rs794728591

chr1-156134811-C-T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1 PM2 PM5 PP2 PP3_Moderate PP5

The NM_170707.4(LMNA):c.646C>T(p.Arg216Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,614,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R216H) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0000055 (0 hom.)
• Consequence: LMNA NM_170707.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:2
• Conservation: PhyloP100: 2.65

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 10 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 12 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 chr1-156134812-G-A is described in Lovd as [Likely_pathogenic].
• PP2: Missense variant where missense usually causes diseases, LMNA
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.894
• PP5: Variant 1-156134811-C-T is Pathogenic according to our data. Variant chr1-156134811-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 200938.We mark this variant Likely_pathogenic, oryginal submissions are: {Pathogenic=3, Likely_pathogenic=3, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LMNA	NM_170707.4	c.646C>T	p.Arg216Cys	missense_variant	4/12	ENST00000368300.9
LMNA	NM_005572.4	c.646C>T	p.Arg216Cys	missense_variant	4/10	ENST00000677389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LMNA	ENST00000368300.9	c.646C>T	p.Arg216Cys	missense_variant	4/12	1	NM_170707.4	P1
LMNA	ENST00000677389.1	c.646C>T	p.Arg216Cys	missense_variant	4/10		NM_005572.4

Frequencies

GnomAD3 genomes AF: 0.00000657 AC: 1 AN: 152174 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251080 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135872

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000327

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000547 AC: 8 AN: 1461882 Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3 AN XY: 727240

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000450

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152174 Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1 AN XY: 74326

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Alfa AF: 0.0000712 Hom.: 0

Bravo AF: 0.00000378

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1 Uncertain:2

Uncertain significance, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Aug 17, 2017	p.Arg216Cys (R216C; c.646C>T) in exon 4 of the LMNA gene (NM_005572.3) Given the suspicious case data and rarity in the general population, we consider this variant a variant of uncertain significance, likely pathogenic. At this time, we do not feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). However, if the patient is able to get her family involved for segregation analysis and it segregates with disease, this variant is a good candidate for pathogenicity. The variant has been seen in at least 13 unrelated cases of cardiomyopathy (not including this patient's family). Most of these patients were seen at other genetic testing labs. Some of these patients have conduction system disease and a family history of sudden cardiac death. The case data is strong; however, segregation and functional data is lacking in any of these families, which leads us to a classification of VUS-likely pathogenic. We have seen this variant in 3 of our patients - one with cardiomyopathy, family history of sudden cardiac death/arrest, conduction system disease, arrhythmias, another with severe dilated cardiomyopathy and a family history of DCM, and another with recurrent VT and family history of VT/SVT and older-onset cardiomyopathy. This variant has been reported in one patient who is part of a multicenter cohort of 269 LMNA-positive individuals recruited in Europe with clinical or family evidence of laminopathy (van Rijsingen I et al., 2013). Ancestry is not provided. Subjects were recruited in Denmark, France, Germany, Italy, Netherlands, UK. The variant was also report in a paper on ablation for laminopathy, however the case amy be redundant with that reported by van Rijsingen et al given overlap in authors and recruitment sites and lack of details to assess potential redundancy. The variant is listed in an LMNA database online, but I can't open the variant's listing (http://www.umd.be/LMNA/W_glossary/Glossary_80C7.shtml). Ito et al (2017) included this variant in some analyses in their paper on impact of LMNA variants on splicing, however it appears it was only evaluated with an in silico algorithm and was not studied further. This is a non-conservative amino acid change, resulting in the replacement of a basic Arginine with a polar Cysteine that is capable of forming disulfide bridges. The Arginine at this location is very highly conserved across vertebrate species (it is an Asparagine in one species of bird and a Histidine in lamprey). Variants in nearby residues (F206L, I210S, L215P, L215V, K219N, K219T, H222P, H222Y, E223K, R225Q, L226V) have been reported in HGMD in association with dilated cardiomyopathy and/or muscular dystrophy, further supporting the functional importance of this region of the protein. According to the Ambry report, in silico analysis with PolyPhen predicts the variant to be “Probably Damaging” with a score of 0.97 and SIFT predicts it to be “Deleterious” with a score of (0.01). Its Grantham score is 180. According to the Invitae report, SIFT, PolyPhen-2, and Align-GVGD all suggest the variant is disruptive. The variant was reported online in 2 of 138585 individuals in the Genome Aggregation Consortium Dataset (gnomAD; http://gnomad.broadinstitute.org/), which currently includes variant calls on >140,000 unrelated individuals of African, Asian, European, Ashkenazi, Latino descent. Specifically, the variant was observed in 1 of 10152 individuals of Ashkenazi Jewish descent (MAF=0.009850%) and 1 of 15391 South Asians (MAF=0.003249%). The phenotype of those individuals is not publicly available. The dataset is comprised of multiple cohorts, some of which were recruited from the general population, others were enriched for common cardiovascular disease. There is one individual of “Other” ancestry with a different variant at the same codon: p.Arg216His. -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Dec 04, 2015	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 22, 2022	Originally reported in one individual who had either clinical or familial evidence of a laminopathy, though specific details were not provided (van Riksingen et al., 2013).; Has been reported in association with a cardiomyopathy or arrhythmia phenotype in multiple unrelated individuals referred for genetic testing at GeneDx, and in published literature (Chen et al., 2018; Armaroli et al., 2020); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 32155092, 23183350, 29943882, 30007954, 28878402, 33673806, 30078822, 34975533, 10939567) -

Charcot-Marie-Tooth disease type 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 15, 2024

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 216 of the LMNA protein (p.Arg216Cys). This variant is present in population databases (rs794728591, gnomAD 0.01%). This missense change has been observed in individuals with conduction disease and/or dilated cardiomyopathy (PMID: 23183350, 27506821, 28878402, 29237675, 29943882, 30007954). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 200938). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt LMNA protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects LMNA function (PMID: 28878402). For these reasons, this variant has been classified as Pathogenic. -

Primary dilated cardiomyopathy;C5392094:Laminopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jun 29, 2018

The p.Arg216Cys variant in LMNA has been reported at least 10 individuals with c ardiomyopathy or other features suggestive of a laminopathy (Al-Saaidi 2018, van Rijsingen 2013, Ambry pers. comm., BluePrint pers. comm, EGL pers. comm., GeneD x pers. comm., Invitae pers. comm., Stanford pers. comm., LMM data) and segregat ed with disease in 18 affected individuals from one large family with DCM (Al-Sa aidi 2018). It has also been identified in 2/277170 chromosomes by the Genome Ag gregation Database (gnomAD, http://gnomad.broadinstitute.org) and has been repor ted in ClinVar (Variation ID:200938). Computational prediction tools and conserv ation analysis suggest that the p.Arg216Cys variant may impact the protein, thou gh this information is not predictive enough to determine pathogenicity. In summ ary, although additional studies are required to fully establish its clinical si gnificance, the p.Arg216Cys variant is likely pathogenic. ACMG/AMP Criteria appl ied: PP1_Strong, PS4_Moderate, PM2, PP3. -

Primary familial dilated cardiomyopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Oct 02, 2021

Variant summary: LMNA c.646C>T (p.Arg216Cys) results in a non-conservative amino acid change located in the Intermediate filament, rod domain (IPR039008) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251080 control chromosomes. c.646C>T has been widely reported in the literature in multiple comprehensively genotyped individuals affected with a variety of cardiac phenotypes such as, unspecified cardiac disease (van Rijsingen_2013), confirmed LMNA cardiomyopathy (Kumar_2016), RVA pacing induced HF with reduced left ventricular ejection fraction (LVEF) (Liu_2017), Atrial Firbillation and Atrioventricular block (Nishiuchi_2017), co-segregation with disease among all affected family members with DCM features of arrythmia and/or cardiomegaly (Chen_2018) and a comprehensively genotyped laboratory referral genetic testing cohort with suspected clinical diagnosis of HCM (Hathaway_2021). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in disrupted Lamin A/C nuclear location and increased apoptotic rate under environmental stress of serum starvation in a neonatal rat cardiomyocyte cell system (example, Liu_2017). Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments (Pathogenic/Likely pathogenic, n=5; VUS, n=2). Some submitters cite overlapping evidence utilized in the context of this evaluation. Based on the evidence outlined above, the variant was classified as pathogenic. -

Primary dilated cardiomyopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Blueprint Genetics

Mar 19, 2015

- -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 05, 2019

The p.R216C pathogenic mutation (also known as c.646C>T), located in coding exon 4 of the LMNA gene, results from a C to T substitution at nucleotide position 646. The arginine at codon 216 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been identified in multiple individuals with dilated cardiomyopathy, cardiac conduction disease, and/or other laminopathy phenotypes, and it has been shown to segregate with disease in two large families (van Rijsingen IA et al. Eur J Heart Fail. 2013;15(4):376-84; Kumar S et al. Circ Arrhythm Electrophysiol. 2016;9:e004357; Nishiuchi S et al. Circ Cardiovasc Genet. 2017;10:e001603; Al-Saaidi RA et al. Eur. J. Heart Fail. 2018;ejhf.1241; Chen L et al. J Biomed Res, 2018 Jul;32:314-316; BluePrint pers. comm.; EGL pers. comm.; GeneDx pers. comm.; LMM pers. comm.; Invitae pers. comm.; Stanford pers. comm., Ambry Internal Data). In one study, neonatal rat cardiomyocytes expressing p.R216C exhibited differences in the size and distribution of lamin aggregates compared with cardiomyocytes expressing wildtype LMNA (Liu N et al. Sci Rep. 2017;7:10676). In a second study, authors showed reduced efficiency of incorporation of this alteration in the cytoskeletal fraction of patient fibroblasts (Al-Saaidi RA et al. Eur. J. Heart Fail. 2018;ejhf.1241). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.73
CardioboostCm	Uncertain	0.75
BayesDel_addAF	Pathogenic	0.37	D
BayesDel_noAF	Pathogenic	0.39
Cadd	Pathogenic	33
Dann	Pathogenic	1.0
Eigen	Pathogenic	0.68
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Pathogenic	0.99	D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.62	D
MetaRNN	Pathogenic	0.89	D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.80	D
MutationAssessor	Pathogenic	2.9	M;.;M;M;M;.;.;.;.
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D
PrimateAI	Pathogenic	0.85	D
PROVEAN	Pathogenic	-6.0	D;D;D;D;D;D;D;D;D
REVEL	Pathogenic	0.83
Sift	Pathogenic	0.0	D;D;D;D;D;D;D;D;D
Sift4G	Pathogenic	0.0010	D;D;D;D;D;D;D;D;D
Polyphen		1.0	D;.;D;D;.;.;D;.;.
Vest4		0.90
MutPred		0.62		Loss of MoRF binding (P = 0.0067);Loss of MoRF binding (P = 0.0067);Loss of MoRF binding (P = 0.0067);Loss of MoRF binding (P = 0.0067);Loss of MoRF binding (P = 0.0067);.;.;.;.;
MVP		0.98
MPC		2.4
ClinPred		1.0	D
GERP RS		5.3
RBP_binding_hub_radar		1.0
RBP_regulation_power_radar		2.8
Varity_R		0.65
gMVP		0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs794728591; hg19: chr1-156104602; COSMIC: COSV105905866; COSMIC: COSV105905866;