rs777841827
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The ENST00000368300.9(LMNA):c.1879C>T(p.Arg627Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,580 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R627H) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000368300.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LMNA | NM_170707.4 | c.1879C>T | p.Arg627Cys | missense_variant | 11/12 | ENST00000368300.9 | NP_733821.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LMNA | ENST00000368300.9 | c.1879C>T | p.Arg627Cys | missense_variant | 11/12 | 1 | NM_170707.4 | ENSP00000357283 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152246Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248608Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135018
GnomAD4 exome AF: 0.0000417 AC: 61AN: 1461334Hom.: 0 Cov.: 32 AF XY: 0.0000385 AC XY: 28AN XY: 726978
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152246Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74382
ClinVar
Submissions by phenotype
not provided Uncertain:6
Uncertain significance, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Aug 15, 2024 | PM2 - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 25, 2021 | Variant summary: LMNA c.1879C>T (p.Arg627Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 248646 control chromosomes (gnomAD and publication data). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.1879C>T has been reported in the literature in individuals affected with Dilated Cardiomyopathy and Primary Electrical Disease as well as in one carrier (Houben_2012, Hazebroek_2015, Proost_2017, Hoorntje_2017, van Lint_2019). These reports do not provide unequivocal conclusions about association of the variant with Dilated Cardiomyopathy. At least one publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (van Tienen_2018). Two ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Nov 16, 2023 | This missense variant replaces arginine with cysteine at codon 627 of the LMNA protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have shown that there were no nuclear envelope or morphology abnormalities in fibroblasts of carrier individuals (PMID: 28790152, 30420677). This variant has been reported in two individuals affected with dilated cardiomyopathy (PMID: 22918509, 30847666). One of these individuals also carried a pathogenic variant in the RBM20 gene that could explain the observed phenotype (PMID: 30847666). This variant has been reported in an individual affected with cardiac arrhythmia (PMID: 27884249), in an individual affected with primary electrical disease (PMID: 28341588), in an individual affected with unspecified cardiomyopathy (PMID: 28790152), and in an individual affected with sudden infant death (PMID: 37589201). This variant has also been reported in an individual with left ventricular dysfunction (PMID: 29540472); this individual also carried a different pathogenic variant in the LMNA gene that could explain the observed phenotype. This variant has been identified in 8/248608 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. - |
Charcot-Marie-Tooth disease type 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 27, 2023 | 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. This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 627 of the LMNA protein (p.Arg627Cys). This variant is present in population databases (rs777841827, gnomAD 0.006%). This missense change has been observed in individual(s) with cardiac arrhythmias, dilated cardiomyopathy, and/or unspecified cardiomyopathy (PMID: 22918509, 27884249, 28341588, 29540472, 30847666). ClinVar contains an entry for this variant (Variation ID: 543199). Experimental studies have shown that this missense change does not substantially affect LMNA function (PMID: 28790152, 30420677). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Primary dilated cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Dec 13, 2023 | This missense variant replaces arginine with cysteine at codon 627 of the LMNA protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). Functional studies have shown that there were no nuclear envelope or morphology abnormalities in fibroblasts of carrier individuals (PMID: 28790152, 30420677). This variant has been reported in two individuals affected with dilated cardiomyopathy (PMID: 22918509, 30847666). One of these individuals also carried a pathogenic variant in the RBM20 gene that could explain the observed phenotype (PMID: 30847666). This variant has been reported in an individual affected with cardiac arrhythmia (PMID: 27884249), in an individual affected with primary electrical disease (PMID: 28341588), in an individual affected with unspecified cardiomyopathy (PMID: 28790152), and in an individual affected with sudden infant death (PMID: 37589201). This variant has also been reported in an individual with left ventricular dysfunction (PMID: 29540472); this individual also carried a different pathogenic variant in the LMNA gene that could explain the observed phenotype. This variant has been identified in 8/248608 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 | Sep 26, 2022 | The p.R627C variant (also known as c.1879C>T), located in coding exon 11 of the LMNA gene, results from a C to T substitution at nucleotide position 1879. The arginine at codon 627 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been detected in an individual with dilated cardiomyopathy (who carried a second LMNA alteration p.R331Q (c.992G>A)) and in two individuals with primary electrical disease (Hoorntje ET et al. Circ Cardiovasc Genet, 2017 Aug;10; Proost D et al. J Mol Diagn, 2017 May;19:445-459; Kumar S et al. J. Am. Coll. Cardiol., 2016 Nov;68:2299-2307). In addition, functional studies used immunofluorescence on cultured fibroblasts to show that this alteration did not cause any nuclear envelope abnormalities (Hoorntje ET et al. Circ Cardiovasc Genet, 2017 Aug;10; Houben F et al. Histochem. Cell Biol., 2013 Jan;139:119-34). This amino acid position is well 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at