ClinVar Genomic variation as it relates to human health
NM_170707.4(LMNA):c.1583C>T (p.Thr528Met)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Likely pathogenic(1); Uncertain significance(3)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_170707.4(LMNA):c.1583C>T (p.Thr528Met)
Variation ID: 66851 Accession: VCV000066851.14
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q22 1: 156137207 (GRCh38) [ NCBI UCSC ] 1: 156106998 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Oct 20, 2013 May 1, 2024 Dec 1, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_170707.4:c.1583C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_733821.1:p.Thr528Met missense NM_005572.4:c.1583C>T MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_005563.1:p.Thr528Met missense NM_001257374.3:c.1247C>T NP_001244303.1:p.Thr416Met missense NM_001282624.2:c.1340C>T NP_001269553.1:p.Thr447Met missense NM_001282625.2:c.1583C>T NP_001269554.1:p.Thr528Met missense NM_001282626.2:c.1583C>T NP_001269555.1:p.Thr528Met missense NM_170708.4:c.1583C>T NP_733822.1:p.Thr528Met missense NC_000001.11:g.156137207C>T NC_000001.10:g.156106998C>T NG_008692.2:g.59635C>T LRG_254:g.59635C>T LRG_254t2:c.1583C>T - Protein change
- T528M, T416M, T447M
- Other names
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- Canonical SPDI
- NC_000001.11:156137206:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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The Genome Aggregation Database (gnomAD), exomes 0.00001
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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LMNA | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
1845 | 2125 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Uncertain significance (4) |
criteria provided, single submitter
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Nov 3, 2016 | RCV000057330.10 | |
Uncertain significance (1) |
criteria provided, single submitter
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Mar 12, 2020 | RCV001182566.3 | |
Uncertain significance (1) |
criteria provided, single submitter
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Dec 1, 2023 | RCV003996505.3 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Sep 25, 2023 | RCV004018988.2 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Nov 03, 2016)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Eurofins Ntd Llc (ga)
Accession: SCV000703215.2
First in ClinVar: Apr 02, 2018 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Sex: mixed
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Uncertain significance
(Mar 12, 2020)
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criteria provided, single submitter
Method: clinical testing
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Cardiomyopathy
Affected status: unknown
Allele origin:
germline
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Color Diagnostics, LLC DBA Color Health
Accession: SCV001348060.2
First in ClinVar: Jun 22, 2020 Last updated: Jan 12, 2022 |
Comment:
This missense variant replaces threonine with methionine at codon 528 of the lamin A/C proteins. Computational prediction suggests that this variant may have deleterious impact … (more)
This missense variant replaces threonine with methionine at codon 528 of the lamin A/C proteins. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant causes abnormal nuclei with aggregates (PMID: 22413764), nuclear rupture and loss of compartmentalization (PMID: 21831885). However, clinical relevance of these observations is not clear. This variant has been reported in an individual affected with non-valvular atrial fibrillation (PMID: 22413764), as well as in an individual affected with familial partial lipodystrophy (PMID: 28641778). This variant has also been reported in compound heterozygous state with other variants in the LMNA gene in individuals affected with Hutchinson-Gilford progeria syndrome (PMID: 16825282), familial partial lipodystrophy (PMID: 15298354, 29078011), or mandibuloacral dysplasia with type A lipodystrophy (Xiang et al., 2014). Heterozygous carriers of this variant in these families were reported to be unaffected. This variant has been identified in 2/214466 chromosomes in the general population by the Genome Aggregation Database (gnomAD). While this variant has been observed in multiple individuals affected with laminopathy, the available evidence is insufficient to determine the role of this variant in autosomal dominant cardiomyopathy conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. (less)
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Likely pathogenic
(Sep 25, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cardiovascular phenotype
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV005030834.1
First in ClinVar: May 01, 2024 Last updated: May 01, 2024 |
Comment:
The p.T528M variant (also known as c.1583C>T), located in coding exon 9 of the LMNA gene, results from a C to T substitution at nucleotide … (more)
The p.T528M variant (also known as c.1583C>T), located in coding exon 9 of the LMNA gene, results from a C to T substitution at nucleotide position 1583. The threonine at codon 528 is replaced by methionine, an amino acid with similar properties. This alteration has been reported in individuals with laminopathies, including cardiac conduction disease, cardiomyopathy, and lipodystrophy (Saj M et al. Mol Diagn Ther, 2012 Apr;16:99-107; Akinci B et al. Metabolism, 2017 Jul;72:109-119; Neubauer J et al. Eur J Hum Genet, 2017 Apr;25:404-409; van Tienen FHJ et al. Eur J Hum Genet, 2019 Mar;27:389-399; Araújo-Vilar D et al. J Clin Med, 2021 Apr;10:[ePub ahead of print]; Vasandani C et al. J Endocr Soc, 2022 Oct;6:bvac155). Additionally, this alteration has been identified in a case report of a proband who was compound heterozygous with an additional alteration in LMNA, who had classical symptoms of Hutchinson–Gilford progeria syndrome (Verstraeten VL et al. Hum Mol Genet, 2006 Aug;15:2509-22). Two other alterations at the same codon, p.T528R (c.1583C>G) and p.T528K (c.1583C>A), have been detected in numerous individuals with laminopathies, including individuals with Emery Dreifuss muscular dystrophy (EDMD) (Vytopil M et al. J Med Genet, 2003 Dec;40:e132; Scharner J et al. Hum Mutat, 2011 Feb;32:152-67; Zhang L et al. Mol Med Rep, 2015 Oct;12:5065-71; Lee Y et al. J Clin Neurol, 2017 Oct;13:405-410; Sivitskaya LN et al. Acta Myol, 2017 Dec;36:207-212; Stehlíková K et al. Clin Genet, 2017 Mar;91:463-469; Peretto G et al. Ann Intern Med, 2019 Oct;171:458-463; Ben Yaou R et al. Brain Commun, 2021 Jul;3:fcab075). This amino acid position is highly conserved in available vertebrate species. 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 laminopathies; however, its clinical significance for Hutchinson–Gilford progeria syndrome is unclear. (less)
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Uncertain Significance
(Dec 01, 2023)
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criteria provided, single submitter
Method: clinical testing
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Primary dilated cardiomyopathy
(Autosomal dominant inheritance)
Affected status: unknown
Allele origin:
germline
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All of Us Research Program, National Institutes of Health
Accession: SCV004818017.1
First in ClinVar: Apr 20, 2024 Last updated: Apr 20, 2024
Comment:
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of … (more)
This study involves interpretation of variants in research participants for the purpose of population health screening. Participant phenotype was not available at the time of variant classification. Additional details can be found in publication PMID: 35346344, PMCID: PMC8962531 (less)
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Comment:
This missense variant replaces threonine with methionine at codon 528 of the lamin A/C proteins. Computational prediction suggests that this variant may have deleterious impact … (more)
This missense variant replaces threonine with methionine at codon 528 of the lamin A/C proteins. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant causes abnormal nuclei with aggregates (PMID: 22413764), nuclear rupture and loss of compartmentalization (PMID: 21831885). However, clinical relevance of these observations is not clear. This variant has been reported in an individual affected with non-valvular atrial fibrillation (PMID: 22413764), as well as in an individual affected with familial partial lipodystrophy (PMID: 28641778). This variant has also been reported in compound heterozygous state with other variants in the LMNA gene in individuals affected with Hutchinson-Gilford progeria syndrome (PMID: 16825282), familial partial lipodystrophy (PMID: 15298354, 29078011), or mandibuloacral dysplasia with type A lipodystrophy (Xiang et al., 2014). Heterozygous carriers of this variant in these families were reported to be unaffected. This variant has been identified in 2/214466 chromosomes in the general population by the Genome Aggregation Database (gnomAD). While this variant has been observed in multiple individuals affected with laminopathy, the available evidence is insufficient to determine the role of this variant in autosomal dominant cardiomyopathy conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. (less)
Number of individuals with the variant: 1
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Uncertain significance
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001743048.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 2021 |
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Uncertain significance
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001953784.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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not provided
(-)
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no classification provided
Method: not provided
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not provided
Affected status: not provided
Allele origin:
not provided
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Epithelial Biology; Institute of Medical Biology, Singapore
Accession: SCV000088443.1
First in ClinVar: Oct 20, 2013 Last updated: Oct 20, 2013 |
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Phenotypic Differences Among Familial Partial Lipodystrophy Due to LMNA or PPARG Variants. | Vasandani C | Journal of the Endocrine Society | 2022 | PMID: 36397776 |
Variable Expressivity and Allelic Heterogeneity in Type 2 Familial Partial Lipodystrophy: The p.(Thr528Met) LMNA Variant. | Araújo-Vilar D | Journal of clinical medicine | 2021 | PMID: 33916827 |
Cardiac phenotype in familial partial lipodystrophy. | Eldin AJ | Clinical endocrinology | 2021 | PMID: 33502018 |
Assessment of fibroblast nuclear morphology aids interpretation of LMNA variants. | van Tienen FHJ | European journal of human genetics : EJHG | 2019 | PMID: 30420677 |
Bone mineral density in familial partial lipodystrophy. | Fernández-Pombo A | Clinical endocrinology | 2018 | PMID: 29078011 |
Clinical presentations, metabolic abnormalities and end-organ complications in patients with familial partial lipodystrophy. | Akinci B | Metabolism: clinical and experimental | 2017 | PMID: 28641778 |
Post-mortem whole-exome analysis in a large sudden infant death syndrome cohort with a focus on cardiovascular and metabolic genetic diseases. | Neubauer J | European journal of human genetics : EJHG | 2017 | PMID: 28074886 |
Mapping disease-related missense mutations in the immunoglobulin-like fold domain of lamin A/C reveals novel genotype-phenotype associations for laminopathies. | Scharner J | Proteins | 2014 | PMID: 24375749 |
Cytoplasmic localization of PML particles in laminopathies. | Houben F | Histochemistry and cell biology | 2013 | PMID: 22918509 |
Variants of the lamin A/C (LMNA) gene in non-valvular atrial fibrillation patients: a possible pathogenic role of the Thr528Met mutation. | Saj M | Molecular diagnosis & therapy | 2012 | PMID: 22413764 |
Repetitive disruptions of the nuclear envelope invoke temporary loss of cellular compartmentalization in laminopathies. | De Vos WH | Human molecular genetics | 2011 | PMID: 21831885 |
Compound heterozygosity for mutations in LMNA causes a progeria syndrome without prelamin A accumulation. | Verstraeten VL | Human molecular genetics | 2006 | PMID: 16825282 |
Familial partial lipodystrophy associated with compound heterozygosity for novel mutations in the LMNA gene. | Savage DB | Diabetologia | 2004 | PMID: 15298354 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=LMNA | - | - | - | - |
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Text-mined citations for rs57629361 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.