rs869069617

Variant names:

• chr1-156130709-C-T
• rs869069617
• NM_170707.4:c.449C>T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_001406993.1(LMNA):​c.-110C>T variant causes a 5 prime UTR premature start codon gain 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 Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: LMNA NM_001406993.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:3
• Conservation: PhyloP100: 7.91

Genes affected

LMNA (HGNC:6636): (lamin A/C) The protein encoded by this gene is part of the nuclear lamina, a two-dimensional matrix of proteins located next to the inner nuclear membrane. The lamin family of proteins make up the matrix and are highly conserved in evolution. During mitosis, the lamina matrix is reversibly disassembled as the lamin proteins are phosphorylated. Lamin proteins are thought to be involved in nuclear stability, chromatin structure and gene expression. Vertebrate lamins consist of two types, A and B. Alternative splicing results in multiple transcript variants. Mutations in this gene lead to several diseases: Emery-Dreifuss muscular dystrophy, familial partial lipodystrophy, limb girdle muscular dystrophy, dilated cardiomyopathy, Charcot-Marie-Tooth disease, and Hutchinson-Gilford progeria syndrome. [provided by RefSeq, May 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.875

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LMNA	NM_170707.4	c.449C>T	p.Thr150Ile	missense_variant	Exon 2 of 12	ENST00000368300.9	NP_733821.1
LMNA	NM_005572.4	c.449C>T	p.Thr150Ile	missense_variant	Exon 2 of 10	ENST00000677389.1	NP_005563.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMNA	ENST00000368300.9	c.449C>T	p.Thr150Ile	missense_variant	Exon 2 of 12	1	NM_170707.4	ENSP00000357283.4
LMNA	ENST00000677389.1	c.449C>T	p.Thr150Ile	missense_variant	Exon 2 of 10		NM_005572.4	ENSP00000503633.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Cardiomyopathy Pathogenic:1

May 16, 2023

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

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Uncertain:1

Apr 09, 2015

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant classified as Uncertain Significance - Favor Pathogenic. The p.Thr150Ile variant in LMNA has been previously reported in 1 individual with DCM (Hirtle-L ewis 2013) and was absent from large population studies. In addition, another di sease-causing variant at this position (p.Thr150Pro) has been reported in 2 indi viduals with Emery-Dreifuss muscular dystrophy with conduction system disease (F elice 2000, Schamer 2011) and was identified by our laboratory in 4 family membe rs with clinical features of LMNA-related cardiomyopathy (DCM, muscle weakness, and/or conduction system disease; LMM unpublished data), suggesting that a chang e at this position may not be tolerated. Computational prediction tools and cons ervation analysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, whi le there is some suspicion for a pathogenic role, the clinical significance of t he p.Thr150Ile variant is uncertain. -

not provided Uncertain:1

Aug 01, 2023

GeneDx

Significance: Uncertain significance

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; Reported in individuals with dilated cardiomyopathy (Hirtle-Lewis et al., 2013; Chami et al., 2014); This variant is associated with the following publications: (PMID: 24037902, 1300868, 30402260, 25448463, 10939567, 20848652, 10908904) -

Cardiovascular phenotype Uncertain:1

Jan 18, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.T150I variant (also known as c.449C>T), located in coding exon 2 of the LMNA gene, results from a C to T substitution at nucleotide position 449. The threonine at codon 150 is replaced by isoleucine, an amino acid with similar properties. This variant has been detected in individuals from dilated cardiomyopathy cohorts (Hirtle-Lewis M et al. Clin Cardiol, 2013 Oct;36:628-33; Chami N et al. Can J Cardiol, 2014 Dec;30:1655-61; Adler A et al. Circ Arrhythm Electrophysiol, 2016 Jan;9:e003440; Mazzarotto F et al. Circulation, 2020 Feb;141:387-398). Another alteration at the same codon, p.T150P (c.448A>C), has been reported in association with phenotypes consistent with laminopathies (Felice KJ. Neurology. 2000 Jul;55(2):275-80). 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 available evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
CardioboostCm	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.35	D
BayesDel_noAF	Pathogenic	0.26
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.96	.;.;.;D;.;.;.;D;.
Eigen	Pathogenic	0.91
Eigen_PC	Pathogenic	0.87
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Uncertain	0.88	D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.62	D
MetaRNN	Pathogenic	0.88	D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.60	D
MutationAssessor	Pathogenic	4.0	H;.;H;H;H;.;.;.;.
PrimateAI	Pathogenic	0.81	D
PROVEAN	Uncertain	-4.3	D;D;D;D;D;D;D;D;D
REVEL	Pathogenic	0.87
Sift	Uncertain	0.0010	D;D;D;D;D;D;D;D;D
Sift4G	Benign	0.069	T;T;T;T;T;T;T;D;T
Polyphen		0.93	P;.;D;P;.;.;D;.;.
Vest4		0.84
MutPred		0.51		Loss of phosphorylation at T150 (P = 0.0398);Loss of phosphorylation at T150 (P = 0.0398);Loss of phosphorylation at T150 (P = 0.0398);Loss of phosphorylation at T150 (P = 0.0398);Loss of phosphorylation at T150 (P = 0.0398);.;.;.;.;
MVP		0.91
MPC		2.2
ClinPred		1.0	D
GERP RS		5.6
Varity_R		0.80
gMVP		0.90

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: rs869069617; hg19: chr1-156100500;