1-156135268-C-T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP2PP3_StrongPP5

The NM_170707.4(LMNA):​c.892C>T​(p.Arg298Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,613,516 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R298H) has been classified as Likely pathogenic.

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000044 ( 0 hom. )

Consequence

LMNA
NM_170707.4 missense

Scores

17
2
1

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:13U:3O:1

Conservation

PhyloP100: 3.19
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 12 ACMG points.

PM1
In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 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 chr1-156135269-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 2159261.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=1}.
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), LMNA. . Gene score misZ 2.3673 (greater than the threshold 3.09). Trascript score misZ 3.0905 (greater than threshold 3.09). GenCC has associacion of gene with familial partial lipodystrophy, Dunnigan type, autosomal recessive Emery-Dreifuss muscular dystrophy, LMNA-related cardiocutaneous progeria syndrome, atrioventricular block, dilated cardiomyopathy 1A, Emery-Dreifuss muscular dystrophy 2, autosomal dominant, atypical Werner syndrome, restrictive dermopathy 1, autosomal semi-dominant severe lipodystrophic laminopathy, Emery-Dreifuss muscular dystrophy 3, autosomal recessive, dilated cardiomyopathy, Charcot-Marie-Tooth disease type 2B1, dilated cardiomyopathy-hypergonadotropic hypogonadism syndrome, arrhythmogenic right ventricular cardiomyopathy, familial isolated dilated cardiomyopathy, mandibuloacral dysplasia with type A lipodystrophy, autosomal dominant Emery-Dreifuss muscular dystrophy, heart-hand syndrome, Slovenian type, congenital muscular dystrophy due to LMNA mutation, lethal restrictive dermopathy, Hutchinson-Gilford progeria syndrome.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.99
PP5
Variant 1-156135268-C-T is Pathogenic according to our data. Variant chr1-156135268-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 14498.We mark this variant Likely_pathogenic, oryginal submissions are: {not_provided=1, Pathogenic=10, Uncertain_significance=4}. Variant chr1-156135268-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
LMNANM_170707.4 linkuse as main transcriptc.892C>T p.Arg298Cys missense_variant 5/12 ENST00000368300.9
LMNANM_005572.4 linkuse as main transcriptc.892C>T p.Arg298Cys missense_variant 5/10 ENST00000677389.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
LMNAENST00000368300.9 linkuse as main transcriptc.892C>T p.Arg298Cys missense_variant 5/121 NM_170707.4 P1P02545-1
LMNAENST00000677389.1 linkuse as main transcriptc.892C>T p.Arg298Cys missense_variant 5/10 NM_005572.4 P02545-2

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152244
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.000478
GnomAD3 exomes
AF:
0.0000359
AC:
9
AN:
250398
Hom.:
0
AF XY:
0.0000442
AC XY:
6
AN XY:
135628
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000290
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:
0.0000619
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000438
AC:
64
AN:
1461272
Hom.:
0
Cov.:
34
AF XY:
0.0000399
AC XY:
29
AN XY:
726946
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000224
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000232
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000531
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152244
Hom.:
0
Cov.:
32
AF XY:
0.0000269
AC XY:
2
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.000478
Alfa
AF:
0.0000688
Hom.:
0
Bravo
AF:
0.0000151
ExAC
AF:
0.0000412
AC:
5
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:13Uncertain:3Other:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Pathogenic:6Other:1
Pathogenic, criteria provided, single submitterclinical testingRevvity Omics, RevvityMay 03, 2021- -
Pathogenic, no assertion criteria providedclinical testingLaboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)-- -
Pathogenic, no assertion criteria providedclinical testingClinical Genetics, Academic Medical Center-- -
Pathogenic, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenMay 01, 2017- -
Pathogenic, criteria provided, single submitterclinical testingGeneDxFeb 17, 2023Published functional studies demonstrate a damaging effect as cells from R298C homozygous knock in mice showed downregulation of LMNA at both the protein and mRNA level (Poitelon et al., 2012); 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: 12467734, 14607793, 11799477, 18549403, 17347251, 17536044, 35383421, 16809772, 10939567, 30340945, 34862408, 35449878, 22331516, 31383942) -
Pathogenic, criteria provided, single submitterclinical testingInstitute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU DresdenNov 03, 2021- -
not provided, no classification providedliterature onlyEpithelial Biology; Institute of Medical Biology, Singapore-- -
Charcot-Marie-Tooth disease type 2B1 Pathogenic:3
Pathogenic, no assertion criteria providedliterature onlyOMIMDec 01, 2007- -
Pathogenic, criteria provided, single submitterclinical testingBaylor GeneticsDec 20, 2022- -
Pathogenic, criteria provided, single submitterclinical testingAthena DiagnosticsNov 18, 2014- -
Charcot-Marie-Tooth disease type 2 Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingInvitaeJan 21, 2024This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 298 of the LMNA protein (p.Arg298Cys). This variant is present in population databases (rs59885338, gnomAD 0.005%). This missense change has been observed in individual(s) with autosomal recessive Charcot-Marie-Tooth disease (PMID: 14607793, 17347251, 18549403). It is commonly reported in individuals of North African ancestry (PMID: 11799477, 14607793, 17347251, 18549403). ClinVar contains an entry for this variant (Variation ID: 14498). 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%. For these reasons, this variant has been classified as Pathogenic. -
Cardiovascular phenotype Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsNov 22, 2022The p.R298C pathogenic mutation (also known as c.892C>T), located in coding exon 5 of the LMNA gene, results from a C to T substitution at nucleotide position 892. The arginine at codon 298 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant has been detected in multiple homozygous individuals with autosomal recessive Charcot-Marie-Tooth disease, has shown segregation with disease in multiple families of Algerian or Moroccan descent, and has been described as a north western African founder mutation (Tazir M et al. Brain, 2004 Jan;127:154-63; Chaouch M et al. Neuromuscul Disord, 2003 Jan;13:60-7; Bouhouche A et al. Brain, 2007 Apr;130:1062-75; Hamadouche T et al. Ann Hum Genet, 2008 Sep;72:590-7). In vitro studies indicate this variant may impact protein function and lead to abnormal nuclear aggregates in some mammalian cell lines (Dreuillet C et al. Biol Cell, 2008 Jan;100:51-61; Anderson CL et al. NPJ Genom Med, 2021 Dec;6:103). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this variant is expected to be causative of autosomal recessive Charcot-Marie-Tooth disease when present along with a second pathogenic variant on the other allele; however, its clinical significance for autosomal dominant cardiomyopathy and other laminopathies is unclear. -
Autosomal recessive axonal hereditary motor and sensory neuropathy Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 02, 2018The p.Arg298Cys variant in LMNA has been reported as homozygous in at least 25 N orth African consanguineous families with clinical features of Charcot Marie Too th Disease variant 2B1 (CMT2B1) and has been described as a founder variant in t his population (De Sandre-Giovannoli 2002, Chaouch 2003, Bouhouche 2007, Ben Yao u 2007, Hamadouche 2008). Animal models of this homozygous variant are associate d with some molecular findings but not the phenotypic abnormalities seen in CMT2 B1 patients (Poitelon 2012). This variant has been identified in 6/1111132 of Eu ropean chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.bro adinstitute.org; dbSNP rs59885338) and reported in ClinVar (Variation ID# 14498) ; however its frequency is low enough to be consistent with a recessive carrier frequency. In addition, computational prediction tools and conservation analysis suggest that the p.Arg298Cys variant may impact the protein. In summary, this v ariant meets criteria to be classified as pathogenic for CMT2B1 in an autosomal recessive manner based upon segregation studies, low frequency in controls, and functional evidence. ACMG/AMP Criteria applied: PS4; PP1_Strong; PM2_Supporting; PP3. -
Hutchinson-Gilford syndrome Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingMendelicsMay 28, 2019- -
Cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingColor Diagnostics, LLC DBA Color HealthMay 15, 2023This missense variant replaces arginine with cysteine at codon 298 of the lamin A/C proteins. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant is a well-known founder mutation in North African countries and has been reported to segregate with autosomal recessive Charcot-Marie-Tooth type 2 in affected families (PMID: 11799477, 12467734, 14607793, 17347251; Clinvar variation ID: 14498). Cardiac systems were normal in all of over 20 homozygotes assessed (PMID: 12467734, 14607793). Over 40 heterozygous carriers were reported from these families, who were all asymptomatic except for one individual with nonspecific cardiac abnormalities (PMID: 17536044). This variant has also been reported in another two heterozygous individuals referred for cardiac catheterization (PMID: 32792077). This variant has been identified in 9/250398 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as a Variant of Uncertain Significance for autosomal dominant cardiomyopathy, although it is known to cause autosomal recessive Charcot-Marie-Tooth type 2 (ClinVar variation ID:14498). -
Familial partial lipodystrophy, Dunnigan type Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingNew York Genome CenterDec 17, 2020The heterozygous c.892C>T (p.Arg298Cys) variant in LMNA is a known pathogenic variant for autosomal recessive Charcot-Marie-Tooth disease, type 2B1(CMT2B1), and has been reported as homozygous in multiple consanguineous families affected with CMT2B1 [PMID: 11799477;PMID: 14607793;PMID: 12467734]. Family-members carrying heterozygous p.Arg298Cys variant were apparently normal [PMID: 11799477;PMID: 14607793;PMID: 12467734]. The variant has been reported in ClinVar database as pathogenic for recessive CMT2B1 disease [Variation ID:14498]. The p.Arg298Cys variant has 0.00002627 allele frequency in the gnomAD(v3) database (4 out of 152,244 heterozygous alleles, no homozygotes) suggesting it is not a common benign variant in the general population. The variant affects an evolutionarily conserved residue and is predicted deleterious by multiple in silico prediction tools. Given that heterozygous carriers of p.Arg298Cys were apparently normal, and due to the absence of evidence supporting its pathogenicity in heterozygous state, the p.Arg298Cys variant in the LMNA gene is reported as a variant of uncertain significance for autosomal dominant familial partial lipodystrophy. -
Primary dilated cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAll of Us Research Program, National Institutes of HealthFeb 05, 2024This missense variant replaces arginine with cysteine at codon 298 of the lamin A/C proteins. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant is a well-known founder mutation in North African countries and has been reported to segregate with autosomal recessive Charcot-Marie-Tooth type 2 in affected families (PMID: 11799477, 12467734, 14607793, 17347251; Clinvar variation ID: 14498). Cardiac systems were normal in all of over 20 homozygotes assessed (PMID: 12467734, 14607793). Over 40 heterozygous carriers were reported from these families, who were all asymptomatic except for one individual with nonspecific cardiac abnormalities (PMID: 17536044). This variant has also been reported in another two heterozygous individuals referred for cardiac catheterization (PMID: 32792077). This variant has been identified in 9/250398 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as a Variant of Uncertain Significance for autosomal dominant cardiomyopathy, although it is known to cause autosomal recessive Charcot-Marie-Tooth type 2 (ClinVar variation ID:14498). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.87
CardioboostCm
Pathogenic
0.98
BayesDel_addAF
Pathogenic
0.34
D
BayesDel_noAF
Pathogenic
0.40
CADD
Pathogenic
32
DANN
Pathogenic
1.0
DEOGEN2
Pathogenic
0.97
.;.;.;D;.;.;.;.
Eigen
Pathogenic
0.75
Eigen_PC
Pathogenic
0.69
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.94
D;D;D;D;D;D;D;D
M_CAP
Pathogenic
0.84
D
MetaRNN
Pathogenic
0.99
D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
0.92
D
MutationAssessor
Pathogenic
3.2
M;.;M;M;M;.;.;.
MutationTaster
Benign
1.0
A;A;A;A;A;A;A;A;A
PrimateAI
Uncertain
0.78
T
PROVEAN
Pathogenic
-7.6
D;D;D;D;D;D;D;D
REVEL
Pathogenic
0.88
Sift
Pathogenic
0.0
D;D;D;D;D;D;D;D
Sift4G
Pathogenic
0.0
D;D;D;D;D;D;D;D
Polyphen
1.0
D;.;P;D;.;.;D;.
Vest4
0.89
MutPred
0.85
Loss of MoRF binding (P = 0.0116);Loss of MoRF binding (P = 0.0116);Loss of MoRF binding (P = 0.0116);Loss of MoRF binding (P = 0.0116);Loss of MoRF binding (P = 0.0116);.;.;.;
MVP
0.96
MPC
2.1
ClinPred
0.99
D
GERP RS
5.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.8
Varity_R
0.81
gMVP
0.97

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs59885338; hg19: chr1-156105059; COSMIC: COSV61543499; COSMIC: COSV61543499; API