rs397515825

Variant names:

• chr15-48537785-TA-T
• rs397515825
• NM_000138.5:c.561delT

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000138.5(FBN1):​c.561delT​(p.Phe187LeufsTer3) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FBN1 NM_000138.5 frameshift
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.849

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 12 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 15-48537785-TA-T is Pathogenic according to our data. Variant chr15-48537785-TA-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 42389.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBN1	NM_000138.5	c.561delT	p.Phe187LeufsTer3	frameshift_variant	Exon 7 of 66	ENST00000316623.10	NP_000129.3
FBN1	NM_001406716.1	c.561delT	p.Phe187LeufsTer3	frameshift_variant	Exon 6 of 65		NP_001393645.1
FBN1	NM_001406717.1	c.561delT	p.Phe187LeufsTer3	frameshift_variant	Exon 7 of 9		NP_001393646.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBN1	ENST00000316623.10	c.561delT	p.Phe187LeufsTer3	frameshift_variant	Exon 7 of 66	1	NM_000138.5	ENSP00000325527.5
FBN1	ENST00000559133.6	n.561delT		non_coding_transcript_exon_variant	Exon 7 of 67	1		ENSP00000453958.2
FBN1	ENST00000537463.6	n.561delT		non_coding_transcript_exon_variant	Exon 7 of 31	5		ENSP00000440294.2
FBN1	ENST00000674301.2	n.561delT		non_coding_transcript_exon_variant	Exon 7 of 68			ENSP00000501333.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Marfan syndrome Pathogenic:1

Feb 17, 2014

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Phe187fs variant in FBN1 has now been identified by our laboratory in two in dividuals with clinical features of Marfan syndrome, and was shown to have occur red de novo in one of these individuals (LMM unpublished data). This frameshift variant is predicted to alter the protein?s amino acid sequence beginning at pos ition 187 and lead to a premature termination codon 3 amino acids downstream. Th is alteration is then predicted to lead to a truncated or absent protein. In sum mary, this variant is likely to be pathogenic, though additional studies are req uired to fully establish its clinical significance. -

Computational scores

Source: dbNSFP v4.3

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: rs397515825; hg19: chr15-48829982;