ClinVar Genomic variation as it relates to human health
NM_000530.8(MPZ):c.293G>A (p.Arg98His)
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_000530.8(MPZ):c.293G>A (p.Arg98His)
Variation ID: 14176 Accession: VCV000014176.52
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q23.3 1: 161306863 (GRCh38) [ NCBI UCSC ] 1: 161276653 (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, 2015 Oct 20, 2024 May 29, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000530.8:c.293G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000521.2:p.Arg98His missense NM_001315491.2:c.293G>A NP_001302420.1:p.Arg98His missense NC_000001.11:g.161306863C>T NC_000001.10:g.161276653C>T NG_008055.1:g.8110G>A LRG_256:g.8110G>A LRG_256t1:c.293G>A LRG_256p1:p.Arg98His P25189:p.Arg98His - Protein change
- R98H
- Other names
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- Canonical SPDI
- NC_000001.11:161306862: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
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00000
The Genome Aggregation Database (gnomAD) 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
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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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MPZ | - | - |
GRCh38 GRCh37 |
647 | 682 |
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
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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 (2) |
criteria provided, single submitter
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Feb 23, 2023 | RCV000015239.27 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 8, 2024 | RCV000196172.10 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Sep 19, 2014 | RCV000415463.3 | |
Pathogenic (6) |
criteria provided, multiple submitters, no conflicts
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May 29, 2024 | RCV000376287.37 | |
Pathogenic (1) |
criteria provided, single submitter
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- | RCV001173692.2 | |
Pathogenic (1) |
criteria provided, single submitter
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Mar 25, 2020 | RCV002433457.3 | |
MPZ-related disorder
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Pathogenic (1) |
criteria provided, single submitter
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Oct 21, 2022 | RCV004528112.2 |
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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Likely pathogenic
(Sep 19, 2014)
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criteria provided, single submitter
Method: clinical testing
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Decreased nerve conduction velocity
Distal lower limb amyotrophy Distal muscle weakness Pes cavus Sensory neuropathy
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV000492978.1
First in ClinVar: Jan 13, 2017 Last updated: Jan 13, 2017 |
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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: SCV001336802.1
First in ClinVar: Jun 14, 2020 Last updated: Jun 14, 2020 |
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Pathogenic
(Mar 12, 2015)
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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: SCV000614105.3
First in ClinVar: Dec 06, 2016 Last updated: Jan 26, 2021 |
Comment:
Not found in the total gnomAD dataset, and the data is high quality. Found in multiple individuals with expected phenotype for this gene. This variant … (more)
Not found in the total gnomAD dataset, and the data is high quality. Found in multiple individuals with expected phenotype for this gene. This variant occurs as the most likely explanation for disease in a significant number of internal cases, suggesting this variant is associated with disease. Assessment of experimental evidence suggests this variant results in abnormal protein function. Segregates with disease in multiple families (less)
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Pathogenic
(Oct 21, 2022)
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criteria provided, single submitter
Method: clinical testing
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MPZ-related condition
Affected status: unknown
Allele origin:
germline
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PreventionGenetics, part of Exact Sciences
Accession: SCV004103382.1
First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023 |
Comment:
The MPZ c.293G>A variant is predicted to result in the amino acid substitution p.Arg98His. This variant has been reported in many individuals and families with … (more)
The MPZ c.293G>A variant is predicted to result in the amino acid substitution p.Arg98His. This variant has been reported in many individuals and families with Charcot-Marie-Tooth disease, type 1B (Ohnishi et al. 1999. PubMed ID: 10581375; Lee et al. 2010. PubMed ID: 20461396; Hsu et al. 2019. PubMed ID: 31211173; Volodarsky et al. 2020. PubMed ID: 32376792; Hayasaka et al. 1993. PubMed ID: 7688964; Gabreëls-Festen et al. 1996. PubMed ID: 8797476). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. (less)
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Pathogenic
(Feb 23, 2023)
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criteria provided, single submitter
Method: clinical testing
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Charcot-Marie-Tooth disease type 1B
Affected status: yes
Allele origin:
unknown
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3billion
Accession: SCV003842081.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
The variant is not observed in the gnomAD v2.1.1 dataset. In silico tool predictions suggest damaging effect of the variant on gene or gene product … (more)
The variant is not observed in the gnomAD v2.1.1 dataset. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.68; 3Cnet: 1.00). Same nucleotide change resulting in same amino acid change (ClinVar ID: VCV000014176) and different missense changes at the same codon (p.Arg98Cys, p.Arg98Leu, p.Arg98Pro / ClinVar ID: VCV000014174, VCV000014175, VCV000586152) Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Distal lower limb muscle weakness (present) , Distal upper limb muscle weakness (present) , Proximal muscle weakness in lower limbs (present) , Reduced tendon reflexes … (more)
Distal lower limb muscle weakness (present) , Distal upper limb muscle weakness (present) , Proximal muscle weakness in lower limbs (present) , Reduced tendon reflexes (present) , Distal amyotrophy (present) , Hypotrophy of the small hand muscles (present) (less)
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Pathogenic
(Jan 20, 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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Mayo Clinic Laboratories, Mayo Clinic
Accession: SCV001713094.2
First in ClinVar: Jun 15, 2021 Last updated: Jun 03, 2023 |
Comment:
PM1, PM2, PS3, PS4
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Pathogenic
(Jan 08, 2024)
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criteria provided, single submitter
Method: clinical testing
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Charcot-Marie-Tooth disease, type I
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000253842.8
First in ClinVar: Oct 11, 2015 Last updated: Feb 28, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 98 of the MPZ protein (p.Arg98His). … (more)
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 98 of the MPZ protein (p.Arg98His). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Charcot-Marie-Tooth disease type 1 (PMID: 7688964, 8644725, 10581375, 12477701, 20215982). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 14176). 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 MPZ protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects MPZ function (PMID: 20461396). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Mar 25, 2020)
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criteria provided, single submitter
Method: clinical testing
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Inborn genetic diseases
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV002747828.2
First in ClinVar: Nov 29, 2022 Last updated: May 01, 2024 |
Comment:
The p.R98H pathogenic mutation (also known as c.293G>A), located in coding exon 3 of the MPZ gene, results from a G to A substitution at … (more)
The p.R98H pathogenic mutation (also known as c.293G>A), located in coding exon 3 of the MPZ gene, results from a G to A substitution at nucleotide position 293. The arginine at codon 98 is replaced by histidine, an amino acid with highly similar properties. This alteration has been reported in multiple individuals with demyelinating Charcot-Marie Tooth disease and to co-segregate with disease in multiple families (Lagueny A et al. Neuromuscul. Disord., 1999 Oct;9:361-7; Ohnishi A et al. J. Neurol. Sci., 1999 Dec;171:97-109; Rouger H et al. Am. J. Hum. Genet., 1996 Mar;58:638-41). Additionally, in vitro functional studies have shown that protein with this alteration fails to localize to the cell membrane and increases the unfolded protein response in the cell (Bai Y et al. Ann Clin Transl Neurol, 2018 Apr;5:445-455; Lee YC et al. J. Neurol., 2010 Oct;257:1661-8). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. (less)
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Pathogenic
(May 29, 2024)
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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: SCV000329714.10
First in ClinVar: Dec 06, 2016 Last updated: Sep 16, 2024 |
Comment:
Published functional studies demonstrate a damaging effect on cell adhesiveness (PMID: 20461396); Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in … (more)
Published functional studies demonstrate a damaging effect on cell adhesiveness (PMID: 20461396); Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are a common cause of disease and they are underrepresented in the general population; 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: 31211173, 33179255, 31372974, 12221176, 8797476, 7688964, 10737979, 20215982, 10581375, 11437164, 29687021, 32376792, 33726816, 36203352, 37273706, 29136549, 10545037, 37581289, 15729519, 34925207, 12477701, 26310628, 20461396, 8644725, 21840889, 22689911) (less)
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Pathogenic
(Oct 01, 2021)
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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: SCV001249786.24
First in ClinVar: May 12, 2020 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 2
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Pathogenic
(Sep 10, 2002)
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no assertion criteria provided
Method: literature only
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CHARCOT-MARIE-TOOTH DISEASE, TYPE 1B
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000035498.3
First in ClinVar: Apr 04, 2013 Last updated: Mar 14, 2018 |
Comment on evidence:
Among 20 unrelated French Charcot-Marie-Tooth disease type 1B (CMT1B; 118200) patients without 17p11.2 duplications, Rouger et al. (1996) found 3 different mutations at codon 98. … (more)
Among 20 unrelated French Charcot-Marie-Tooth disease type 1B (CMT1B; 118200) patients without 17p11.2 duplications, Rouger et al. (1996) found 3 different mutations at codon 98. No other mutation in exon 3 of the MPZ gene was detected. The mutation was demonstrated to be de novo in 1 of the cases and suspected of being de novo in the other 2, suggesting that mutations occur with a high rate at codon 98. In 1 patient an arg98-to-pro (R98P; 159440.0009) mutation was caused by a 293G-C transversion, whereas in another patient an arg98-to-cys substitution (R98C; 159440.0010) was caused by a 292C-T transition. The third mutation was a 293G-A transition, resulting in an arg98-to-his substitution. Rouger et al. (1996) noted that this mutation had previously been reported in a Japanese family by Hayasaka et al. (1993). The patient with the R98C mutation showed a more severe clinical and electrophysiologic phenotype than the others with a codon 98 mutation, partly compatible with Dejerine-Sottas syndrome with very early onset (1 year), and a very low nerve conduction velocity, but only mild functional disability at age 8 years. All 3 mutations in codon 98 implied a C-to-T transition (1 on the sense and 2 on the antisense strand), suggesting that they may result from the deamination of a methylcytosine to a thymine. The authors stated that this could explain the high rate of mutations on codon 98. The R98H mutation, characterized by direct sequencing in 2 cases, was not detected by the SSCP technique. Since SSCP analysis was used as the initial screening technique in most previous studies, the frequency of mutations at codon 98 may have been underestimated. The 3 codon 98 mutations represented 20% of the CMT1 patients without duplications and probably a much higher proportion of those with MPZ mutations. These mutations can be picked up by CfoI restriction of exon 3 of the MPZ gene; this approach should be the first step in screening CMT1 patients without duplications. Watanabe et al. (2002) reported partial symptom relief with corticosteroid treatment in a patient with demyelinating CMT1B and a heterozygous R98H mutation in the MPZ gene. Although this response is rare in such patients, Watanabe et al. (2002) hypothesized that poor myelin compaction by the MPZ protein, caused by the mutation, may have allowed circulating immune elements access to normally sequestered endoneurial components, thus accounting for the response to corticosteroid treatment. (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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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: SCV002037333.1 First in ClinVar: Dec 21, 2021 Last updated: Dec 21, 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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Clinical Genetics, Academic Medical Center
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV002034563.1 First in ClinVar: Dec 18, 2021 Last updated: Dec 18, 2021 |
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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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Genetic spectrum and clinical profiles in a southeast Chinese cohort of Charcot-Marie-Tooth disease. | Chen CX | Clinical genetics | 2019 | PMID: 31372974 |
Mutation spectrum of Charcot-Marie-Tooth disease among the Han Chinese in Taiwan. | Hsu YH | Annals of clinical and translational neurology | 2019 | PMID: 31211173 |
Myelin protein zero mutations and the unfolded protein response in Charcot Marie Tooth disease type 1B. | Bai Y | Annals of clinical and translational neurology | 2018 | PMID: 29687021 |
The spectrum of Charcot-Marie-Tooth disease due to myelin protein zero: An electrodiagnostic, nerve ultrasound and histological study. | Fabrizi GM | Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology | 2018 | PMID: 29136549 |
Cellular characterization of MPZ mutations presenting with diverse clinical phenotypes. | Lee YC | Journal of neurology | 2010 | PMID: 20461396 |
Asymmetric phenotype associated with rare myelin protein zero mutation. | Souayah N | Journal of clinical neuromuscular disease | 2010 | PMID: 20215982 |
Demyelinating and axonal features of Charcot-Marie-Tooth disease with mutations of myelin-related proteins (PMP22, MPZ and Cx32): a clinicopathological study of 205 Japanese patients. | Hattori N | Brain : a journal of neurology | 2003 | PMID: 12477701 |
Corticosteroid- responsive asymmetric neuropathy with a myelin protein zero gene mutation. | Watanabe M | Neurology | 2002 | PMID: 12221176 |
Mutation analysis in Chariot-Marie Tooth disease type 1: point mutations in the MPZ gene and the GJB1 gene cause comparable phenotypic heterogeneity. | Young P | Journal of neurology | 2001 | PMID: 11437164 |
Screening for mutations in the peripheral myelin genes PMP22, MPZ and Cx32 (GJB1) in Russian Charcot-Marie-Tooth neuropathy patients. | Mersiyanova IV | Human mutation | 2000 | PMID: 10737979 |
Myelinated fibers in Charcot-Marie-Tooth disease type 1B with Arg98His mutation of Po protein. | Ohnishi A | Journal of the neurological sciences | 1999 | PMID: 10581375 |
Peripheral myelin modification in CMT1B correlates with MPZ gene mutations. | Lagueny A | Neuromuscular disorders : NMD | 1999 | PMID: 10545037 |
Two divergent types of nerve pathology in patients with different P0 mutations in Charcot-Marie-Tooth disease. | Gabreëls-Festen AA | Neurology | 1996 | PMID: 8797476 |
High frequency of mutations in codon 98 of the peripheral myelin protein P0 gene in 20 French CMT1 patients. | Rouger H | American journal of human genetics | 1996 | PMID: 8644725 |
Mutation of the myelin P0 gene in Charcot-Marie-tooth neuropathy type 1. | Hayasaka K | Biochemical and biophysical research communications | 1993 | PMID: 7688964 |
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Text-mined citations for rs121913589 ...
HelpRecord last updated Oct 27, 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.