ClinVar Genomic variation as it relates to human health
NM_152263.4(TPM3):c.502C>T (p.Arg168Cys)
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_152263.4(TPM3):c.502C>T (p.Arg168Cys)
Variation ID: 12454 Accession: VCV000012454.36
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q21.3 1: 154172972 (GRCh38) [ NCBI UCSC ] 1: 154145448 (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 May 3, 2013 Oct 20, 2024 Mar 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_152263.4:c.502C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_689476.2:p.Arg168Cys missense NM_001043351.2:c.391C>T NP_001036816.1:p.Arg131Cys missense NM_001043352.2:c.391C>T NP_001036817.1:p.Arg131Cys missense NM_001043353.2:c.391C>T NP_001036818.1:p.Arg131Cys missense NM_001278188.2:c.193C>T NP_001265117.1:p.Arg65Cys missense NM_001278189.2:c.391C>T NP_001265118.1:p.Arg131Cys missense NM_001278190.2:c.391C>T NP_001265119.1:p.Arg131Cys missense NM_001278191.2:c.121C>T NP_001265120.1:p.Arg41Cys missense NM_001349679.2:c.391C>T NP_001336608.1:p.Arg131Cys missense NM_001364679.2:c.502C>T NP_001351608.1:p.Arg168Cys missense NM_001364680.2:c.502C>T NP_001351609.1:p.Arg168Cys missense NM_001364681.2:c.502C>T NP_001351610.1:p.Arg168Cys missense NM_001364682.1:c.502C>T NP_001351611.1:p.Arg168Cys missense NM_001364683.1:c.391C>T NP_001351612.1:p.Arg131Cys missense NM_153649.4:c.391C>T NP_705935.1:p.Arg131Cys missense NR_103461.2:n.490C>T non-coding transcript variant NC_000001.11:g.154172972G>A NC_000001.10:g.154145448G>A NG_008621.1:g.24162C>T LRG_681:g.24162C>T LRG_681t1:c.391C>T LRG_681p1:p.Arg131Cys LRG_681t2:c.502C>T LRG_681p2:p.Arg168Cys LRG_681t3:c.391C>T LRG_681p3:p.Arg131Cys P06753:p.Arg168Cys - Protein change
- R168C, R131C, R41C, R65C
- Other names
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- Canonical SPDI
- NC_000001.11:154172971:G:A
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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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- 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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TPM3 | - | - |
GRCh38 GRCh37 |
368 | 387 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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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
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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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not provided (1) |
no classification provided
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- | RCV000013269.33 | |
Pathogenic (2) |
criteria provided, single submitter
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- | RCV000054416.24 | |
Pathogenic (1) |
criteria provided, single submitter
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Jun 7, 2016 | RCV000624745.3 | |
Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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Dec 28, 2022 | RCV000128700.27 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 1, 2024 | RCV004585999.1 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 19, 2024 | RCV000637291.9 |
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
(Apr 11, 2017)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: not provided
Allele origin:
de novo
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Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics
Accession: SCV000609700.1
First in ClinVar: Dec 06, 2016 Last updated: Dec 06, 2016 |
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Pathogenic
(Nov 29, 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: SCV000703292.2
First in ClinVar: Apr 02, 2018 Last updated: Dec 15, 2018 |
Number of individuals with the variant: 1
Zygosity: Single Heterozygote
Sex: mixed
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Pathogenic
(Jun 21, 2019)
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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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Revvity Omics, Revvity
Accession: SCV002022397.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Mar 01, 2024)
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criteria provided, single submitter
Method: research
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Nemaline myopathy
Affected status: yes
Allele origin:
de novo
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Muscle and Diseases Team, Institut de Génétique et Biologie Moléculaire et Cellulaire
Accession: SCV005038510.1
First in ClinVar: Jul 15, 2024 Last updated: Jul 15, 2024 |
Comment:
PS3+PM1+PM2+PM5+PM6+PP2+PP3
Number of individuals with the variant: 1
Sex: male
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Pathogenic
(Jun 07, 2016)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: yes
Allele origin:
germline
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Ambry Genetics
Accession: SCV000741605.3
First in ClinVar: Apr 15, 2018 Last updated: Jan 07, 2023 |
Number of individuals with the variant: 1
Clinical Features:
Muscular hypotonia (present) , Global developmental delay (present) , Myopathic facies (present) , Dysphagia (present) , Sleep apnea (present) , Pneumothorax (present) , Hyperbilirubinemia (present) … (more)
Muscular hypotonia (present) , Global developmental delay (present) , Myopathic facies (present) , Dysphagia (present) , Sleep apnea (present) , Pneumothorax (present) , Hyperbilirubinemia (present) , Decreased muscle mass (present) , Difficulty running (present) (less)
Sex: male
Ethnicity/Population group: Caucasian/Asian
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Pathogenic
(Dec 28, 2022)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000329559.7
First in ClinVar: Dec 06, 2016 Last updated: Jan 07, 2023 |
Comment:
Published functional studies demonstrate a decreased affinity for actin and reduced calcium-induced ATPase activation (Robaszkiewicz et al., 2012); Not observed at significant frequency in large … (more)
Published functional studies demonstrate a decreased affinity for actin and reduced calcium-induced ATPase activation (Robaszkiewicz et al., 2012); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24692096, 24642510, 24456932, 20301436, 12467750, 32675003, 22749829, 19181092, 26307083, 18300303, 20554445, 24095155, 24507666, 19487656, 24239060, 20179953, 22172422, 23584160, 27363342, 29669168, 23886664, 22798622, 21357678, 19953533, 19553118, 17376686, 12601110, 12196661, 12163190, 10619715, 33646172, 33064836, 33652732, 33333461) (less)
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Pathogenic
(Jan 19, 2024)
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criteria provided, single submitter
Method: clinical testing
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Congenital myopathy with fiber type disproportion
Congenital myopathy 4B, autosomal recessive
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: SCV000758739.7
First in ClinVar: May 28, 2018 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 168 of the TPM3 protein … (more)
This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 168 of the TPM3 protein (p.Arg168Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with congenital myopathy, cap myopathy, nemaline myopathy, and congenital fiber type disproportion (PMID: 18300303, 19487656, 19953533, 20554445, 24095155, 24507666, 24642510, 24692096, 26307083, 27363342). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 12454). 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 TPM3 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects TPM3 function (PMID: 22749829, 26307083). This variant disrupts the p.Arg168 amino acid residue in TPM3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 12467750, 17376686, 19553118, 21357678, 22749829, 22798622, 23886664, 24507666, 24692096). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(-)
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criteria provided, single submitter
Method: clinical testing
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Congenital myopathy 4A, autosomal dominant
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
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Suma Genomics
Accession: SCV005341000.1
First in ClinVar: Oct 13, 2024 Last updated: Oct 13, 2024 |
Comment:
A missense variant c.502C>T, p.(Arg168Cys) is observed in exon 5 of TPM3 in heterozygous state. This variant is not observed in the gnomAD database. This … (more)
A missense variant c.502C>T, p.(Arg168Cys) is observed in exon 5 of TPM3 in heterozygous state. This variant is not observed in the gnomAD database. This variant was reported earlier in the ClinVar database as pathogenic (ClinVar id. 12454). ACMG criteria: PS2, PS3, PM1, PM2_Supporting, PM6 and PP3 (less)
Zygosity: Single Heterozygote
Age: 0-9 years
Sex: male
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Pathogenic
(Sep 01, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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CeGaT Center for Human Genetics Tuebingen
Accession: SCV002585155.15
First in ClinVar: Oct 22, 2022 Last updated: Oct 20, 2024 |
Comment:
TPM3: PM2, PM5, PM6, PS4:Moderate, PP3, PP4, PS3:Supporting
Number of individuals with the variant: 1
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Pathogenic
(Dec 01, 2013)
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no assertion criteria provided
Method: literature only
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CONGENITAL MYOPATHY 4A, AUTOSOMAL DOMINANT
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000033516.6
First in ClinVar: Apr 04, 2013 Last updated: Jul 23, 2024 |
Comment on evidence:
In a woman with congenital myopathy-4A (CMYO4A; 609284), Clarke et al. (2008) identified a heterozygous c.502C-T transition (c.502C-T, NM_152263.2) in exon 5 of the TPM3 … (more)
In a woman with congenital myopathy-4A (CMYO4A; 609284), Clarke et al. (2008) identified a heterozygous c.502C-T transition (c.502C-T, NM_152263.2) in exon 5 of the TPM3 gene, resulting in an arg168-to-cys (R168C) substitution in the alpha-helix domain. The patient had poor head control before 1 year of age, but normal walking at age 9 months, and could run in childhood. At age 32, she could walk stairs with difficulty and had impaired nocturnal ventilation, moderate proximal weakness, ptosis, and severe kyphoscoliosis. Skeletal muscle biopsy showed fiber-type disproportion (CFTD). The authors noted that several other mutations had been identified in this codon (see, e.g., R168G, 191030.0008). Ohlsson et al. (2009) identified a heterozygous R168C mutation in a 38-year-old woman with CMYO4A associated with cap structures on skeletal muscle biopsy. She had previously been reported by Fidzianska (2002). She had slowly progressive muscle weakness and scoliosis since childhood, but was not examined until age 18 years. At that time, she had long narrow face, high-arched palate, chest deformity, and thin underdeveloped muscles. Other features included impaired nocturnal ventilation. Skeletal muscle biopsy showed that 20 to 30% of muscle fibers had granular cap structures devoid of ATPase activities. Myofibrils forming the caps were clearly demarcated from the remaining fibers and had an abnormal sarcomere pattern. Nemaline rods and fiber-type disproportion were not observed. The findings illustrated the phenotypic and histologic variability associated with TPM3 mutations, and suggested that cap disease is related to nemaline myopathy and CFTD. Waddell et al. (2010) reported a young man with CMYO4A due to a de novo heterozygous R168C mutation. He had mildly delayed motor development in early childhood, generalized hypotonia, and muscle weakness, particularly of the proximal lower limbs, ankle dorsiflexors, and neck. He had a long myopathic face with open mouth, high-arched palate, retrognathia, narrow chest, and mild scoliosis. At age 20 years, his pulmonary vital capacity was 37% of that predicted. Muscle biopsy taken at age 3 years showed increased variation in fiber size and subsarcolemmal protein inclusions in 25% of fibers, typical of caps. There was also type 1 fiber predominance. Caps stained strongly for several proteins, including tropomyosin, and electron microscopy showed disorganized thin filament structures containing Z-band remnants. Nemaline rods were not present. Two-dimensional gel electrophoresis showed that the mutant protein accounted for about 50% of the TPM3 protein in sarcomeres, and Waddell et al. (2010) postulated a dominant-negative effect, perhaps resulting from altered protein-protein interactions. These findings indicated that the fiber type distribution pattern as well as the pattern of protein inclusions can vary widely even among patients with the same TPM3 mutation. Malfatti et al. (2013) reported a man of French Canadian origin, with early-onset myopathy and a de novo heterozygous R168C mutation in the TPM3 gene. He had typical clinical features of the disorder, with mildly delayed motor milestones, generalized hypotonia, proximal and distal muscle weakness, impaired respiratory function, long, narrow face, and high-arched palate. Muscle biopsy showed type 1 fiber uniformity, subsarcolemmal caps in about 20% of fibers, typical nemaline rods in about 10% of fibers, and both caps and rods in about 5% of fibers. Electron microscopy demonstrated that the cap structures were composed of disorganized myofibrils and thickened Z-bands; the nemaline rods had longitudinal and transverse striations and were surrounded by thin filaments. Some of the caps contained structures resembling small rods, and the intermyofibrillary network adjacent to caps or nemaline rods was irregular with jagged Z lines. Malfatti et al. (2013) emphasized that the combination of rods and caps had not previously been reported in the same patient, which suggested that the 2 patterns are pathogenetically related. The findings confirmed that nemaline myopathy and cap myopathy resulting from TPM3 mutations are part of a disease spectrum. (less)
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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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TPM3 homepage - Leiden Muscular Dystrophy pages
Accession: SCV000172340.1
First in ClinVar: Jul 23, 2014 Last updated: Jul 23, 2014 |
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not provided
(-)
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no classification provided
Method: literature only
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Congenital myopathy with fiber type disproportion
Affected status: not provided
Allele origin:
unknown
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GeneReviews
Accession: SCV000058560.2
First in ClinVar: May 03, 2013 Last updated: Oct 01, 2022 |
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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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Exome sequencing in undiagnosed congenital myopathy reveals new genes and refines genes-phenotypes correlations. | de Feraudy Y | Genome medicine | 2024 | DOI: 10.1186/s13073-024-01353-0 |
Discovery of pathogenic variants in a large Korean cohort of inherited muscular disorders. | Park HJ | Clinical genetics | 2017 | PMID: 27363342 |
Muscle weakness in TPM3-myopathy is due to reduced Ca2+-sensitivity and impaired acto-myosin cross-bridge cycling in slow fibres. | Yuen M | Human molecular genetics | 2015 | PMID: 26307083 |
Mutation update and genotype-phenotype correlations of novel and previously described mutations in TPM2 and TPM3 causing congenital myopathies. | Marttila M | Human mutation | 2014 | PMID: 24692096 |
Congenital fiber type disproportion myopathy caused by LMNA mutations. | Kajino S | Journal of the neurological sciences | 2014 | PMID: 24642510 |
Frequency and phenotype of patients carrying TPM2 and TPM3 gene mutations in a cohort of 94 patients with congenital myopathy. | Citirak G | Neuromuscular disorders : NMD | 2014 | PMID: 24507666 |
Combined cap disease and nemaline myopathy in the same patient caused by an autosomal dominant mutation in the TPM3 gene. | Malfatti E | Neuromuscular disorders : NMD | 2013 | PMID: 24095155 |
Mutations in repeating structural motifs of tropomyosin cause gain of function in skeletal muscle myopathy patients. | Marston S | Human molecular genetics | 2013 | PMID: 23886664 |
Congenital Fiber-Type Disproportion – RETIRED CHAPTER, FOR HISTORICAL REFERENCE ONLY. | Adam MP | - | 2013 | PMID: 20301436 |
Congenital myopathy-causing tropomyosin mutations induce thin filament dysfunction via distinct physiological mechanisms. | Ochala J | Human molecular genetics | 2012 | PMID: 22798622 |
Functional effects of congenital myopathy-related mutations in gamma-tropomyosin gene. | Robaszkiewicz K | Biochimica et biophysica acta | 2012 | PMID: 22749829 |
Changes in cross-bridge cycling underlie muscle weakness in patients with tropomyosin 3-based myopathy. | Ottenheijm CA | Human molecular genetics | 2011 | PMID: 21357678 |
Evidence for a dominant negative disease mechanism in cap myopathy due to TPM3. | Waddell LB | Neuromuscular disorders : NMD | 2010 | PMID: 20554445 |
Mutations of tropomyosin 3 (TPM3) are common and associated with type 1 myofiber hypotrophy in congenital fiber type disproportion. | Lawlor MW | Human mutation | 2010 | PMID: 19953533 |
A TPM3 mutation causing cap myopathy. | De Paula AM | Neuromuscular disorders : NMD | 2009 | PMID: 19553118 |
TPM3 mutation in one of the original cases of cap disease. | Ohlsson M | Neurology | 2009 | PMID: 19487656 |
Mutations in TPM3 are a common cause of congenital fiber type disproportion. | Clarke NF | Annals of neurology | 2008 | PMID: 18300303 |
A second pedigree with autosomal dominant nemaline myopathy caused by TPM3 mutation: a clinical and pathological study. | Pénisson-Besnier I | Neuromuscular disorders : NMD | 2007 | PMID: 17376686 |
De novo missense mutation in a constitutively expressed exon of the slow alpha-tropomyosin gene TPM3 associated with an atypical, sporadic case of nemaline myopathy. | Durling HJ | Neuromuscular disorders : NMD | 2002 | PMID: 12467750 |
"Cap disease"--a failure in the correct muscle fibre formation. | Fidziańska A | Journal of the neurological sciences | 2002 | PMID: 12163190 |
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=TPM3 | - | - | - | - |
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Text-mined citations for rs121964854 ...
HelpRecord last updated Nov 10, 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.