chr5-128349396-G-T

Variant names:

• chr5-128349396-G-T
• NM_001999.4:c.2940C>A

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_001999.4(FBN2):​c.2940C>A​(p.Cys980*) variant causes a stop gained change involving the alteration of a non-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 Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. C980C) has been classified as Benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: FBN2 NM_001999.4 stop_gained
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.669

Genes affected

FBN2 (HGNC:3604): (fibrillin 2) The protein encoded by this gene is a component of connective tissue microfibrils and may be involved in elastic fiber assembly. Mutations in this gene cause congenital contractural arachnodactyly. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Pathogenic. Variant got 10 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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBN2	NM_001999.4	c.2940C>A	p.Cys980*	stop_gained	Exon 23 of 65	ENST00000262464.9	NP_001990.2
FBN2	XM_017009228.3	c.2787C>A	p.Cys929*	stop_gained	Exon 22 of 64		XP_016864717.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBN2	ENST00000262464.9	c.2940C>A	p.Cys980*	stop_gained	Exon 23 of 65	1	NM_001999.4	ENSP00000262464.4
FBN2	ENST00000508989.5	c.2841C>A	p.Cys947*	stop_gained	Exon 22 of 33	2		ENSP00000425596.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital contractural arachnodactyly Uncertain:1

Sep 21, 2024

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as VUS-3A. Following criteria are met: 0105 - The mechanism of disease for this gene is not clearly established. However, dominant negative is a likely mechanism of disease (PMID: 31316167). Loss of function has recently been suggested as a possible mechanism of disease, although additional functional studies are required to confirm this hypothesis (PMID: 20301560). (I) 0107 - This gene is associated with autosomal dominant disease. There are also rare reports of a severe form of congenital contractural arachnodactyly due to biallelic variants (PMID: 33571691). (I) 0115 - Variants in this gene are known to have variable expressivity. Intrafamilial and interfamilial variability are both well-reported for this gene (PMID: 20301560). (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0710 - Other null variants comparable to the one identified in this case have inconclusive previous evidence for pathogenicity. Four NMD-predicted variants have been classified as likely pathogenic and pathogenic in ClinVar. Where additional information was provided, these variants were identified in individuals with contractures or multiple spontaneous pneumothorax (ClinVar, GeneDx personal communication, Greenwood Genetic Centre personal communication). Additionally, p.(Glu1328X) was also identified in the proband's maternal grandmother who has contractures (Greenwood Genetic Centre personal communication). However, it should be noted that the vast majority of NMD-predicted variants in ClinVar are described as variants of uncertain significance, while only a single NMD-predicted variant suggested to result in aberrant splicing was identified in the literature in an individual with congenital contractural arachnodactyly (PMID: 11754102). (I) 0807 - This variant has no previous evidence of pathogenicity. (I) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.55	D
BayesDel_noAF	Pathogenic	0.55
CADD	Pathogenic	35
DANN	Uncertain	0.99
Eigen	Uncertain	0.28
Eigen_PC	Benign	0.090
FATHMM_MKL	Uncertain	0.77	D
Vest4		0.91
GERP RS		1.6

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-127685088;