ClinVar Genomic variation as it relates to human health
NM_001540.5(HSPB1):c.116C>T (p.Pro39Leu)
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_001540.5(HSPB1):c.116C>T (p.Pro39Leu)
Variation ID: 533814 Accession: VCV000533814.38
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 7q11.23 7: 76302828 (GRCh38) [ NCBI UCSC ] 7: 75932145 (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 28, 2018 Oct 20, 2024 Dec 28, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001540.5:c.116C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001531.1:p.Pro39Leu missense NC_000007.14:g.76302828C>T NC_000007.13:g.75932145C>T NG_008995.1:g.5271C>T LRG_248:g.5271C>T LRG_248t1:c.116C>T - Protein change
- P39L
- Other names
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- Canonical SPDI
- NC_000007.14:76302827: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 0.00000
Exome Aggregation Consortium (ExAC) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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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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HSPB1 | - | - |
GRCh38 GRCh37 |
370 | 410 |
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
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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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Dec 28, 2023 | RCV000641079.9 | |
Pathogenic (2) |
criteria provided, single submitter
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- | RCV000789058.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 24, 2019 | RCV001197515.3 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Nov 1, 2022 | RCV002060745.22 | |
HSPB1-related axonal neuropathies
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Pathogenic (1) |
criteria provided, single submitter
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Jun 16, 2021 | RCV001796974.5 |
HSPB1-related disorder
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Pathogenic (1) |
no assertion criteria provided
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Mar 5, 2024 | RCV004544855.2 |
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
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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
(-)
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criteria provided, single submitter
Method: clinical testing
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Charcot-Marie-Tooth disease
Affected status: yes
Allele origin:
germline
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Molecular Genetics Laboratory, London Health Sciences Centre
Accession: SCV001337299.1
First in ClinVar: Jun 14, 2020 Last updated: Jun 14, 2020 |
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Pathogenic
(Jan 24, 2019)
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criteria provided, single submitter
Method: clinical testing
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Neuronopathy, distal hereditary motor, type 2B
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV001368291.2
First in ClinVar: Jul 04, 2020 Last updated: Jul 04, 2020 |
Comment:
This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3.
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Pathogenic
(Jun 16, 2021)
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criteria provided, single submitter
Method: clinical testing
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HSPB1-related axonal neuropathies
Affected status: unknown
Allele origin:
unknown
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Illumina Laboratory Services, Illumina
Accession: SCV002038568.1
First in ClinVar: Dec 23, 2021 Last updated: Dec 23, 2021 |
Comment:
The HSPB1 c.116C>T (p.Pro39Leu) variant is a missense variant that has been reported in at least three studies, in which it was found in a … (more)
The HSPB1 c.116C>T (p.Pro39Leu) variant is a missense variant that has been reported in at least three studies, in which it was found in a heterozygous state in at least eight unrelated individuals with Charcot-Marie-Tooth disease type 2 or distal hereditary motor neuropathy (Capponi et al. 2011; Echaniz-Laguna et al. 2017; Tanabe et al. 2018). In several families, multiple affected individuals were heterozygous for the variant and in at least one individual, the variant was shown to be de novo. The p.Pro39Leu variant is reported at a frequency of 0.00001 in the European (non-Finnish) population from the Genome Aggregation Database (version 2.1.1), though this is based on one allele in a region of good sequence coverage, so the variant is presumed to be rare. Physicochemical studies of the p.Pro39Leu variant noted a decrease in phosphorylation-dependent dissociation of large oligomers and decreased chaperoning activity compared to wildtype (Muranova et al. 2015). Furthermore, the p.Pro39Leu variant was associated with mitochondrial dysfunction in motor neurons and increased vulnerability to oxidative stress (Kalmar et al. 2017). Based on the available evidence, the p.Pro39Leu variant is classified as pathogenic for HSPB1-related axonal neuropathies. (less)
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Pathogenic
(Sep 09, 2021)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
unknown
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Athena Diagnostics
Accession: SCV002770664.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
Comment:
The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated individuals with clinical … (more)
The frequency of this variant in the general population is consistent with pathogenicity (http://gnomad.broadinstitute.org). This variant has been identified in multiple unrelated individuals with clinical features associated with this gene. This variant appears to occur de novo in one individual with clinical features associated with this gene. Assessment of experimental evidence suggests this variant results in abnormal protein function. Expression of this variant in a motor neuron cell line resulted in impaired mitochondrial function and transport (PMID: 28592321). (less)
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Pathogenic
(Apr 18, 2022)
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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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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV003800118.2
First in ClinVar: Feb 13, 2023 Last updated: Mar 04, 2023 |
Comment:
The HSBP1 c.116C>T; p.Pro39Leu variant (rs557327165) is reported in the literature in multiple individuals and families affected with Charcot-Marie-Tooth disease type 2 and distal hereditary … (more)
The HSBP1 c.116C>T; p.Pro39Leu variant (rs557327165) is reported in the literature in multiple individuals and families affected with Charcot-Marie-Tooth disease type 2 and distal hereditary motor neuropathy (Capponi 2011, Echaniz-Laguna 2017, Kalmar 2017, Rossor 2017). Functional analyses of the variant protein show increased protein aggregation, increased resistance to dissociation, reduced chaperone-like activity (Muranova 2015) and mitochondrial dysfunction (Kalmer 2017). This variant is reported in ClinVar (Variation ID: 533814) and is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. Based on available information, this variant is considered to be pathogenic. References: Capponi S et al. HSPB1 and HSPB8 in inherited neuropathies: study of an Italian cohort of dHMN and CMT2 patients. J Peripher Nerv Syst. 2011 Dec;16(4):287-94. PMID: 22176143. Echaniz-Laguna A et al. Axonal Neuropathies due to Mutations in Small Heat Shock Proteins: Clinical, Genetic, and Functional Insights into Novel Mutations. Hum Mutat. 2017 May;38(5):556-568. PMID: 28144995. Kalmar B et al. Mitochondrial deficits and abnormal mitochondrial retrograde axonal transport play a role in the pathogenesis of mutant Hsp27-induced Charcot Marie Tooth Disease. Hum Mol Genet. 2017 Sep 1;26(17):3313-3326. PMID: 28595321. Muranova et al. Characterization of Mutants of Human Small Heat Shock Protein HspB1 Carrying Replacements in the N-Terminal Domain and Associated with Hereditary Motor Neuron Diseases. PLoS One. 2015 May 12;10(5):e0126248. PMID: 25965061. Rossor AM et al. Pilot phenotype and natural history study of hereditary neuropathies caused by mutations in the HSPB1 gene. Neuromuscul Disord. 2017 Jan;27(1):50-56. PMID: 27816334. (less)
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Pathogenic
(Dec 28, 2023)
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criteria provided, single submitter
Method: clinical testing
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Charcot-Marie-Tooth disease axonal type 2F
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000762697.7
First in ClinVar: May 28, 2018 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 39 of the HSPB1 protein (p.Pro39Leu). … (more)
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 39 of the HSPB1 protein (p.Pro39Leu). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individuals with autosomal dominant Charcot-Marie-Tooth disease (PMID: 22176143, 27816334, 28144995). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 533814). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on HSPB1 protein function. Experimental studies have shown that this missense change affects HSPB1 function (PMID: 25965061, 28595321). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Nov 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: SCV002497523.18
First in ClinVar: Apr 08, 2022 Last updated: Oct 20, 2024 |
Comment:
HSPB1: PP1:Strong, PM2, PS4:Moderate, PP4, PS3:Supporting
Number of individuals with the variant: 2
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Uncertain significance
(-)
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no assertion criteria provided
Method: literature only
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Charcot-Marie-Tooth disease
Affected status: yes
Allele origin:
germline
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Inherited Neuropathy Consortium
Accession: SCV000928407.1
First in ClinVar: Jul 27, 2019 Last updated: Jul 27, 2019 |
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Pathogenic
(Mar 05, 2024)
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no assertion criteria provided
Method: clinical testing
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HSPB1-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004764438.2
First in ClinVar: Mar 16, 2024 Last updated: Oct 08, 2024 |
Comment:
The HSPB1 c.116C>T variant is predicted to result in the amino acid substitution p.Pro39Leu. This variant was reported in individuals with autosomal dominant Charcot-Marie-Tooth disease, … (more)
The HSPB1 c.116C>T variant is predicted to result in the amino acid substitution p.Pro39Leu. This variant was reported in individuals with autosomal dominant Charcot-Marie-Tooth disease, type 2 (Houlden et al 2008. PubMed ID: 18832141; Volodarsky et al 2020. PubMed ID: 32376792; Tanabe et al. 2018. PubMed ID: 29381233). Functional studies suggest that the p.Pro39Leu variant led to abnormal mitochondrial axonal transport and abnormal phosphorylation (Kalmar et al 2017. PubMed ID: 28595321; Muranova et al 2015. PubMed ID: 25965061). This variant is reported in 0.00099% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic. (less)
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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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Small heat shock proteins in neurodegenerative diseases. | Vendredy L | Cell stress & chaperones | 2020 | PMID: 32323160 |
Mutations in HspB1 and hereditary neuropathies. | Muranova LK | Cell stress & chaperones | 2020 | PMID: 32301006 |
Interplay of disordered and ordered regions of a human small heat shock protein yields an ensemble of 'quasi-ordered' states. | Clouser AF | eLife | 2019 | PMID: 31573509 |
Small heat shock proteins: multifaceted proteins with important implications for life. | Carra S | Cell stress & chaperones | 2019 | PMID: 30758704 |
Clinical and genetic features of Charcot-Marie-Tooth disease 2F and hereditary motor neuropathy 2B in Japan. | Tanabe H | Journal of the peripheral nervous system : JPNS | 2018 | PMID: 29381233 |
Mitochondrial deficits and abnormal mitochondrial retrograde axonal transport play a role in the pathogenesis of mutant Hsp27-induced Charcot Marie Tooth Disease. | Kalmar B | Human molecular genetics | 2017 | PMID: 28595321 |
Axonal Neuropathies due to Mutations in Small Heat Shock Proteins: Clinical, Genetic, and Functional Insights into Novel Mutations. | Echaniz-Laguna A | Human mutation | 2017 | PMID: 28144995 |
Pilot phenotype and natural history study of hereditary neuropathies caused by mutations in the HSPB1 gene. | Rossor AM | Neuromuscular disorders : NMD | 2017 | PMID: 27816334 |
High diagnostic yield of clinical exome sequencing in Middle Eastern patients with Mendelian disorders. | Yavarna T | Human genetics | 2015 | PMID: 26077850 |
In silico evaluation of human small heat shock protein HSP27: homology modeling, mutation analyses and docking studies. | Fossa P | Bioorganic & medicinal chemistry | 2015 | PMID: 25999205 |
Characterization of Mutants of Human Small Heat Shock Protein HspB1 Carrying Replacements in the N-Terminal Domain and Associated with Hereditary Motor Neuron Diseases. | Muranova LK | PloS one | 2015 | PMID: 25965061 |
Barcoding heat shock proteins to human diseases: looking beyond the heat shock response. | Kakkar V | Disease models & mechanisms | 2014 | PMID: 24719117 |
Neuropathy- and myopathy-associated mutations in human small heat shock proteins: Characteristics and evolutionary history of the mutation sites. | Benndorf R | Mutation research. Reviews in mutation research | 2014 | PMID: 24607769 |
Mutations of small heat shock proteins and human congenital diseases. | Datskevich PN | Biochemistry. Biokhimiia | 2012 | PMID: 23379525 |
The family of mammalian small heat shock proteins (HSPBs): implications in protein deposit diseases and motor neuropathies. | Boncoraglio A | The international journal of biochemistry & cell biology | 2012 | PMID: 22484489 |
Alteration of protein folding and degradation in motor neuron diseases: Implications and protective functions of small heat shock proteins. | Carra S | Progress in neurobiology | 2012 | PMID: 21971574 |
HSPB1 and HSPB8 in inherited neuropathies: study of an Italian cohort of dHMN and CMT2 patients. | Capponi S | Journal of the peripheral nervous system : JPNS | 2011 | PMID: 22176143 |
Mutations in the HSP27 (HSPB1) gene cause dominant, recessive, and sporadic distal HMN/CMT type 2. | Houlden H | Neurology | 2008 | PMID: 18832141 |
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Text-mined citations for rs557327165 ...
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.