ClinVar Genomic variation as it relates to human health
NM_001927.4(DES):c.38C>T (p.Ser13Phe)
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.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001927.4(DES):c.38C>T (p.Ser13Phe)
Variation ID: 44260 Accession: VCV000044260.23
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 2q35 2: 219418500 (GRCh38) [ NCBI UCSC ] 2: 220283222 (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 19, 2013 Feb 28, 2024 Mar 16, 2022 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001927.4:c.38C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001918.3:p.Ser13Phe missense NC_000002.12:g.219418500C>T NC_000002.11:g.220283222C>T NG_008043.1:g.5124C>T NG_046330.1:g.18892C>T LRG_380:g.5124C>T LRG_380t1:c.38C>T P17661:p.Ser13Phe - Protein change
- S13F
- Other names
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- Canonical SPDI
- NC_000002.12:219418499: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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Trans-Omics for Precision Medicine (TOPMed) 0.00000
- 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
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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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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DES | - | - |
GRCh38 GRCh37 |
1064 | 1110 |
Conditions - Germline
Condition
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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
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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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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Pathogenic (1) |
criteria provided, single submitter
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Sep 7, 2011 | RCV000037240.12 | |
Pathogenic (5) |
criteria provided, single submitter
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Mar 2, 2017 | RCV000056801.22 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Mar 16, 2022 | RCV001389153.13 |
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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Pathogenic
(Nov 26, 2013)
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criteria provided, single submitter
Method: clinical testing
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Myofibrillar myopathy 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Baylor Genetics
Study: Adult_WES
Accession: SCV000245471.1 First in ClinVar: Sep 29, 2015 Last updated: Sep 29, 2015 |
Comment:
This variant has been previously reported as disease-causing and was found once in our laboratory in a 46-year-old male with arrhythmia, hypertrophic cardiomyopathy, EMG evidence … (more)
This variant has been previously reported as disease-causing and was found once in our laboratory in a 46-year-old male with arrhythmia, hypertrophic cardiomyopathy, EMG evidence of distal myopathy with myotonic discharges, progressive balance issues, short stature, scolisos, small hands, maternal family history of heart problems. Myotonia was likely explained by additional variants in this individual. (less)
Number of individuals with the variant: 1
Age: 40-49 years
Sex: male
Ethnicity/Population group: Causasians
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Pathogenic
(Dec 15, 2014)
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criteria provided, single submitter
Method: clinical testing
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Desmin-related myofibrillar myopathy
Affected status: yes
Allele origin:
germline
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Blueprint Genetics
Accession: SCV000263827.2
First in ClinVar: Feb 27, 2016 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
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Pathogenic
(Mar 02, 2017)
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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: SCV000332859.4
First in ClinVar: Dec 06, 2016 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 2
Sex: mixed
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Pathogenic
(Sep 07, 2011)
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criteria provided, single submitter
Method: clinical testing
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Primary dilated cardiomyopathy
(Autosomal dominant inheritance)
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000060897.5
First in ClinVar: May 03, 2013 Last updated: Jan 31, 2015 |
Comment:
The Ser13Phe variant has been reported in several families showing significant s egregation with desmin-related myopathy (> than 10 affected family members posit ive) and … (more)
The Ser13Phe variant has been reported in several families showing significant s egregation with desmin-related myopathy (> than 10 affected family members posit ive) and was absent from > 400 control chromosomes (Bergman 2007, Pica 2008, van Tintelen 2009). Serine (Ser) at position 13 is highly conserved across evoluti onarily distant species, suggesting that a change in the amino acid may not be t olerated. In addition, in vitro studies show that this variant impacts the stru cture and function of desmin protein (Pica 2008, Sharma 2009). Therefore, the S er13Phe variant meets our criteria for pathogenicity (http://pcpgm.partners.org/ lmm) based on segregation studies, absence from controls, and functional evidenc e. (less)
Number of individuals with the variant: 3
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Pathogenic
(Mar 16, 2022)
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criteria provided, single submitter
Method: clinical testing
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Desmin-related myofibrillar myopathy
Desmin-related myofibrillar myopathy
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001590419.4
First in ClinVar: May 10, 2021 Last updated: Feb 28, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects DES function (PMID: 19763525, 22403400). Algorithms … (more)
For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects DES function (PMID: 19763525, 22403400). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C15"). ClinVar contains an entry for this variant (Variation ID: 44260). This missense change has been observed in individuals with autosomal dominant dilated cardiomyopathy and/or skeletal myopathy (PMID: 17720647, 18061454, 19879535, 23349452, 26097489). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 13 of the DES protein (p.Ser13Phe). (less)
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Pathogenic
(Nov 01, 2009)
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no assertion criteria provided
Method: literature only
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MYOPATHY, MYOFIBRILLAR, 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000188575.4
First in ClinVar: Aug 22, 2014 Last updated: May 14, 2018 |
Comment on evidence:
In affected members of 2 distantly related Dutch families segregating autosomal dominant myofibrillar myopathy-1 (MFM1; 601419) with a highly heterogeneous clinical picture, varying from isolated … (more)
In affected members of 2 distantly related Dutch families segregating autosomal dominant myofibrillar myopathy-1 (MFM1; 601419) with a highly heterogeneous clinical picture, varying from isolated dilated cardiomyopathy to more generalized skeletal myopathy and mild respiratory problems, Bergman et al. (2007) identified heterozygosity for a c.38C-T transition in exon 1 of the DES gene, resulting in a ser13-to-phe (S13F) substitution within a highly conserved nonapeptide motif in the 'head' domain. The authors noted that the serine at position 13 serves as a phosphorylation site for protein kinase C (176960) and is required for appropriate dimer-dimer formation. The mutation was not found in unaffected family members or in 216 ethnically matched controls. Haplotype analysis confirmed the distant relationship between the 2 families, who resided in nearby villages. In a 39-year-old Chinese man who presented with complete heart block and mild proximal and distal limb weakness, Pica et al. (2008) identified heterozygosity for the S13F mutation in the DES gene. His mother and 2 sibs, who were also heterozygous for the mutation, had somewhat milder limb weakness. His affected brother also reported 2 episodes of unexplained syncope, whereas his affected sister reported episodes of palpitations. The mutation was not found in his unaffected father or in 100 unrelated controls. Transfection studies in BHK21 and MCF7 cells demonstrated a fine filamentous desmin network with both mutant and wildtype DES; however, there were significantly more large accumulations of desmin material with the S13F mutant compared to wildtype. Van Tintelen et al. (2009) restudied the Dutch kindred with MFM1 reported by Bergman et al. (2007) and expanded it to include 3 distantly related families. The authors described 2 more affected Dutch families whose ancestors could be traced to the same small, poorly populated region in which the common ancestral couple of the large Dutch kindred had lived. All 27 affected individuals were heterozygous for the S13F mutation, which was not found in 300 ethnically matched chromosomes. Based on haplotype analysis, the mutation was estimated to be between 220 and 495 years old. All affected family members demonstrated a fully penetrant yet variable, predominantly cardiologic phenotype, characterized by conduction disease at an early age and right ventricular involvement, including right bundle branch block (RBBB) and/or right ventricular tachycardias and ARVC phenocopies. Immunofluorescence of patient cardiomyocytes showed abnormal intercalated discs with a convoluted and elongated shape in a strong zigzag pattern, compared to the straight, robust lines of high intensity seen in control myocardia. These highly irregular and twisted intercalated discs were also observed on electron microscopy; however, Z discs appeared to be aligned. (less)
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Pathogenic
(-)
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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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Clinical Genetics, Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001925003.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 2021 |
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Pathogenic
(-)
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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: SCV001952696.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(-)
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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: SCV001740070.3 First in ClinVar: Jul 07, 2021 Last updated: Sep 08, 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: SCV000087914.1
First in ClinVar: Oct 19, 2013 Last updated: Oct 19, 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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Molecular diagnostic experience of whole-exome sequencing in adult patients. | Posey JE | Genetics in medicine : official journal of the American College of Medical Genetics | 2016 | PMID: 26633545 |
Desmin common mutation is associated with multi-systemic disease manifestations and depletion of mitochondria and mitochondrial DNA. | McCormick EM | Frontiers in genetics | 2015 | PMID: 26097489 |
Genetic analysis in 418 index patients with idiopathic dilated cardiomyopathy: overview of 10 years' experience. | van Spaendonck-Zwarts KY | European journal of heart failure | 2013 | PMID: 23349452 |
Dual color photoactivation localization microscopy of cardiomyopathy-associated desmin mutants. | Brodehl A | The Journal of biological chemistry | 2012 | PMID: 22403400 |
Recurrent and founder mutations in the Netherlands: the cardiac phenotype of DES founder mutations p.S13F and p.N342D. | van Spaendonck-Zwarts KY | Netherlands heart journal : monthly journal of the Netherlands Society of Cardiology and the Netherlands Heart Foundation | 2012 | PMID: 22215463 |
Severe cardiac phenotype with right ventricular predominance in a large cohort of patients with a single missense mutation in the DES gene. | van Tintelen JP | Heart rhythm | 2009 | PMID: 19879535 |
Disease mutations in the "head" domain of the extra-sarcomeric protein desmin distinctly alter its assembly and network-forming properties. | Sharma S | Journal of molecular medicine (Berlin, Germany) | 2009 | PMID: 19763525 |
Characterization of a novel S13F desmin mutation associated with desmin myopathy and heart block in a Chinese family. | Pica EC | Neuromuscular disorders : NMD | 2008 | PMID: 18061454 |
Two related Dutch families with a clinically variable presentation of cardioskeletal myopathy caused by a novel S13F mutation in the desmin gene. | Bergman JE | European journal of medical genetics | 2007 | PMID: 17720647 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=DES | - | - | - | - |
Text-mined citations for rs62636495 ...
HelpRecord last updated Nov 25, 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.