rs142191737
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1PM2PP2
The NM_170707.4(LMNA):c.1634G>A(p.Arg545His) variant causes a missense change. The variant allele was found at a frequency of 0.000284 in 1,555,522 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R545C) has been classified as Uncertain significance.
Frequency
Genomes: 𝑓 0.00024 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00029 ( 0 hom. )
Consequence
LMNA
NM_170707.4 missense
NM_170707.4 missense
Scores
6
7
6
Clinical Significance
Conservation
PhyloP100: 6.09
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM1
?
In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 benign, 14 uncertain in NM_170707.4
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, LMNA
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| LMNA | NM_170707.4 | c.1634G>A | p.Arg545His | missense_variant | 10/12 | ENST00000368300.9 | |
| LMNA | NM_005572.4 | c.1634G>A | p.Arg545His | missense_variant | 10/10 | ENST00000677389.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LMNA | ENST00000368300.9 | c.1634G>A | p.Arg545His | missense_variant | 10/12 | 1 | NM_170707.4 | P1 | |
| LMNA | ENST00000677389.1 | c.1634G>A | p.Arg545His | missense_variant | 10/10 | NM_005572.4 |
Frequencies
GnomAD3 genomes ? AF: 0.000243 AC: 37AN: 152150Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000228 AC: 37AN: 162612Hom.: 0 AF XY: 0.000245 AC XY: 21AN XY: 85698
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:2Uncertain:28Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:9
| Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
| Uncertain significance, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2023 | LMNA: PS3:Moderate - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 03, 2017 | - - |
| Uncertain significance, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
| Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 26, 2023 | Reported in the heterozygous state in individuals with dilated cardiomyopathy, unspecified arrhythmia, cathecholaminergic polymorphic ventricular tachycardia, isolated atrial fibrillation, left ventricle non-compaction, or metabolic syndrome and lipodystrophy, with or without cardiomyopathy and proximal myopathy, but full familial segregation information was generally not provided (Klauke et al., 2017; van Lint et al., 2019; van Tienen et al., 2019; Chan et al., 2016; Guillin-Amarelle et al., 2018; Magno et al., 2021, Pessente et al., 2022; Lenarduzzi et al., 2023); Reported in the apparent homozygous state in two siblings with lipodystrophy with near-generalized loss of subcutaneous fat, diabetes mellitus, extreme hypertriglyceridemia, hepatic steatosis, as well as intellectual disability, short stature, joint contractures, and cataracts; two heterozygous relatives were overweight and had acanthosis nigricans, but no evidence of lipodystrophy (Patni et al., 2020); Identified, both independently and/or in conjunction with additional variants, in other unrelated individuals referred for genetic testing at GeneDx, including one individual with a de novo pathogenic variant in another gene that was sufficient to explain their phenotype.; In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 27498076, 30564623, 28663758, 26332594, 23183350, 29557732, 28255936, 27919367, 28074886, 29253866, 30847666, 31383942, 30420677, 34426522, 31857427, 33803191, 32041611, 34806324, 35205065, 33713793, 10939567, 35449878, 35846372, 35772917, 29791652, 36788754) - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 11, 2022 | PP3 - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | May 03, 2021 | - - |
Dilated cardiomyopathy 1A Uncertain:3
| Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | Jul 15, 2022 | - - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 11, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
| Uncertain significance, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jan 01, 2019 | - - |
Cardiomyopathy Uncertain:2
| Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Nov 14, 2023 | This missense variant replaces arginine with histidine at codon 545 of the LMNA protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). In a functional study, homozygous LMNA-R545H knock-in mice were reported to have reduced sodium current and increased sinus arrhythmias (Wu et al, 2020). A separate study correlated the presence of cytoplasmically located PML nuclear bodies with cells from patients with laminopathies (PMID: 22918509). However, clinical relevance of this observation is unknown. This variant has been observed in individuals affected with possible LMNA-related diseases (PMID: 22918509, 23183350, 27529282, 27919367, 29557732, 29791652, 30420677, 31857427, 33803191, 35449878; Wu et al, 2020). This variant has been identified in 48/193996 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. - |
| Uncertain significance, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Sep 04, 2018 | - - |
Dilated cardiomyopathy 1S Pathogenic:1
| Likely pathogenic, no assertion criteria provided | clinical testing | Institut für Laboratoriums- und Transfusionsmedizin, Herz- und Diabeteszentrum Nordrhein-Westfalen | May 01, 2016 | - - |
Hypercholesterolemia;C0152423:Microtia;C0349588:Short stature;C0432055:2-3 finger syndactyly;C1839546:Microretrognathia;C4021959:Round ear;C5574742:Decreased body weight Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Nov 02, 2021 | _x000D_ Criteria applied: PS3, PS4, PM5_STR, PP3 - |
Charcot-Marie-Tooth disease type 2B1 Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 11, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
LMNA-related disorder Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 10, 2024 | The LMNA c.1634G>A variant is predicted to result in the amino acid substitution p.Arg545His. This variant has been reported in individuals who had cardiac disease (Table S1, van Rijsingen et al. 2013. PubMed ID: 23183350; Table S4, Neubauer et al. 2017. PubMed ID: 28074886; Table S5, Klauke et al. 2017. PubMed ID: 29253866; Guillín-Amarelle et al. 2018. PubMed ID: 29791652). This variant has also been reported in individuals with lipodystrophy or dyslipidemias (Chan et al. 2016. PubMed ID: 27919367; Table S4, Dron et al. 2020. PubMed ID: 32041611). This variant is reported in 0.051% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has conflicting interpretations of pathogenicity in ClinVar ranging from likely benign to pathogenic (http://www.ncbi.nlm.nih.gov/clinvar/variation/163878). Different substitutions that affect the same amino acid (p.Arg545Cys and p.Arg545Ser) have also been documented in association with Emery-Dreifuss muscular dystrophy and dilated cardiomyopathy (Kandert et al. 2009. PubMed ID: 19589617; Zhang et al. 2020. PubMed ID: 32041989). At this time, the clinical significance of the c.1634G>A (p.Arg545His) variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Congenital muscular dystrophy due to LMNA mutation Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 11, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Hutchinson-Gilford syndrome Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 11, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
not specified Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 12, 2018 | The p.Arg545His variant in LMNA has been reported in at least 2 individuals with sudden death, 1 individual with partial lipodystrophy, 1 individual with lipody strophy and myopathy, 4 individuals with laminopathy-associated features, and se gregated with disease in 1 affected relative (LMM data, Houben 2013, van Rijsing en 2013, Chan 2016, Campuzano 2017, Neubauer 2017, Guillin-Amarelle 2018, Olaopa 2018). This variant has been reported in ClinVar (Variation ID: 163878) and has been identified in 0.05% (38/75898) of European chromosomes by the Genome Aggre gation Database (gnomAD, http://gnomad.broadinstitute.org/; dbSNP rs142191737). Please note that for diseases with clinical variability, reduced penetrance, or recessive inheritance, pathogenic variants may be present at a low frequency in the general population. In vitro functional studies provide some evidence that t he p.Arg545His variant may reduce sodium current (Olaopa 2018). However, these types of assays may not accurately represent biological function.Computational p rediction tools and conservation analysis do not provide strong support for or a gainst an impact to the protein. In summary, due to conflicting evidence and var iable phenotypes of affected individuals carrying the variant, the clinical sign ificance of the p.Arg545His variant is uncertain.ACMG/AMP criteria applied: PS3_ Moderate, PS4_Moderate. - |
Peripheral neuropathy Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Claritas Genomics | Aug 22, 2016 | - - |
Mandibuloacral dysplasia with type A lipodystrophy Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 11, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Autosomal semi-dominant severe lipodystrophic laminopathy Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | Aug 01, 2023 | This sequence change in LMNA is predicted to replace arginine with histidine at codon 545, p.(Arg545His). The arginine residue is highly conserved (100 vertebrates, UCSC), and is located in the lamin tail domain. There is a small physicochemical difference between arginine and histidine. The highest population minor allele frequency in the population database gnomAD v2.1 is 0.05% (41/79,748 alleles) in the European (non-Finnish) population. This variant has been reported in individuals with LMNA-related disorders, including cardiomyopathy and lipodystrophy but has also been identified in unaffected individuals (PMID: 30420677, 31857427, 33803191, 35772917). The variant has been identified as homozygous in two siblings with lipodystrophy (PMID: 31857427). A homozygous knock-in mouse model of the variant demonstrated reduced voltage-gated sodium current, prolonged PR and QTc intervals, and increased sinus arrhythmias, which were absent in the heterozygous knock-in model (Wu et al. https://doi.org/10.1161/circ.142.suppl_3.12627Circulation). Computational evidence predicts a deleterious effect for the missense substitution (REVEL = 0.769). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.6.1, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE. Following criteria are met: PP3, PS3_Supporting. - |
Lethal tight skin contracture syndrome Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 11, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Lipoatrophy with Diabetes, Hepatic Steatosis, Hypertrophic Cardiomyopathy, and Leukomelanodermic Papules Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 11, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Lipodystrophy Uncertain:1
| Uncertain significance, criteria provided, single submitter | curation | Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard | Jan 22, 2020 | The p.Arg545His variant in LMNA has been reported in 1 individual with lipodystrophy (PMID: 28074886), but has been identified in 0.05% (41/79748) of European (non-Finnish) chromosomes and other populations at lesser frequencies by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs142191737). This variant has been seen in the general population at a frequency high enough to rule out a pathogenic role. This variant has also been reported in ClinVar as having conflicting interpretations of pathogenicity (Variation ID: 163878). In vitro functional studies provide some evidence that the p.Arg545His variant may slightly impact protein function (PMID: 22918509). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. Multiple variants in the same region as p.Arg545His have been reported in association with disease in the literature and the variant is located in a region of LMNA that is thought to be essential to protein folding and stability, suggesting that this variant is in a functional domain and slightly supports pathogenicity (PMID: 28663758). In summary, the clinical significance of the p.Arg545His variant is uncertain. ACMG/AMP Criteria applied: PP3, PS3_supporting, PM1_supporting, BA1 (Richards 2015). - |
Primary dilated cardiomyopathy Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Feb 05, 2024 | This missense variant replaces arginine with histidine at codon 545 of the LMNA protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). In a functional study, homozygous LMNA-R545H knock-in mice were reported to have reduced sodium current and increased sinus arrhythmias (Wu et al, 2020). A separate study correlated the presence of cytoplasmically located PML nuclear bodies with cells from patients with laminopathies (PMID: 22918509). However, clinical relevance of this observation is unknown. This variant has been observed in individuals affected with possible LMNA-related diseases (PMID: 22918509, 23183350, 27529282, 27919367, 29557732, 29791652, 30420677, 31857427, 33803191, 35449878; Wu et al, 2020). This variant has been identified in 48/193996 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. - |
Cardiovascular phenotype Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2023 | The p.R545H variant (also known as c.1634G>A), located in coding exon 10 of the LMNA gene, results from a G to A substitution at nucleotide position 1634. The arginine at codon 545 is replaced by histidine, an amino acid with highly similar properties. This alteration has been reported as heterozygous and homozygous in association with different types of LMNA-related disease (van Rijsingen IA et al. Eur. J. Heart Fail., 2013 Apr;15:376-84; Chan D et al. J Clin Lipidol. 2016 Sep;10:1488-1491; Neubauer J et al. Eur. J. Hum. Genet., 2017 04;25:404-409; Guillín-Amarelle C et al. Arch Endocrinol Metab, 2018 Jun;62:376-382; Patni N et al. J Med Genet, 2020 06;57:422-426). This variant has also been detected in 125 participants from a biobank cohort; however, details were limited (Lazarte J et al. J Am Coll Cardiol. 2022 Jul;80(1):50-59). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Emery-Dreifuss muscular dystrophy 2, autosomal dominant Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 11, 2018 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Charcot-Marie-Tooth disease type 2 Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
CardioboostCm
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Pathogenic
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M;.;M;M;.;.;.
MutationTaster
Benign
D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N;N;N;N;N
REVEL
Pathogenic
Sift
Benign
T;.;D;D;D;D;D
Sift4G
Benign
T;D;T;T;T;T;T
Polyphen
D;.;D;.;.;D;.
Vest4
MVP
MPC
0.48
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at