ClinVar Miner

Submissions for variant NM_170707.4(LMNA):c.976T>A (p.Ser326Thr)

gnomAD frequency: 0.00009  dbSNP: rs56851164
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV000212504 SCV000065076 uncertain significance not specified 2018-03-19 criteria provided, single submitter clinical testing Variant classified as Uncertain Significance - Favor Pathogenic. The Ser326Thr v ariant in LMNA has been reported in 7 individuals with a range of cardio-muscula r manifestations, including 5 individuals with DCM and/or conduction system dise ase (CSD), 1 with late-onset scapular myopathy and CSD, and 1 with early-onset X -linked EDMD that also carried a pathogenic EMD variant (Muntoni 2006, Meune 200 6, Ito 2017, Hasselberg 2018). This variant has also been identified in 15/12614 6 European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad .broadinstitute.org; dbSNP rs56851164). In vitro functional studies provide some evidence that the p.Ser326Thr variant may not impact protein function (Gangemi 2013). However, these types of assays may not accurately represent biological fu nction. In addition, serine (Ser) at position 326 is not conserved in evolution with 5 species carrying a threonine (Thr), suggesting that this change may be to lerated. In summary, while there is some suspicion for a pathogenic role, the cl inical significance of the p.Ser326Thr variant is uncertain due to conflicting e vidence. ACMG/AMP Criteria applied: PM6; PS4; BP4, BS3_Supporting.
GeneDx RCV000057494 SCV000234689 uncertain significance not provided 2023-06-01 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 22071332, 23142632, 16585054, 27532257, 16407522, 20627339, 28663758, 9536090, 22224630, 28518168, 31019283, 29095976, 29237690, 28679633, 24846508, 10939567, 34862408, 34240052, 36975868, 33673806, 31476771, 24503780)
Eurofins Ntd Llc (ga) RCV000057494 SCV000337761 uncertain significance not provided 2015-12-08 criteria provided, single submitter clinical testing
Invitae RCV000544253 SCV000657831 likely benign Charcot-Marie-Tooth disease type 2 2024-01-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV000621488 SCV000736913 uncertain significance Cardiovascular phenotype 2022-08-24 criteria provided, single submitter clinical testing The p.S326T variant (also known as c.976T>A), located in coding exon 6 of the LMNA gene, results from a T to A substitution at nucleotide position 976. The serine at codon 326 is replaced by threonine, an amino acid with similar properties. This alteration has been detected in individuals reported to have conduction system disease and various myopathies, including dilated cardiomyopathy, late-onset scapular myopathy, and Emery-Dreifuss muscular dystrophy; however, some patients had variants in other genes and, in some cases, clinical detail and/or gene analysis were limited (Muntoni F et al. Brain. 2006;129:1260-8; Hasselberg NE et al. Eur Heart J. 2018 03;39(10):853-860Pugh TJ et al. Genet. Med. 2014;16:601-8; Peretto G et al. Ann Intern Med. 2019 10;171(7):458-463). This variant has also been detected in a hypertrophic cardiomyopathy genetic testing cohort and in cohorts not selected for the presence of LMNA-related disease, but clinical details were limited (Florwick A et al. Front Genet. 2017;8:79; Thauvin-Robinet C et al. Eur J Hum Genet. 2019 08;27(8):1197-1214; Hathaway J et al. BMC Cardiovasc Disord. 2021 03;21(1):126). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV000755678 SCV000883086 uncertain significance Dilated cardiomyopathy 1A 2018-11-21 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000212504 SCV001157710 uncertain significance not specified 2018-07-03 criteria provided, single submitter clinical testing The LMNA c.976T>A; p.Ser326Thr variant (rs56851164), is reported in the literature in individuals affected with dilated cardiomyopathy and Emery-Dreifuss muscular dystrophy (Hasselberg 2018, Muntoni 2006, Pugh 2014), and is reported in ClinVar (Variation ID: 48097). In a family with X-linked Emery-Dreifuss muscular dystrophy segregating with a STA p.Tyr105Ter variant, a presumed de novo LMNA c.976T>A; p.Ser326Thr variant was identified in one affected individual presenting with much more severe clinical symptoms than two other affected family members. This variant occurs in the functionally important coil 2B domain that mediates lamin A/C oligomerization; however, molecular dynamics modeling of the LMNA c.976T>A; p.Ser326Thr variant suggested no effect on protein dimerization, although the authors concede other mechanisms could still account for pathogenicity (Gangemi 2013). This variant is found in the non-Finnish European population with an overall allele frequency of 0.012% (15/126146 alleles) in the Genome Aggregation Database, and a recent study classified this variant as likely benign due to its population frequency above a maximum allele frequency threshold (MAF < 0.01%) expected for pathogenic variants (Walsh 2017). The serine at codon 326 is weakly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is tolerated. Due to conflicting information, the clinical significance of the LMNA c.976T>A; p.Ser326Thr variant is uncertain at this time.
Color Diagnostics, LLC DBA Color Health RCV001192112 SCV001360088 uncertain significance Cardiomyopathy 2022-12-15 criteria provided, single submitter clinical testing This missense variant replaces serine with threonine at codon 326 of the lamin A/C proteins. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with unspecified LMNA-associated muscular phenotype (PMID: 16407522), and in three unrelated individuals affected with dilated cardiomyopathy (PMID: 24503780, 27532257, 29095976). This variant has been reported as de novo in an individual affected with Emery-Dreifuss muscular dystrophy (PMID: 16585054). This and two other affected individuals from this family carried a pathogenic p.Tyr105* variant in the same gene. This variant has been reported in three additional individuals affected with Emery-Dreifuss muscular dystrophy, one individual affected with late-onset scapular myopathy and two individuals affected with dilated cardiomyopathy (PMID: 16585054). This variant has also been identified in 15/281330 chromosomes in the general population by the Genome Aggregation Database (gnomAD). In summary, this is a variant of unknown impact on function that has been observed in affected individuals as well as in the general population. 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000212504 SCV004029935 uncertain significance not specified 2023-07-31 criteria provided, single submitter clinical testing Variant summary: LMNA c.976T>A (p.Ser326Thr) results in a conservative amino acid change located in the Intermediate filament, rod domain (IPR039008) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 5.6e-05 in 249958 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in LMNA causing Dilated Cardiomyopathy (5.6e-05 vs 0.0001), allowing no conclusion about variant significance. c.976T>A has been reported in the literature in individuals affected with Cardiomyopathy or muscle laminopathy without strong evidence of causality (e.g. Muntoni_2006, Pugh_2014, Walsh_2017, Ben Yaou_2021, Hathaway_2021, Park_2020). 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, finding no effect of the variant on laminim A aggregation (Anderson_2021). The following publications have been ascertained in the context of this evaluation (PMID: 16585054, 23142632, 24503780, 27532257, 31019283, 34862408, 34240052, 33673806, 31383942, 25274841, 22071332). Nine submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified it as uncertain significance (n=7), likely pathogenic (n=1) or likely benign (n=1). Based on the evidence outlined above, the variant was classified as uncertain significance.
Mayo Clinic Laboratories, Mayo Clinic RCV000057494 SCV004224656 uncertain significance not provided 2023-01-16 criteria provided, single submitter clinical testing
Institute of Immunology and Genetics Kaiserslautern RCV000755678 SCV004363611 uncertain significance Dilated cardiomyopathy 1A 2024-02-02 criteria provided, single submitter clinical testing ACMG Criteria: PM2_P, PP5; Variant was found in heterozygous state
Epithelial Biology; Institute of Medical Biology, Singapore RCV000057494 SCV000088608 not provided not provided no assertion provided not provided
Blueprint Genetics RCV000208012 SCV000264011 likely pathogenic Primary familial hypertrophic cardiomyopathy 2015-09-14 flagged submission clinical testing

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