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NM_001540.5(HSPB1):c.404C>T (p.Ser135Phe) AND Charcot-Marie-Tooth disease axonal type 2F

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Jun 17, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000007904.10

Allele description [Variation Report for NM_001540.5(HSPB1):c.404C>T (p.Ser135Phe)]

NM_001540.5(HSPB1):c.404C>T (p.Ser135Phe)

Gene:
HSPB1:heat shock protein family B (small) member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q11.23
Genomic location:
Preferred name:
NM_001540.5(HSPB1):c.404C>T (p.Ser135Phe)
HGVS:
  • NC_000007.14:g.76303841C>T
  • NG_008995.1:g.6284C>T
  • NM_001540.5:c.404C>TMANE SELECT
  • NP_001531.1:p.Ser135Phe
  • LRG_248t1:c.404C>T
  • LRG_248:g.6284C>T
  • LRG_248p1:p.Ser135Phe
  • NC_000007.13:g.75933158C>T
  • NM_001540.3:c.404C>T
  • P04792:p.Ser135Phe
Protein change:
S135F; SER135PHE
Links:
UniProtKB: P04792#VAR_018507; OMIM: 602195.0001; dbSNP: rs28939680
NCBI 1000 Genomes Browser:
rs28939680
Molecular consequence:
  • NM_001540.5:c.404C>T - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Charcot-Marie-Tooth disease axonal type 2F (CMT2F)
Synonyms:
Charcot-Marie-Tooth disease type 2F; CMT 2F; Charcot-Marie-Tooth disease, neuronal, Type 2F; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011687; MedGen: C1847823; Orphanet: 99940; OMIM: 606595

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000028109OMIM
no assertion criteria provided
Pathogenic
(Nov 18, 2008)
germlineliterature only

PubMed (4)
[See all records that cite these PMIDs]

SCV001586034Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jun 17, 2023)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV0025212443billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 22, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineyes1not providednot provided1not providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A new locus for autosomal dominant Charcot-Marie-Tooth disease type 2 (CMT2F) maps to chromosome 7q11-q21.

Ismailov SM, Fedotov VP, Dadali EL, Polyakov AV, Van Broeckhoven C, Ivanov VI, De Jonghe P, Timmerman V, Evgrafov OV.

Eur J Hum Genet. 2001 Aug;9(8):646-50.

PubMed [citation]
PMID:
11528513

Targeted next-generation sequencing reveals further genetic heterogeneity in axonal Charcot-Marie-Tooth neuropathy and a mutation in HSPB1.

Ylikallio E, Johari M, Konovalova S, Moilanen JS, Kiuru-Enari S, Auranen M, Pajunen L, Tyynismaa H.

Eur J Hum Genet. 2014 Apr;22(4):522-7. doi: 10.1038/ejhg.2013.190. Epub 2013 Aug 21.

PubMed [citation]
PMID:
23963299
PMCID:
PMC3953916
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000028109.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (4)

Description

In affected members of a Russian family with Charcot-Marie-Tooth disease type 2F (CMT2F; 606595) previously reported by Ismailov et al. (2001), Evgrafov et al. (2004) identified a heterozygous c.404C-T transition in exon 2 of the HSPB1 gene, resulting in a ser135-to-phe (S135F) substitution. In affected members of an unrelated family from the United Kingdom with autosomal dominant distal hereditary motor neuronopathy 3 (HMND3; 608634), the authors identified the same mutation in heterozygosity. The S135F mutation occurs in a highly conserved alpha-crystallin domain of the protein. In vitro expression of the mutant protein resulted in reduced viability of neuronal cells and impaired neurofilament assembly. Evgrafov et al. (2004) suggested that these deficits may be responsible for premature axonal degeneration, which underlies both CMT and dHMN.

Houlden et al. (2008) identified a heterozygous S135F mutation in affected members of a large family with HMND3. The mean age at onset was 21 years, and sensory abnormalities were not present.

Variant Function

In cultured mouse motor neurons, Zhai et al. (2007) showed that expression of S135F-mutant HSPB1 led to progressive degeneration of motor neurons with disruption of the neurofilament network and aggregation of NEFL (162280) protein. The 2 proteins were found to associate together, and the S135F mutant had a dominant effect. Similarly, expression of NEFL mutants (e.g., 162280.0003) also led to disruption of the neurofilament network and aggregation of NEFL, and wildtype HSPB1 induced reversal of NEFL aggregates. Zhai et al. (2007) suggested that disruption of the neurofilament network with aggregation of NEFL is a common triggering event of motor neuron degeneration in CMT2E (607684) and CMT2F.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV001586034.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

This sequence change replaces serine, which is neutral and polar, with phenylalanine, which is neutral and non-polar, at codon 135 of the HSPB1 protein (p.Ser135Phe). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Ser135 amino acid residue in HSPB1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 23963299). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects HSPB1 function (PMID: 15122254, 17881652). 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 HSPB1 protein function. ClinVar contains an entry for this variant (Variation ID: 7478). This missense change has been observed in individual(s) with autosomal dominant axonal Charcot-Marie-Tooth (CMT2) and distal hereditary motor neuronopathy type 2B (dHMN2B) (PMID: 15122254, 18832141). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV002521244.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.94; 3Cnet: 0.99). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000007478). Different missense changes at the same codon (p.Ser135Cys, p.Ser135Tyr) have been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000533813, VCV000637060). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

Last Updated: Feb 20, 2024