rs267607591

chr1-156135274-G-A

Variant summary

Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1 PM2 PM5 PP2 PP3_Moderate PP5_Very_Strong

The NM_170707.4(LMNA):c.898G>A(p.Asp300Asn) 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. D300G) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LMNA NM_170707.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:3 O:1
• Conservation: PhyloP100: 9.99

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 Pathogenic. Variant got 17 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 14 uncertain in NM_170707.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr1-156135275-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 217451.Status of the report is no_assertion_criteria_provided, 0 stars.
• PP2: Missense variant where missense usually causes diseases, LMNA
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.877
• PP5: Variant 1-156135274-G-A is Pathogenic according to our data. Variant chr1-156135274-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 66952.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMNA	NM_170707.4	c.898G>A	p.Asp300Asn	missense_variant	5/12	ENST00000368300.9
LMNA	NM_005572.4	c.898G>A	p.Asp300Asn	missense_variant	5/10	ENST00000677389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMNA	ENST00000368300.9	c.898G>A	p.Asp300Asn	missense_variant	5/12	1	NM_170707.4	P1
LMNA	ENST00000677389.1	c.898G>A	p.Asp300Asn	missense_variant	5/10		NM_005572.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:3 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Charcot-Marie-Tooth disease type 2 Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Invitae

Feb 08, 2022

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 300 of the LMNA protein (p.Asp300Asn). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of autosomal dominant LMNA-related conditions (PMID: 19095983, 25327215, 29047356, 32548202). ClinVar contains an entry for this variant (Variation ID: 66952). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C15"). Experimental studies have shown that this missense change affects LMNA function (PMID: 30696354). This variant disrupts the p.Asp300 amino acid residue in LMNA. Other variant(s) that disrupt this residue have been observed in individuals with LMNA-related conditions (PMID: 23666920, 30123186, 32954377), which suggests that this may be a clinically significant amino acid residue. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Lipodystrophy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Genetic Services Laboratory, University of Chicago

Jun 24, 2014

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Dilated cardiomyopathy 1A Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

New York Genome Center

Apr 08, 2022

The c.898G>A variant in LMNA has previously been reported in a heterozygous state in over ten individuals with variable features of laminopathies such as lipodystrophy, progeria, diabetes, non-alcoholic fatty liver disease, and early onset coronary artery disease and cardiomyopathy [PMID:19095983, 28938416,29047356, 32413188, 32548202, 32901917, 33502018], and it has been deposited in ClinVar [ClinVar ID: 66952] as Variant of Uncertain Significance for Charcot-Marie-Tooth disease, type 2 and Likely Pathogenic for Lipodystrophy. The c.898G>A variant is absent from population databases (gnomAD v2.1.1 and v3.1.2,TOPMed Freeze 8, All of Us), suggesting it is not a common benign variant in the populations represented in those databases. The c.898G>A variant is located inexon 5 of this 12-exon gene, and predicted to replace an evolutionarily conserved aspartate amino acid with asparagine at position 300 within the intermediate filament domain of the encoded protein [UniProtKB ID: P02545]. In silico predictions are moderately in favor of damaging effect for p.(Asp300Asn) [CADD v1.6 = 29.9,REVEL = 0.606]. Cardiac myocytes of mice models carrying p.Asp300Asn allele were shown to result in myocardial fibrosis, apoptosis, and cardiac dysfunction [PMID:30696354]. Variants affecting the same residue (p.(Asp300Gly) and p.(Asp300His)) have also been reported in literature in individuals with laminopathies [PMID:22991222, 23666920, 25327215, 30123186, 32954377]. Based on available evidence this c.898G>A p.(Asp300Asn) variant identified in LMNA in is classified as Pathogenic. -

not provided Other:1

not provided, no classification provided

literature only

Epithelial Biology; Institute of Medical Biology, Singapore

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.82
CardioboostCm	Uncertain	0.30
BayesDel_addAF	Uncertain	0.11	D
BayesDel_noAF	Uncertain	-0.080
Cadd	Pathogenic	31
Dann	Pathogenic	1.0
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.65
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.92	D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.36	D
MetaRNN	Pathogenic	0.88	D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.44	D
MutationAssessor	Benign	1.6	L;.;L;L;L;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D
PrimateAI	Uncertain	0.61	T
PROVEAN	Uncertain	-2.5	D;D;D;D;D;N;N;N
REVEL	Uncertain	0.61
Sift	Benign	0.033	D;D;D;D;D;D;D;D
Sift4G	Uncertain	0.012	D;D;D;D;D;D;D;D
Polyphen		0.18	B;.;P;P;.;.;D;.
Vest4		0.72
MutPred		0.76		Gain of MoRF binding (P = 0.0327);Gain of MoRF binding (P = 0.0327);Gain of MoRF binding (P = 0.0327);Gain of MoRF binding (P = 0.0327);Gain of MoRF binding (P = 0.0327);.;.;.;
MVP		0.83
MPC		1.0
ClinPred		0.92	D
GERP RS		5.6
Varity_R		0.22
gMVP		0.89

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: rs267607591; hg19: chr1-156105065;