ClinVar Genomic variation as it relates to human health
NM_005472.5(KCNE3):c.248G>A (p.Arg83His)
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.
Uncertain significance(4); Benign(5); Likely benign(5)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_005472.5(KCNE3):c.248G>A (p.Arg83His)
Variation ID: 5541 Accession: VCV000005541.66
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 11q13.4 11: 74457316 (GRCh38) [ NCBI UCSC ] 11: 74168361 (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 Apr 4, 2013 Oct 20, 2024 Jan 31, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_005472.5:c.248G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_005463.1:p.Arg83His missense NC_000011.10:g.74457316C>T NC_000011.9:g.74168361C>T NG_011833.1:g.15240G>A LRG_439:g.15240G>A LRG_439t1:c.248G>A LRG_439p1:p.Arg83His Q9Y6H6:p.Arg83His - Protein change
- R83H
- Other names
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p.R83H:CGC>CAC
- Canonical SPDI
- NC_000011.10:74457315: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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0.00100 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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1000 Genomes Project 0.00100
1000 Genomes Project 30x 0.00109
Exome Aggregation Consortium (ExAC) 0.00297
The Genome Aggregation Database (gnomAD), exomes 0.00300
The Genome Aggregation Database (gnomAD) 0.00338
Trans-Omics for Precision Medicine (TOPMed) 0.00388
- 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
Help
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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KCNE3 | - | - |
GRCh38 GRCh37 |
106 | 118 | |
LIPT2 | - | - |
GRCh38 GRCh37 |
55 | 129 |
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
Help
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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Conflicting interpretations of pathogenicity (5) |
criteria provided, conflicting classifications
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May 1, 2023 | RCV000005879.41 | |
Benign (1) |
criteria provided, single submitter
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Jun 24, 2013 | RCV000171813.3 | |
Conflicting interpretations of pathogenicity (4) |
criteria provided, conflicting classifications
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Jan 31, 2024 | RCV000538199.24 | |
Uncertain significance (1) |
criteria provided, single submitter
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Jul 3, 2014 | RCV000415218.3 | |
Likely benign (1) |
criteria provided, single submitter
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Jan 10, 2019 | RCV000852657.2 | |
Benign (1) |
criteria provided, single submitter
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May 28, 2019 | RCV000988595.2 | |
Conflicting interpretations of pathogenicity (4) |
criteria provided, conflicting classifications
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Jan 1, 2024 | RCV000223897.12 | |
Likely benign (1) |
criteria provided, single submitter
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May 11, 2018 | RCV000253742.6 |
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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Benign
(Jun 24, 2013)
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criteria provided, single submitter
Method: research
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Periodic paralysis
Affected status: unknown
Allele origin:
unknown
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Biesecker Lab/Clinical Genomics Section, National Institutes of Health
Study: ClinSeq
Accession: SCV000050824.1 First in ClinVar: Jun 04, 2015 Last updated: Jun 04, 2015
Comments (2):
The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See Pubmed ID:23861362 for … (more)
The study set was not selected for affection status in relation to any cancer. Pathogenicity categories were based on literature curation. See Pubmed ID:23861362 for details. (less)
Medical sequencing
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Number of individuals with the variant: 12
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Uncertain significance
(Jul 03, 2014)
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criteria provided, single submitter
Method: clinical testing
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Syncope
Ventricular fibrillation
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV000492900.1
First in ClinVar: Jan 13, 2017 Last updated: Jan 13, 2017 |
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Uncertain significance
(Mar 29, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000539422.1
First in ClinVar: Apr 08, 2017 Last updated: Apr 08, 2017 |
Comment:
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or … (more)
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Several pubs, including possible segs and functional studies, but frequency is too high for disease and wrong phenotype. ExAC: 0.4% (289/66352) European chromosomes (less)
Method: Genome/Exome Filtration
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Likely benign
(Oct 09, 2014)
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criteria provided, single submitter
Method: clinical testing
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Brugada syndrome 6
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, University Medical Center Utrecht
Study: VKGL Data-share Consensus
Accession: SCV000743882.1 First in ClinVar: Dec 26, 2017 Last updated: Dec 26, 2017 |
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Likely benign
(Jan 10, 2019)
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criteria provided, single submitter
Method: clinical testing
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Cardiomyopathy
Affected status: yes
Allele origin:
germline
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Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego
Accession: SCV000995363.1
First in ClinVar: Oct 12, 2019 Last updated: Oct 12, 2019 |
Number of individuals with the variant: 2
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Benign
(May 28, 2019)
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criteria provided, single submitter
Method: clinical testing
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Encephalopathy, neonatal severe, with lactic acidosis and brain abnormalities
Affected status: unknown
Allele origin:
unknown
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Mendelics
Accession: SCV001138374.1
First in ClinVar: Jan 09, 2020 Last updated: Jan 09, 2020 |
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Uncertain significance
(Jan 01, 2016)
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criteria provided, single submitter
Method: clinical testing
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Brugada syndrome 6
Affected status: yes
Allele origin:
unknown
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Centre for Mendelian Genomics, University Medical Centre Ljubljana
Accession: SCV001367235.2
First in ClinVar: Jul 06, 2020 Last updated: Dec 12, 2020 |
Comment:
This variant was classified as: Uncertain significance.
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Likely benign
(Oct 03, 2023)
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criteria provided, single submitter
Method: clinical testing
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Brugada syndrome 6
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000884045.3
First in ClinVar: Oct 11, 2015 Last updated: Feb 20, 2024 |
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Likely benign
(May 11, 2018)
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criteria provided, single submitter
Method: clinical testing
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Cardiovascular phenotype
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000318064.7
First in ClinVar: Oct 02, 2016 Last updated: May 01, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
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Benign
(May 01, 2023)
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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: SCV000574898.32
First in ClinVar: Oct 11, 2015 Last updated: Oct 20, 2024 |
Comment:
KCNE3: BS1, BS2
Number of individuals with the variant: 3
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Uncertain significance
(Jul 15, 2020)
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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: SCV001714385.1
First in ClinVar: Jun 15, 2021 Last updated: Jun 15, 2021 |
Number of individuals with the variant: 1
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Benign
(Jul 13, 2018)
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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: SCV000223524.9
First in ClinVar: May 23, 2015 Last updated: Mar 04, 2023 |
Comment:
This variant is associated with the following publications: (PMID: none, 11207363, 11874988, 24055113, 12414843, 14504341, 15037716, 20051516)
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Benign
(Jan 31, 2024)
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criteria provided, single submitter
Method: clinical testing
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Brugada syndrome 6
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000648490.8
First in ClinVar: Dec 26, 2017 Last updated: Feb 20, 2024 |
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Likely benign
(Jan 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004803732.1
First in ClinVar: Mar 30, 2024 Last updated: Mar 30, 2024 |
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Uncertain significance
(Dec 11, 2012)
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no assertion criteria provided
Method: clinical testing
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not specified
Affected status: not provided
Allele origin:
germline
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Stanford Center for Inherited Cardiovascular Disease, Stanford University
Accession: SCV000280114.1
First in ClinVar: Jun 01, 2016 Last updated: Jun 01, 2016 |
Comment:
Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case … (more)
Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. KCNE3 p.Arg83His Based on the data reviewed below we consider it a variant of uncertain significance, probably benign. The variant has been reported in cases of periodic paralysis (Abbot et al 2001, Dias Da Silva et al 2002, Sterberg et al 2003). However, it was then later found in controls, suggesting it is likely benign and was identified in these cases because it is present in 0.1-1% of all individuals (reviewed in more detail below). Hedley et al (2011) investigated the KCNE genes as putative HCM genes. In their cohort of 93 unrelated HCM patients two individuals had p.Arg83His in KCNE3. However, the authors concluded it was not causative since one of the patients also had a presumed pathogenic TNNT2 variant (specific variant not cited) and because of the prevalence in the general population. In silico analysis with PolyPhen-2 predicts the variant to be benign. The arginine at codon 83 is not conserved across species and in the marmoset is in fact a histidine. The KCNE3 gene has been associated with Brugada syndrome type 6 (Deplon et al 2008) and periodic paralysis (Abbott et al 2001). In total the variant has not been seen with allele frequencies of 0.1-1.1% in individuals in general population samples (rs17215437). Another variant, c.248G>T has been seen with allele frequencies of 0.14-1.52% in 1000 genomes. The variant was recently reported online in 50 of 5379 individuals in the NHLBI Exome Sequencing Project dataset (as of December 11th, 2012). The phenotype of those individuals is not publicly available, however the cohorts that were merged to create this dataset were all either general population samples or samples recruited for common cardiovascular disease such as hypertension. (less)
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Uncertain significance
(Apr 01, 2007)
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no assertion criteria provided
Method: literature only
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RECLASSIFIED - VARIANT OF UNKNOWN SIGNIFICANCE
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000026061.1
First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013 |
Comment on evidence:
This variant, formerly titled HYPOKALEMIC PERIODIC PARALYSIS, HYPERKALEMIC PERIODIC PARALYSIS, and SUSCEPTIBILITY TO THYROTOXIC PERIODIC PARALYSIS based on the findings of Abbott et al. (2001) … (more)
This variant, formerly titled HYPOKALEMIC PERIODIC PARALYSIS, HYPERKALEMIC PERIODIC PARALYSIS, and SUSCEPTIBILITY TO THYROTOXIC PERIODIC PARALYSIS based on the findings of Abbott et al. (2001) and Dias Da Silva et al. (2002), has been reclassified based on the findings of Sternberg et al. (2003) and Jurkat-Rott and Lehmann-Horn (2004). Abbott et al. (2001) identified a 340G-A transition in the KCNE3 gene, resulting in an arg83-to-his (R83H) substitution in 2 of 100 patients with atypical forms of hyperkalemic periodic paralysis (HYPP; 170500) and hypokalemic periodic paralysis (HOKPP; 170400), respectively. However, Sternberg et al. (2003) and Jurkat-Rott and Lehmann-Horn (2004) concluded that the R83H variant does not play a causative role in periodic paralysis and that it is a polymorphism. Abbott et al. (2001) reported a male proband with atypical HYPP who was negative for mutations in the SCN4A gene and who carried the R83H variant. He presented at 22 months of age with episodic weakness of the extremities. Most episodes came on during sleep and were brief (12 hours), although they occasionally lasted for days. Serum potassium levels during attacks were normal. High carbohydrate meals helped resolve attacks, and treatment with a carbonic anhydrase inhibitor prevented attacks. The age at onset, frequent nature of attacks, and improvement with carbohydrate loading were all consistent with HYPP; however, provocative testing with potassium had not been performed. Frequent attacks upon awakening and absence of myotonia were considered atypical for this diagnosis. Abbott et al. (2001) reported a male proband with atypical HOKPP who was negative for mutations in the SCN4A and CACNA1S genes and who carried the R83H variant. He had onset of episodic paralytic weakness at the age of 14 years. Episodes were characterized by weakness primarily affecting the lower extremities and lasting hours to days, and were usually precipitated by strenuous exercise followed by rest or after prolonged sitting. Carbohydrate ingestion did not precipitate attacks, alcohol intake appeared to facilitate recovery from an attack, and potassium had no effect. He was classified as having hypokalemic periodic paralysis because of the typical age of onset, paralytic attacks that most often occurred after exercise, a low potassium level during a spontaneous attack, and the ability to precipitate an attack with insulin and glucose on 1 occasion. Atypical for this diagnosis was that a second provocative test was negative and that attacks usually occurred while awake. The variant was not found in DNA from a control population of 120 unaffected individuals, suggesting to them that it does not represent a polymorphism. Abbott et al. (2001) reported functional expression studies that showed that the mutant R83H KCNE3-Kv3.4 complexes exhibited reduced current density and diminished capacity to set resting membrane potential as a dominant-negative effect compared to wildtype. In in vitro studies, Abbott et al. (2006) found that the R83H variant shifts the voltage-dependence of channel activation in response to pH change. The current through the mutant channel decreased compared to wildtype as intracellular pH was lowered. The authors suggested that R83H acts as a regulatory domain, and concluded that the variation may predispose to the development of periodic paralysis. In contrast, Sternberg et al. (2003) did not identify the R83H mutation in 64 probands with either HYPP or HOKPP in whom mutations in the SCN4A and CACNA1S genes had been excluded. One patient with HOKPP had the R83H change, but he also had a mutation in the SCN4A gene (R672H; 603967.0016). His father, who had the same clinical phenotype and the SCN4A mutation, did not carry the R83H mutation, whereas the asymptomatic mother carried the R83H variant. The findings yielded a frequency of 0.0096 in patients with periodic paralysis (1 in 104) and 0.0158 (8 of 506) in healthy controls. Likewise, Jurkat-Rott and Lehmann-Horn (2004) identified the R83H mutation in 1 of 76 patients with HYPP, in 1 of 61 patients with paramyotonia congenita (608390), in 5 unaffected relatives, in 0 of 8 patients with TTPP, and in 3 of 321 healthy controls, suggesting that it is a polymorphism. Provocation of an unaffected carrier with glucose or potassium administration did not induce weakness. The authors offered a formula for determining causality of a mutation based on reduced penetrance, but concluded that the R83H mutation does not cause these muscle disorders. Dias Da Silva et al. (2002) identified the R83H substitution in 1 of 15 patients with thyrotoxic hypokalemic periodic paralysis (188580). The patient was a 44-year-old Caucasian man of Portuguese descent who experienced episodic paralysis for 2 years before developing thyrotoxicosis caused by Graves disease (275000). Two of his 3 offspring, all asymptomatic, were found to have the same variant. Tang et al. (2004) did not identify the R83H substitution, or any mutations in the KCNE3 gene, among 79 Chinese patients with thyrotoxic hypokalemic periodic paralysis. Jurkat-Rott and Lehmann-Horn (2007) again refuted the pathogenicity of the R83H variant, noting that it had been identified in 1.17% of patients and 1.16% of healthy controls, which does not support disease causality. (less)
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Likely benign
(-)
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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: SCV001956677.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Benign
(-)
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no assertion criteria provided
Method: clinical testing
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not specified
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: SCV001918148.1 First in ClinVar: Sep 24, 2021 Last updated: Sep 24, 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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Genotype-phenotype correlation and therapeutic rationale in hyperkalemic periodic paralysis. | Jurkat-Rott K | Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics | 2007 | PMID: 17395131 |
Phosphorylation and protonation of neighboring MiRP2 sites: function and pathophysiology of MiRP2-Kv3.4 potassium channels in periodic paralysis. | Abbott GW | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 2006 | PMID: 16449802 |
No mutation in the KCNE3 potassium channel gene in Chinese thyrotoxic hypokalaemic periodic paralysis patients. | Tang NL | Clinical endocrinology | 2004 | PMID: 15212652 |
Periodic paralysis mutation MiRP2-R83H in controls: Interpretations and general recommendation. | Jurkat-Rott K | Neurology | 2004 | PMID: 15037716 |
Lack of association of the potassium channel-associated peptide MiRP2-R83H variant with periodic paralysis. | Sternberg D | Neurology | 2003 | PMID: 14504341 |
A mutation in the KCNE3 potassium channel gene is associated with susceptibility to thyrotoxic hypokalemic periodic paralysis. | Dias Da Silva MR | The Journal of clinical endocrinology and metabolism | 2002 | PMID: 12414843 |
MiRP2 forms potassium channels in skeletal muscle with Kv3.4 and is associated with periodic paralysis. | Abbott GW | Cell | 2001 | PMID: 11207363 |
Text-mined citations for rs17215437 ...
HelpRecord last updated Oct 20, 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.