at K72 (P = 0.068);
MVP		0.97
MPC		1.6
ClinPred		1.0	D
GERP RS		5.1

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

Other links and lift over

dbSNP: rs113604459; hg19: chr15-48905252;